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Kumar P, Khirid S, Jangid DK, Nishad CS, Chauhan P, Kumari P, Meena S, Bose SK, Kumar A, Banerjee B, Dhayal RS. Dithiophosphonate-Protected Eight-Electron Superatomic Ag 21 Nanocluster: Synthesis, Isomerism, Luminescence, and Catalytic Activity. Inorg Chem 2024; 63:13724-13737. [PMID: 38970493 DOI: 10.1021/acs.inorgchem.4c02062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2024]
Abstract
The structure-property relationship considering isomerism-tuned photoluminescence and efficient catalytic activity of silver nanoclusters (NCs) is exclusive. Asymmetrical dithiophosphonate NH4[S2P(OR)(p-C6H4OCH3)] ligated first atomically precise silver NCs [Ag21{S2P(OR)(p-C6H4OCH3)}12]PF6 {where, R = nPr (1), Et (2)} were established by single-crystal X-ray diffraction and characterized by electrospray ionization mass spectrometry, NMR (31P, 1H, 2H), X-ray photoelectron spectroscopy, UV-visible, energy-dispersive X-ray spectroscopy, Fourier transforms infrared, thermogravimetric analysis, etc. NCs 1 and 2 consist of eight silver atoms in a cubic framework and enclose an Ag@Ag12-centered icosahedron to constitute an Ag21 core of Th symmetry, which is concentrically inscribed within the S24 snub-cube, P12 cuboctahedron, and the O12 truncated tetrahedron formed by 12 dithiophosphonate ligands. These NCs facilitate to be an eight-electron superatom (1S21P6), in which eight capping Ag atoms exhibit structural isomerism with documented isoelectronic [Ag21{S2P(OiPr)2}12]PF6, 3. In contrast to 3, the stapling of dithiophosphonates in 1 and 2 triggered bluish emission within the 400 to 500 nm region at room temperature. The density functional theory study rationalized isomerization and optical properties of 1, 2, and 3. Both (1, and 2) clusters catalyzed a decarboxylative acylarylation reaction for rapid oxindole synthesis in 99% yield under ambient conditions and proposed a multistep reaction pathway. Ultimately, this study links nanostructures to their physical and catalytic properties.
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Affiliation(s)
- Pankaj Kumar
- Department of Chemistry, Central University of Punjab, Bathinda 151401, India
| | - Samreet Khirid
- Department of Chemistry, Central University of Punjab, Bathinda 151401, India
| | - Dilip Kumar Jangid
- Department of Chemistry, Central University of Punjab, Bathinda 151401, India
| | | | - Poonam Chauhan
- Department of Physics, Central University of Punjab, Bathinda 151401, India
| | - Priti Kumari
- Department of Chemistry, Central University of Punjab, Bathinda 151401, India
| | - Sangeeta Meena
- Department of Chemistry, Central University of Punjab, Bathinda 151401, India
| | - Shubhankar Kumar Bose
- Centre for Nano and Material Sciences (CNMS), Jain (Deemed-to-be-University), Jain Global Campus, Bangalore 562112, India
| | - Ashok Kumar
- Department of Physics, Central University of Punjab, Bathinda 151401, India
| | - Biplab Banerjee
- Department of Chemistry, Central University of Punjab, Bathinda 151401, India
| | - Rajendra S Dhayal
- Department of Chemistry, Central University of Punjab, Bathinda 151401, India
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2
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Jamdar SN, Yadav P, Kulkarni BS, Sudesh, Kumar A, Makde RD. Crystal structure of a newly identified M61 family aminopeptidase with broad substrate specificity that is solely responsible for recycling acidic amino acids. FEBS J 2024; 291:3211-3232. [PMID: 38646733 DOI: 10.1111/febs.17133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 02/10/2024] [Accepted: 03/25/2024] [Indexed: 04/23/2024]
Abstract
Aminopeptidases with varied substrate specificities are involved in different crucial physiological processes of cellular homeostasis. They also have wide applications in food and pharma industries. Within the bacterial cell, broad specificity aminopeptidases primarily participate in the recycling of amino acids by degrading oligopeptides generated via primary proteolysis mediated by cellular ATP-dependent proteases. However, in bacteria, a truly broad specificity enzyme, which can cleave off acidic, basic, Gly and hydrophobic amino acid residues, is extremely rare. Here, we report structure-function of a putative glycyl aminopeptidase (M61xc) from Xanthomonas campestris pv campestris (Xcc) belonging to the M61 peptidase family. The enzyme exhibits broad specificity and cleaves Ala, Leu, Asp, Glu, Met, Ser, Phe, Tyr, Gly, Arg, and Lys at the N terminus, optimally of peptides with a length of 3-7 amino acids. Further, we report the high-resolution crystal structure of M61xc in the apo form (2.1 Å) and bestatin-bound form (1.95 Å), detailing its catalytic and substrate preference mechanisms. Comparative analysis of enzyme activity in crude cell extracts from both wild-type and m61xc-knockout mutant strains of Xcc has elucidated the unique intracellular role of M61xc. This study suggests that M61xc is the exclusive enzyme in these bacteria that is responsible for liberating Asp/Glu residues from the N-termini of peptides. Also, in view of its broad specificity and peptide degradation ability, it could be considered equivalent to M1 or other oligomeric peptidases from families like M17, M18, M42 or S9, who have an important auxiliary role in post-proteasomal protein degradation in prokaryotes.
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Affiliation(s)
- Sahayog N Jamdar
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Pooja Yadav
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, India
| | | | - Sudesh
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Ashwani Kumar
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, India
| | - Ravindra D Makde
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, India
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3
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Saha I, Ghosh B, Dasgupta J. Structural insights in to the atypical type-I ABC Glucose-6-phosphate importer VCA0625-27 of Vibrio cholerae. Biochem Biophys Res Commun 2024; 716:150030. [PMID: 38704889 DOI: 10.1016/j.bbrc.2024.150030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 04/28/2024] [Indexed: 05/07/2024]
Abstract
Sugar phosphates are potential sources of carbon and phosphate for bacteria. Despite that the process of internalization of Glucose-6-Phosphate (G6P) through plasma membrane remained elusive in several bacteria. VCA0625-27, made of periplasmic ligand binding protein (PLBP) VCA0625, an atypical monomeric permease VCA0626, and a cytosolic ATPase VCA0627, recently emerged as hexose-6-phosphate uptake system of Vibrio cholerae. Here we report high resolution crystal structure of VCA0625 in G6P bound state that largely resembles AfuA of Actinobacillus pleuropneumoniae. MD simulations on VCA0625 in apo and G6P bound states unraveled an 'open to close' and swinging bi-lobal motions, which are diminished upon G6P binding. Mutagenesis followed by biochemical assays on VCA0625 underscored that R34 works as gateway to bind G6P. Although VCA0627 binds ATP, it is ATPase deficient in the absence of VCA0625 and VCA0626, which is a signature phenomenon of type-I ABC importer. Further, modeling, docking and systematic sequence analysis allowed us to envisage the existence of similar atypical type-I G6P importer with fused monomeric permease in 27 other gram-negative bacteria.
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Affiliation(s)
- Indrila Saha
- Department of Biotechnology, St. Xavier's College (Autonomous), 30, Mother Teresa Sarani, Kolkata, 700016, India
| | - Biplab Ghosh
- Macromolecular Crystallography Section, Beamline Development & Application Section, Bhabha Atomic Research Center, Trombay, Mumbai, 400085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, India.
| | - Jhimli Dasgupta
- Department of Biotechnology, St. Xavier's College (Autonomous), 30, Mother Teresa Sarani, Kolkata, 700016, India.
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4
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Chandravanshi K, Singh R, Bhange GN, Kumar A, Yadav P, Kumar A, Makde RD. Crystal structure and solution scattering of Geobacillus stearothermophilus S9 peptidase reveal structural adaptations for carboxypeptidase activity. FEBS Lett 2024; 598:684-701. [PMID: 38426217 DOI: 10.1002/1873-3468.14834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 03/02/2024]
Abstract
Acylaminoacyl peptidases (AAPs) play a pivotal role in various pathological conditions and are recognized as potential therapeutic targets. AAPs exhibit a wide range of activities, such as acylated amino acid-dependent aminopeptidase, endopeptidase, and less studied carboxypeptidase activity. We have determined the crystal structure of an AAP from Geobacillus stearothermophilus (S9gs) at 2.0 Å resolution. Despite being annotated as an aminopeptidase in the NCBI database, our enzymatic characterization proved S9gs to be a carboxypeptidase. Solution-scattering studies showed that S9gs exists as a tetramer in solution, and crystal structure analysis revealed adaptations responsible for the carboxypeptidase activity of S9gs. The findings present a hypothesis for substrate selection, substrate entry, and product exit from the active site, enriching our understanding of this rare carboxypeptidase.
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Affiliation(s)
| | - Rahul Singh
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, India
| | - Gauri N Bhange
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, India
| | - Ashwani Kumar
- Department of Bioscience and Biomedical Engineering, Indian Institute of Technology Indore, India
| | - Pooja Yadav
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, India
| | - Amit Kumar
- Department of Bioscience and Biomedical Engineering, Indian Institute of Technology Indore, India
| | - Ravindra D Makde
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, India
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5
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Khan S, Upadhyay S, Dave U, Kumar A, Gomes J. Structural and mechanistic insights into ALS patient derived mutations in D-amino acid oxidase. Int J Biol Macromol 2024; 256:128403. [PMID: 38035964 DOI: 10.1016/j.ijbiomac.2023.128403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/19/2023] [Accepted: 11/22/2023] [Indexed: 12/02/2023]
Abstract
The D-amino acid oxidase protein modulates neurotransmission by controlling the levels of D-serine, a co-agonist of N-methyl-D-aspartate receptors. Mutations in the DAO gene have been associated with ALS, with some studies reporting pathogenic mechanisms of the R199W mutation. We have characterized two novel mutations R38H and Q201R found in ALS patients and report certain novel findings related to the R199W mutation. We report the first instance of crystal structure analysis of a patient-derived mutant of DAO, R38H, solved at 2.10 Å. The structure revealed significant perturbations and altered binding with the cofactor (FAD) and the inhibitor benzoate, supported by biochemical assays. Q201R-DAO also exhibited significantly lower ligand binding efficiency. Furthermore, kinetic analysis across all variants revealed reduced oxidase activity and substrate binding. Notably, R38H-DAO exhibited near-WT activity only at high substrate concentrations, while R199W-DAO and Q201R-DAO displayed drastic activity reduction. Additionally, structural perturbations were inferred for R199W-DAO and Q201R-DAO, evident by the higher oligomeric state in the holoenzyme form. We also observed thermal instability in case of R199W-DAO mutant. We hypothesize that the mutant enzymes may be rendered non-functional in a cellular context, potentially leading to NMDAR-associated excitotoxicity. The study provides novel insights into structural and functional aspects of DAO mutations in ALS.
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Affiliation(s)
- Shumayila Khan
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi 110016, India; Indian Council of Medical Research, New Delhi 110029, India
| | - Saurabh Upadhyay
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi 110016, India
| | - Upma Dave
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi 110016, India
| | - Ashwani Kumar
- Macromolecular Crystallography Section, Beamline Development & Application Section, Bhabha Atomic Research Center, Trombay, Mumbai 400085, India
| | - James Gomes
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi 110016, India.
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Kinkar OU, Kumar A, Prashar A, Yadav B, Hadapad AB, Hire RS, Makde RD. The crystal structure of insecticidal protein Txp40 from Xenorhabdus nematophila reveals a two-domain unique binary toxin with homology to the toxin-antitoxin (TA) system. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2024; 164:104045. [PMID: 38040266 DOI: 10.1016/j.ibmb.2023.104045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 11/15/2023] [Accepted: 11/24/2023] [Indexed: 12/03/2023]
Abstract
Txp40 is a ubiquitous, conserved, and novel toxin from Xenorhabdus and Photorhabdus bacteria, toxic to a wide range of insect pests. However, the three-dimensional structure and toxicity mechanism for Txp40 or any of its sequence homologs are not yet known. Here, we are reporting the crystal structure of the insecticidal protein Txp40 from Xenorhabdus nematophila at 2.08 Å resolution. The Txp40 was structurally distinct from currently known insecticidal proteins. Txp40 consists of two structurally different domains, an N-terminal domain (NTD) and a C-terminal domain (CTD), primarily joined by a 33-residue long linker peptide. Txp40 displayed proteolytic propensity. Txp40 gets proteolyzed, removing the linker peptide, which is essential for proper crystal packing. NTD adopts a novel fold composed of nine amphipathic helices and has no shared sequence or structural homology to any known proteins. CTD has structural homology with RNases of type II toxin-antitoxin (TA) complex belonging to the RelE/ParE toxin domain superfamily. NTD and CTD were individually toxic to Galleria mellonella larvae. However, maximal toxicity was observed when both domains were present. Our results suggested that the Txp40 acts as a two-domain binary toxin, which is unique and different from any known binary toxins and insecticidal proteins. Txp40 is also unique because it belongs to the prokaryotic RelE/ParE toxin family with a toxic effect on eukaryotic organisms, in contrast to other members of the same family. Broad insect specificity and unique binary toxin complex formation make Txp40 a viable candidate to overcome the development of resistance in insect pests.
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Affiliation(s)
- Omkar U Kinkar
- Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, Maharashtra, India; Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, 400085, Maharashtra, India.
| | - Ashwani Kumar
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, 400085, Maharashtra, India.
| | - Arpit Prashar
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085, Maharashtra, India.
| | - Beena Yadav
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, 400085, Maharashtra, India.
| | - Ashok B Hadapad
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085, Maharashtra, India.
| | - Ramesh S Hire
- Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, Maharashtra, India; Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085, Maharashtra, India.
| | - Ravindra D Makde
- Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, Maharashtra, India; Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, 400085, Maharashtra, India.
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7
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Kinkar OU, Singh R, Prashar A, Kumar A, Hire RS, Makde RD. 20-kDa accessory protein (P20) from Bacillus thuringiensis subsp. israelensis ISPC-12: Purification, characterization, solution scattering and structural analysis. Int J Biol Macromol 2024; 254:127985. [PMID: 37949263 DOI: 10.1016/j.ijbiomac.2023.127985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 11/12/2023]
Abstract
The 20-kDa accessory protein (P20) from Bacillus thuringiensis subsp. israelensis (Bti) has been identified as an essential molecular chaperone in the enhancement of Cry11Aa and Cyt1Aa toxins production and their bio-crystallization. Additionally, P20 plays a vital role in suppressing the toxic effect of Cyt toxin on the host bacterium and also enhances insecticidal activity of Cry1Ac protein. Thus, the function of P20 is more specific than that of the chaperones. However, P20 is poorly investigated and insufficiently characterized. In the present study, we recombinantly expressed p20 from local isolate Bti ISPC-12 in heterologous bacterium E. coli and P20 protein was purified to homogeneity. Detailed biochemical and biophysical characterization provides crucial insights about in-vitro behavior as well as spatial conformations of P20 protein. Further, structural modelling and analysis provides insights into three-dimensional organization of the protein and shows that P20 is a non-toxic member of cytolytic (Cyt) toxin family similar to Cyt1Ca, with presence of conserved cytolysin fold. Additionally, solution scattering reveals that P20 is present as a dimer in the solution and probable dimeric assembly of P20 is presented. The findings reported here reveal engaging facts about P20 thereby advancing our understanding about this protein, which will expedite future studies.
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Affiliation(s)
- Omkar U Kinkar
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, Maharashtra, India; Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India.
| | - Rahul Singh
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, Maharashtra, India; Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India.
| | - Arpit Prashar
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India.
| | - Ashwani Kumar
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India.
| | - Ramesh S Hire
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, Maharashtra, India; Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India.
| | - Ravindra D Makde
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, Maharashtra, India; Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India.
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8
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Jagdev MK, Tompa DR, Ling LL, Peoples AJ, Dandapat J, Mohapatra C, Lewis K, Vasudevan D. Crystal structure of the N-terminal domain of MtClpC1 in complex with the anti-mycobacterial natural peptide Lassomycin. Int J Biol Macromol 2023; 253:126771. [PMID: 37683752 DOI: 10.1016/j.ijbiomac.2023.126771] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 08/25/2023] [Accepted: 09/05/2023] [Indexed: 09/10/2023]
Abstract
Antibiotics form our frontline therapy against disease-causing bacteria. Unfortunately, antibiotic resistance is becoming more common, threatening a future where these medications can no longer cure infections. Furthermore, the emergence of multidrug-resistant (MDR), totally drug-resistant (TDR), and extensively drug-resistant (XDR) tuberculosis has increased the urgency of discovering new therapeutic leads with unique modes of action. Some natural peptides derived from actinomycetes, such as Cyclomarin A, Lassomycin, Rufomycin I, and Ecumicin, have potent and specific bactericidal activity against Mycobacterium tuberculosis, with the specificity owing to the fact that these peptides target the ClpC1 ATPase, an essential enzyme in mycobacteria, and inhibit/activate the proteolytic activity of the ClpC1/P1/P2 complex that participates in protein homeostasis. Here, we report the high-resolution crystal structure of the N-terminal domain of ClpC1 (ClpC1 NTD) in complex with Lassomycin, showing the specific binding mode of Lassomycin. In addition, the work also compares the Lassomycin complex structure with the previously known structures of ClpC1 NTD in complex with other natural peptides such as Cyclomarin A, Rufomycin I, and Ecumicin.
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Affiliation(s)
- Manas K Jagdev
- Division of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, Odisha, India; Post-Graduate Department of Biotechnology, Utkal University, Bhubaneswar 751004, Odisha, India
| | - Dharma R Tompa
- Division of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, Odisha, India
| | - Losee L Ling
- NovoBiotic Pharmaceuticals, Cambridge, MA 02138, USA
| | | | - Jagneshwar Dandapat
- Post-Graduate Department of Biotechnology, Utkal University, Bhubaneswar 751004, Odisha, India
| | - Chinmayee Mohapatra
- Division of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, Odisha, India
| | - Kim Lewis
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA.
| | - Dileep Vasudevan
- Division of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, Odisha, India; Transdisciplinary Biology Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, Kerala, India.
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Prashar A, Kinkar OU, Kumar A, Hadapad AB, Makde RD, Hire RS. Crystal structures of PirA and PirB toxins from Photorhabdus akhurstii subsp. akhurstii K-1. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2023; 162:104014. [PMID: 37778713 DOI: 10.1016/j.ibmb.2023.104014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/08/2023] [Accepted: 09/25/2023] [Indexed: 10/03/2023]
Abstract
PirAB binary toxin from Photorhabdus is toxic to the larvae of dipteran and lepidopteran insect pests. However, the 3-D structures and their toxicity mechanism are not yet fully understood. Here we report the crystal structures of PirA and PirB proteins from Photorhabdus akhurstii subsp. akhurstii K-1 at 1.6 and 2.1 Å, respectively. PirA comprises of eight β-strands depicting jelly-roll topology while PirB folds into two distinct domains, an N-terminal domain (PirB-N) made up of seven α-helices and a C-terminal domain (PirB-C) consists of ten β-strands. Despite the low sequence identity, PirA adopts similar architecture as domain III and PirB shared similar architecture as domain I/II of the Cry δ-endotoxin of Bacillus thuringiensis, respectively. However, PirA shows significant structural variations as compared to domain III of lepidopteran and dipteran specific Cry toxins (Cry1Aa and Cry11Ba) suggesting its role in virulence among range of insect pests and hence, in receptor binding. High structural resemblance between PirB-N and domain I of Cry toxin raises the possibility that the putative PirAB binary toxin may mimic the toxicity mechanism of the Cry protein, particularly its ability to perform pore formation. The mixture of independently purified PirA and PirB proteins are not toxic to insects. However, PirA-PirB protein complex purified from expression of pir operon with non-coding Enterobacterial Repetitive Intergenic Consensus (ERIC) sequences found toxic to Galleria mellonella larvae with LD50 value of 1.62 μg/larva. This suggests that toxic conformation of PirA and PirB are achieved in-vivo with the help of ERIC sequences.
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Affiliation(s)
- Arpit Prashar
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085, Maharashtra, India.
| | - Omkar U Kinkar
- Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, Maharashtra, India; Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, 400085, Maharashtra, India.
| | - Ashwani Kumar
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, 400085, Maharashtra, India.
| | - Ashok B Hadapad
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085, Maharashtra, India.
| | - Ravindra D Makde
- Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, Maharashtra, India; Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, 400085, Maharashtra, India.
| | - Ramesh S Hire
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085, Maharashtra, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, Maharashtra, India.
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10
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Patel SN, Sonani RR, Chaubey MG, Gupta GD, Singh NK, Kumar V, Madamwar D. Crystal structure of Synechococcus phycocyanin: implications of light-harvesting and antioxidant properties. 3 Biotech 2023; 13:247. [PMID: 37366498 PMCID: PMC10290628 DOI: 10.1007/s13205-023-03665-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 06/07/2023] [Indexed: 06/28/2023] Open
Abstract
Phycobiliproteins is a family of chromophore-containing proteins having light-harvesting and antioxidant capacity. The phycocyanin (PC) is a brilliant blue coloured phycobiliprotein, found in rod structure of phycobilisome and has been widely studied for their therapeutic and fluorescent properties. In the present study, the hexameric assembly structure of phycocyanin (Syn-PC) from Synechococcus Sp. R42DM is characterized by X-ray crystallography to understand its light-harvesting and antioxidant properties. The crystal structure of Syn-PC is solved with 2.15 Å resolution and crystallographic R-factors, Rwork/Rfree, 0.16/0.21. The hexamer of Syn-PC is formed by heterodimer of two polypeptide chains, namely, α- and β-subunits. The structure is analysed at atomic level to reveal the chromophore microenvironment and possible light energy transfer mechanism in Syn-PC. The chromophore arrangement in hexamer, deviation angle and distance between the chromophore contribute to the energy transfer efficiency of protein. The structural attributes responsible for the antioxidant potential of Syn-PC are recognized and annotated on its 3-dimensional structure. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03665-1.
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Affiliation(s)
- Stuti N. Patel
- P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, CHARUSAT Campus, Changa, Anand, Gujarat 388421 India
- Present Address: Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Ravi R. Sonani
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA USA
| | - Mukesh G. Chaubey
- Shri A. N. Patel P. G. Institute of Science and Research, Sardar Patel University, Anand, Gujarat India
| | - Gagan D. Gupta
- Radiation Biology and Health Sciences Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085 India
| | - Niraj Kumar Singh
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, Gujarat 382 011 India
| | - Vinay Kumar
- Radiation Biology and Health Sciences Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085 India
| | - Datta Madamwar
- P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, CHARUSAT Campus, Changa, Anand, Gujarat 388421 India
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11
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Khakerwala Z, Kumar A, Makde RD. Crystal structure of phosphate bound Acyl phosphatase mini-enzyme from Deinococcus radiodurans at 1Å resolution. Biochem Biophys Res Commun 2023; 671:153-159. [PMID: 37302289 DOI: 10.1016/j.bbrc.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/13/2023]
Abstract
Acylphosphatase (Acp) is a hydrolase which specifically cleaves carboxyl-phosphate bond of intermediates of metabolic pathways. It is a small cytosolic enzyme found in both prokaryotic and eukaryotic organisms. Previous crystal structures of acylphosphatase from different organisms have provided insights into the active site but the complete understanding of substrate binding and catalytic mechanisms in acylphosphatase remain elusive. Here we report the crystal structure of phosphate bound acylphosphatase from a mesothermic bacterium, Deinococcus radiodurans (drAcp) at resolution of 1.0 Å. Our structural analysis shows how the terminal phosphate group of substrates is bound to the active site, highlighting the importance of arginine in substrate recognition, role of asparagine in mode of catalysis and shedding light on the reaction mechanism. Additionally, the protein can refold after thermal melting by gradually lowering the temperature. To further explore the dynamics of drAcp, molecular dynamics simulation of drAcp and homologs from thermophilic organisms were carried out which revealed similar root mean square fluctuation profile but drAcp showed comparatively higher fluctuations.
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Affiliation(s)
- Zeenat Khakerwala
- Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, Maharashtra, India; Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, 400085, Maharashtra, India.
| | - Ashwani Kumar
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, 400085, Maharashtra, India.
| | - Ravindra D Makde
- Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, Maharashtra, India; Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, 400085, Maharashtra, India.
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12
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Lahiri D, Agrawal R, Chandravanshi K, Rajput P, Agrawal A, Dwivedi A, Makde RD, Jha SN, Garg N. Assessing the prospect of XAFS experiments of metalloproteins under in vivo conditions at Indus-2 synchrotron facility, India. JOURNAL OF SYNCHROTRON RADIATION 2023; 30:449-456. [PMID: 36891859 PMCID: PMC10000809 DOI: 10.1107/s1600577522011791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/10/2022] [Indexed: 06/18/2023]
Abstract
The feasibility of X-ray absorption fine-structure (XAFS) experiments of ultra-dilute metalloproteins under in vivo conditions (T = 300 K, pH = 7) at the BL-9 bending-magnet beamline (Indus-2) is reported, using as an example analogous synthetic Zn (0.1 mM) M1dr solution. The (Zn K-edge) XAFS of M1dr solution was measured with a four-element silicon drift detector. The first-shell fit was tested and found to be robust against statistical noise, generating reliable nearest-neighbor bond results. The results are found to be invariant between physiological and non-physiological conditions, which confirms the robust coordination chemistry of Zn with important biological implications. The scope of improving spectral quality for accommodation of higher-shell analysis is addressed.
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Affiliation(s)
- Debdutta Lahiri
- High Pressure and Synchrotron Radiation Physics, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Richa Agrawal
- Department of Biochemistry and Molecular Biology, University of Chicago, 929 E 57th Street, Chicago, IL 60637, USA
| | | | - Parasmani Rajput
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Ankur Agrawal
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Ashutosh Dwivedi
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Ravindra D. Makde
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - S. N. Jha
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Nandini Garg
- High Pressure and Synchrotron Radiation Physics, Bhabha Atomic Research Centre, Mumbai 400085, India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
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13
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Gaur NK, Ghosh B, Goyal VD, Kulkarni K, Makde RD. Evolutionary conservation of protein dynamics: insights from all-atom molecular dynamics simulations of 'peptidase' domain of Spt16. J Biomol Struct Dyn 2023; 41:1445-1457. [PMID: 34971347 DOI: 10.1080/07391102.2021.2021990] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Protein function is encoded in its sequence, manifested in its three-dimensional structure, and facilitated by its dynamics. Studies have suggested that protein structures with higher sequence similarity could have more similar patterns of dynamics. However, such studies of protein dynamics within and across protein families typically rely on coarse-grained models, or approximate metrics like crystallographic B-factors. This study uses µs scale molecular dynamics (MD) simulations to explore the conservation of dynamics among homologs of ∼50 kDa N-terminal module of Spt16 (Spt16N). Spt16N from Saccharomyces cerevisiae (Sc-Spt16N) and three of its homologs with 30-40% sequence identities were available in the PDB. To make our data-set more comprehensive, the crystal structure of an additional homolog (62% sequence identity with Sc-Spt16N) was solved at 1.7 Å resolution. Cumulative MD simulations of 6 µs were carried out on these Spt16N structures and on two additional protein structures with varying degrees of similarity to it. The simulations revealed that correlation in patterns of backbone fluctuations vary linearly with sequence identity. This trend could not be inferred using crystallographic B-factors. Further, normal mode analysis suggested a similar pattern of inter-domain (inter-lobe) motions not only among Spt16N homologs, but also in the M24 peptidase structure. On the other hand, MD simulation results highlighted conserved motions that were found unique for Spt16N protein, this along with electrostatics trends shed light on functional aspects of Spt16N.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Neeraj K Gaur
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, India.,Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Biplab Ghosh
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, India
| | - Venuka Durani Goyal
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, India
| | - Kiran Kulkarni
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Ravindra D Makde
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, India
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14
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Bobde RC, Kumar A, Vasudevan D. Plant-specific HDT family histone deacetylases are nucleoplasmins. THE PLANT CELL 2022; 34:4760-4777. [PMID: 36069647 PMCID: PMC9709999 DOI: 10.1093/plcell/koac275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Histone acetyltransferase (HAT)- and histone deacetylase (HDAC)-mediated histone acetylation and deacetylation regulate nucleosome dynamics and gene expression. HDACs are classified into different families, with HD-tuins or HDTs being specific to plants. HDTs show some sequence similarity to nucleoplasmins, the histone chaperones that aid in binding, storing, and loading H2A/H2B dimers to assemble nucleosomes. Here, we solved the crystal structure of the N-terminal domain (NTD) of all four HDTs (HDT1, HDT2, HDT3, and HDT4) from Arabidopsis (Arabidopsis thaliana). The NTDs form a nucleoplasmin fold, exist as pentamers in solution, and are resistant to protease treatment, high temperature, salt, and urea conditions. Structurally, HDTs do not form a decamer, unlike certain classical nucleoplasmins. The HDT-NTD requires an additional A2 acidic tract C-terminal to the nucleoplasmin domain for interaction with histone H3/H4 and H2A/H2B oligomers. We also report the in-solution structures of HDT2 pentamers in complex with histone oligomers. Our study provides a detailed structural and in vitro functional characterization of HDTs, revealing them to be nucleoplasmin family histone chaperones. The experimental confirmation that HDTs are nucleoplasmins may spark new interest in this enigmatic family of proteins.
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Affiliation(s)
- Ruchir C Bobde
- Institute of Life Sciences, Bhubaneswar, Odisha 751023, India
- Regional Centre for Biotechnology, Faridabad 121001, Haryana, India
| | - Ashish Kumar
- Institute of Life Sciences, Bhubaneswar, Odisha 751023, India
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15
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Jangid DK, Dastider SG, Biswas R, Khirid S, Meena S, Kumar P, Sahoo SC, Verma VP, Makde RD, Kumar A, Jangir R, Mondal K, Haldar KK, Dhayal RS. Dithiophosphonate Anchored Heterometallic (Ag(I)/Fe(II)) Molecular Catalysts for Electrochemical Hydrogen Evolution Reaction. Inorg Chem 2022; 61:13342-13354. [PMID: 35959970 DOI: 10.1021/acs.inorgchem.2c01281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The dichalcogenide ligated molecules in catalysis to produce molecular hydrogen through electroreduction of water are rarely explored. Here, a series of heterometallic [Ag4(S2PFc(OR)4] [where Fc = Fe(η5-C5H4)(η5-C5H5), R = Me, 1; Et, 2; nPr, 3; isoAmyl, 4] clusters were synthesized and characterized by IR, absorption spectroscopy, NMR (1H, 31P), and electrospray ionization mass spectrometry. The molecular structures of 1, 2, and 3 clusters were established by single-crystal X-ray crystallographic analysis. The structural elucidation shows that each triangular face of a tetrahedral silver(I) core is capped by a ferrocenyl dithiophosphonate ligand in a trimetallic triconnective (η3; μ2, μ1) pattern. A comparative electrocatalytic hydrogen evolution reaction of 1-5 (R = iPr, 5) was studied in order to demonstrate the potential of these clusters in water splitting activity. The experimental results reveal that catalytic performance decreases with increases in the length of the carbon chain and branching within the alkoxy (-OR) group of these clusters. Catalytic durability was found effective even after 8 h of a chronoamperometric stability test along with 1500 cycles of linear sweep voltammetry performance, and only 15 mV overpotential was increased at 5 mA/cm2 current density for cluster 1. A catalytic mechanism was proposed by applying density functional theory (DFT) on clusters 1 and 2 as a representative. Here, a μ1 coordinated S-site between Ag4 core and ligand was found a reaction center. The experimental results are also in good accordance with the DFT analysis.
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Affiliation(s)
- Dilip Kumar Jangid
- Department of Chemistry, Central University of Punjab, Bathinda 151401, India
| | - Saptarshi G Dastider
- Department of Chemistry, Central University of Punjab, Bathinda 151401, India.,Department of Physics, Central University of Punjab, Bathinda 151401, India
| | | | - Samreet Khirid
- Department of Chemistry, Central University of Punjab, Bathinda 151401, India
| | - Sangeeta Meena
- Department of Chemistry, Central University of Punjab, Bathinda 151401, India
| | - Pankaj Kumar
- Department of Chemistry, Central University of Punjab, Bathinda 151401, India
| | - Subash C Sahoo
- Department of Chemistry, Panjab University, Chandigarh 160014, India
| | - Ved Prakash Verma
- Department of Chemistry, Banasthali University, Newai-Jodhpuriya Road, Vanasthali 304022, India
| | - Ravindra D Makde
- Beamline of Protein Crystallography, Raja Ramanna Centre for Advance Technology, Indore 452013, M.P., India
| | - Ashwani Kumar
- Beamline of Protein Crystallography, Raja Ramanna Centre for Advance Technology, Indore 452013, M.P., India
| | - Ravindra Jangir
- Beamline of Protein Crystallography, Raja Ramanna Centre for Advance Technology, Indore 452013, M.P., India
| | | | | | - Rajendra S Dhayal
- Department of Chemistry, Central University of Punjab, Bathinda 151401, India
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16
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Mathivanan S, Chunchagatta Lakshman PK, Singh M, Giridharan S, Sathish K, Hurakadli MA, Bharatham K, Kamariah N. Structure of a 14-3-3ε:FOXO3a pS253 Phosphopeptide Complex Reveals 14-3-3 Isoform-Specific Binding of Forkhead Box Class O Transcription Factor (FOXO) Phosphoproteins. ACS OMEGA 2022; 7:24344-24352. [PMID: 35874228 PMCID: PMC9301721 DOI: 10.1021/acsomega.2c01700] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The transcriptional activity of Forkhead Box O3 (FOXO3a) is inactivated by AKT-mediated phosphorylation on Serine 253 (S253), which enables FOXO3a binding to 14-3-3. Phosphorylated FOXO3a binding to 14-3-3 facilitates the nuclear exclusion of FOXO3a, causing cancer cell proliferation. The FOXO3a/14-3-3 interaction has, therefore, emerged as an important therapeutic target. Here, we report a comprehensive analysis using fluorescence polarization, isothermal titration calorimetry, small-angle X-ray scattering, X-ray crystallography, and molecular dynamics simulations to gain molecular-level insights into the interaction of FOXO3apS253 phosphopeptide with 14-3-3ε. A high-resolution structure of the fluorophore-labeled FOXO3apS253:14-3-3ε complex revealed a distinct mode of interaction compared to other 14-3-3 phosphopeptide complexes. FOXO3apS253 phosphopeptide showed significant structural difference in the positions of the -3 and -4 Arg residues relative to pSer, compared to that of a similar phosphopeptide, FOXO1pS256 bound to 14-3-3σ. Moreover, molecular dynamics studies show that the significant structural changes and molecular interactions noticed in the crystal structure of FOXO3apS253:14-3-3ε are preserved over the course of the simulation. Thus, this study reveals structural differences between the binding to 14-3-3 isoforms of FOXO1pS256 versus FOXO3apS253, providing a framework for the rational design of isoform-specific FOXO/14-3-3 protein-protein interaction inhibitors for therapy.
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17
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Patel SN, Sonani RR, Gupta GD, Singh NK, Kumar V, Madamwar D. Crystal structure analysis of phycoerythrin from marine cyanobacterium Halomicronema. J Biomol Struct Dyn 2022; 41:3752-3761. [PMID: 35354393 DOI: 10.1080/07391102.2022.2055647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Phycoerythrin (PE) is green light-absorbing pigment-protein that assists in efficient light harvesting in cyanobacteria and red-algae. PE in cyanobacteria stays less studied so far as compared to that in red algae. In this study, PE from marine cyanobacteria Halomicronema sp. R31DM is purified and subjected for its structural characterisation by X-ray crystallography in order to understand its light-harvesting characteristics. The crystal structure is solved to a resolution-limit of 2.21 Å with reasonable R-factors values, 0.16/0.21 (Rwork/ Rfree). PE forms hexamer of hetero-dimers made up of two peptide chains, α- and β-subunits containing 2 and 3 phycoerythrobilin (PEB) chromophores covalently attached to them, respectively. Geometry of five chromophores is analysed along with their relative position within the PE hexamer. Also, their interactions with the surrounding microenvironment are analysed. The plausible energy transfer pathways in hexamer structure have been predicted based on relative position and geometry of chromophores. This structure enriches the structural information of cyanobacterial PE in order to understand its light-harvesting capacity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Stuti N Patel
- P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, Anand, India
| | - Ravi R Sonani
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland.,Radiation Biology and Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Gagan D Gupta
- Radiation Biology and Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Niraj Kumar Singh
- Shri A. N. Patel P. G. Institute of Science and Research, Sardar Patel University, Anand, India
| | - Vinay Kumar
- Radiation Biology and Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Datta Madamwar
- P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, Anand, India
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18
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Kumar A, Singh R, Ghosh B, Makde RD. Crystal structure of aspartyl dipeptidase from Xenopus laevis revealed ligand binding induced loop ordering and catalytic triad assembly. Proteins 2021; 90:299-308. [PMID: 34431561 DOI: 10.1002/prot.26220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 07/30/2021] [Accepted: 08/19/2021] [Indexed: 11/06/2022]
Abstract
Gene encoding aspartyl dipeptidase from Xenopus levies (PepExl) is upregulated by thyroid hormone and is proposed to play a significant role in resorption of tadpole tail during metamorphosis. However, the importance of peptidase activity for the resorption of the tail remain elusive. Here we report the crystal structures of first eukaryotic S51 peptidase, PepExl, in its ligand-free and Asp-bound states at 1.4 and 1.8 Å resolutions, respectively. The active site is located at dimeric interface and the catalytic triad is found to be dissembled in ligand-free and assembled in Asp-bound state. Structural comparison and molecular dynamic simulations of ligand-free and Asp-bound states shows that distinct loop (loop-A) plays an important role in active site shielding, substrate binding and enzyme activation. This study illuminates the Asp-X dipeptide binding in PepExl is associated with ordering of the loop-A and assembly of residues of catalytic triad in active conformation for enzymatic activity.
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Affiliation(s)
- Ashwani Kumar
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, India
| | - Rahul Singh
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, India
| | - Biplab Ghosh
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, India
| | - Ravindra D Makde
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, India
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19
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Kumari P, Sundaram R, Manohar K, Vasudevan D, Acharya N. Interdomain connecting loop and J loop structures determine cross-species compatibility of PCNA. J Biol Chem 2021; 297:100911. [PMID: 34175309 PMCID: PMC8319368 DOI: 10.1016/j.jbc.2021.100911] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/17/2021] [Accepted: 06/22/2021] [Indexed: 11/18/2022] Open
Abstract
Eukaryotic proliferating cell nuclear antigen (PCNA) plays an essential role in orchestrating the assembly of the replisome complex, stimulating processive DNA synthesis, and recruiting other regulatory proteins during the DNA damage response. PCNA and its binding partner network are relatively conserved in eukaryotes, and it exhibits extraordinary structural similarity across species. However, despite this structural similarity, the PCNA of a given species is rarely functional in heterologous systems. In this report, we determined the X-ray crystal structure of Neurospora crassa PCNA (NcPCNA) and compared its structure–function relationship with other available PCNA studies to understand this cross-species incompatibility. We found two regions, the interdomain connecting loop (IDCL) and J loop structures, vary significantly among PCNAs. In particular, the J loop deviates in NcPCNA from that in Saccharomyces cerevisiae PCNA (ScPCNA) by 7 Å. Differences in the IDCL structures result in varied binding affinities of PCNAs for the subunit Pol32 of DNA polymerase delta and for T2-amino alcohol, a small-molecule inhibitor of human PCNA. To validate that these structural differences are accountable for functional incompatibility in S. cerevisiae, we generated NcPCNA mutants mimicking IDCL and J loop structures of ScPCNA. Our genetic analyses suggested that NcPCNA mutants are fully functional in S. cerevisiae. The susceptibility of the strains harboring ScPCNA mimics of NcPCNA to various genotoxic agents was similar to that in yeast cells expressing ScPCNA. Taken together, we conclude that in addition to the overall architecture of PCNA, structures of the IDCL and J loop of PCNA are critical determinants of interspecies functional compatibility.
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Affiliation(s)
- Premlata Kumari
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India; Regional Centre for Biotechnology, Faridabad, India
| | - Rajivgandhi Sundaram
- Laboratory of Macromolecular Crystallography, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India; Manipal Academy of Higher Education, Manipal, India
| | - Kodavati Manohar
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Dileep Vasudevan
- Laboratory of Macromolecular Crystallography, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India.
| | - Narottam Acharya
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India.
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20
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Sundaram R, Manohar K, Patel SK, Acharya N, Vasudevan D. Structural analyses of PCNA from the fungal pathogen Candida albicans identify three regions with species-specific conformations. FEBS Lett 2021; 595:1328-1349. [PMID: 33544878 DOI: 10.1002/1873-3468.14055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 01/11/2023]
Abstract
An assembly of multiprotein complexes achieves chromosomal DNA replication at the replication fork. In eukaryotes, proliferating cell nuclear antigen (PCNA) plays a vital role in the assembly of multiprotein complexes at the replication fork and is essential for cell viability. PCNA from several organisms, including Saccharomyces cerevisiae, has been structurally characterised. However, the structural analyses of PCNA from fungal pathogens are limited. Recently, we have reported that PCNA from the opportunistic fungal pathogen Candida albicans complements the essential functions of ScPCNA in S. cerevisiae. Still, it only partially rescues the loss of ScPCNA when the yeast cells are under genotoxic stress. To understand this further, herein, we have determined the crystal structure of CaPCNA and compared that with the existing structures of other fungal and human PCNA. Our comparative structural and in-solution small-angle X-ray scattering (SAXS) analyses reveal that CaPCNA forms a stable homotrimer, both in crystal and in solution. It displays noticeable structural alterations in the oligomerisation interface, P-loop and hydrophobic pocket regions, suggesting its differential function in a heterologous system and avenues for developing specific therapeutics. DATABASES: The PDB and SASBDB accession codes for CaPCNA are 7BUP and SASDHQ9, respectively.
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Affiliation(s)
- Rajivgandhi Sundaram
- Laboratory of Macromolecular Crystallography, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India.,Manipal Academy of Higher Education, India
| | - Kodavati Manohar
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Shraddheya Kumar Patel
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Narottam Acharya
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Dileep Vasudevan
- Laboratory of Macromolecular Crystallography, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
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21
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22
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Singh R, Deshmukh S, Kumar A, Goyal VD, Makde RD. Crystal structure of XCC3289 from Xanthomonas campestris: homology with the N-terminal substrate-binding domain of Lon peptidase. Acta Crystallogr F Struct Biol Commun 2020; 76:488-494. [PMID: 33006577 PMCID: PMC7531242 DOI: 10.1107/s2053230x20011875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 08/28/2020] [Indexed: 11/13/2023] Open
Abstract
LonA peptidase is a major component of the protein quality-control mechanism in both prokaryotes and the organelles of eukaryotes. Proteins homologous to the N-terminal domain of LonA peptidase, but lacking its other domains, are conserved in several phyla of prokaryotes, including the Xanthomonadales order. However, the function of these homologous proteins (LonNTD-like proteins) is not known. Here, the crystal structure of the LonNTD-like protein from Xanthomonas campestris (XCC3289; UniProt Q8P5P7) is reported at 2.8 Å resolution. The structure was solved by molecular replacement and contains one polypeptide in the asymmetric unit. The structure was refined to an Rfree of 29%. The structure of XCC3289 consists of two domains joined by a long loop. The N-terminal domain (residues 1-112) consists of an α-helix surrounded by β-sheets, whereas the C-terminal domain (residues 123-193) is an α-helical bundle. The fold and spatial orientation of the two domains closely resembles those of the N-terminal domains of the LonA peptidases from Escherichia coli and Mycobacterium avium. The structure is also similar to that of cereblon, a substrate-recognizing component of the E3 ubiquitin ligase complex. The N-terminal domains of both LonA and cereblon are known to be involved in specific protein-protein interactions. This structural analysis suggests that XCC3289 and other LonNTD-like proteins might also be capable of such protein-protein interactions.
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Affiliation(s)
- Rahul Singh
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Sonali Deshmukh
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Ashwani Kumar
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Venuka Durani Goyal
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Ravindra D. Makde
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
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23
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Agrawal R, Goyal VD, Singh R, Kumar A, Jamdar SN, Kumar A, Makde RD. Structural basis for the unusual substrate specificity of unique two-domain M1 metallopeptidase. Int J Biol Macromol 2020; 147:304-313. [PMID: 31923495 DOI: 10.1016/j.ijbiomac.2019.12.239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 12/19/2019] [Accepted: 12/27/2019] [Indexed: 11/30/2022]
Abstract
M1 metallopeptidases regulate many important biological processes such as angiogenesis, tumour growth, hormone regulation, and immune cell development. Knowledge of substrate specificity mechanism in this family is valuable. An M1 peptidase from Deinococcus radiodurans (M1dr) with preference for bulky hydrophobic residues at N-terminus of peptide substrates was recently reported. In contrast to Escherichia coli aminopeptidase N, a previously characterized M1 peptidase, M1dr exhibits reduced activity towards peptides with N-terminal Arg or Ala residue. In order to illuminate structural basis of substrate specificity, we report several crystal structures of M1dr with different amino acids bound to the active site. Structural analysis indicated that the enzyme makes subtle adjustments to multiple residues leading to significant volume change of the active site cavity to accommodate residues of varying sizes (Leu to Trp). This study further reveals that the low preference for Arg at N-terminus of peptide substrate arises from a non-productive conformation in which many of the Arg molecules bind where they block the proton donor essential for the peptidase reaction. Hence, this study illuminates the substrate-binding mechanism and also reveals the structural basis for the substrate specificity of M1dr enzyme.
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Affiliation(s)
- Richa Agrawal
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore 453552, India
| | - Venuka Durani Goyal
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Rahul Singh
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Ashwani Kumar
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Sahayog N Jamdar
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore 453552, India.
| | - Ravindra D Makde
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India.
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Vibrio cholerae YaeO is a Structural Homologue of RNA Chaperone Hfq that Inhibits Rho-dependent Transcription Termination by Dissociating its Hexameric State. J Mol Biol 2019; 431:4749-4766. [PMID: 31628950 DOI: 10.1016/j.jmb.2019.09.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 09/25/2019] [Accepted: 09/26/2019] [Indexed: 11/21/2022]
Abstract
Rho-dependent transcription termination is a well-conserved process in bacteria. The Psu and YaeO proteins are the two established inhibitors of the ATP-dependent RNA helicase Rho protein of Escherichia coli. Here, we show a detailed sequence and phylogenetic analysis demonstrating that Vibrio cholerae YaeO (VcYaeO) is significantly distinct from its E. coli counterpart. VcYaeO induces significant growth defect on in vivo expression and inhibits in vitro functions of the V. cholerae Rho on directly binding to the latter. Through various biophysical techniques, we showed that interaction of VcYaeO disrupts the oligomeric state of the VcRho. Structure of VcYaeO solved at 1.75 Å resolution, the first crystal structure of a YaeO protein, demonstrates a beta-sandwich fold distinct from the NMR structure of the EcYaeO. Interestingly, VcYaeO structurally resembles the Hfq protein, and like the latter, it exhibits ssDNA/RNA-binding properties. Docking studies demonstrate probable interactions of VcYaeO with VcRho and mode of inhibition of RNA binding to Rho. We propose that VcYaeO inhibits the function of the Rho protein via disruption of the latter's hexameric assembly and also likely by sequestering the RNA from the Rho primarybinding sites.
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25
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Sharma M, Kumar V. Crystal structure of BinAB toxin receptor (Cqm1) protein and molecular dynamics simulations reveal the role of unique Ca(II) ion. Int J Biol Macromol 2019; 140:1315-1325. [PMID: 31449868 DOI: 10.1016/j.ijbiomac.2019.08.126] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 08/14/2019] [Accepted: 08/14/2019] [Indexed: 10/26/2022]
Abstract
Glycoside hydrolase 13 (GH13) family represents a large and diverse enzyme family. Cqm1, an amylomaltase of Culex mosquito, belongs to the GH13 family and subfamily 17 (GH13_17). The protein acts as the receptor for mosquito-larvicidal BinAB toxin that is used world-wide for control of the mosquito population. The protein was crystallized in the presence of a mixture of divalent metal ions. Cqm1 crystal structure was solved using the MRSAD method using Cd(II) anomalous at 1.9 Å wavelength and the structure was refined against 1.8 Å synchrotron data. One tightly bound Ca(II) ion in each of the monomer was observed and this site is suggested here to be unique to the GH13_17 family. Molecular dynamics simulations provide clues for the functional role of Ca(II) ion shown earlier to be essential for enzymatic activity. An optimized substrate (maltotriose) bound structure of the complex was constructed based on which 'retaining-type' mechanism can be predicted reliably. It reveals large conformational change in aromatic residues situated at active-site entrance. A Cd(II) ion was observed overlapping with the substrate-binding site. Kinetics data suggests non-competitive inhibition of Cqm1 by Cd(II). This is the first structure from the GH13_17 family and provides template for constructing reliable models for other members.
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Affiliation(s)
- Mahima Sharma
- Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Vinay Kumar
- Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai 400085, India.
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26
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Chakravarty D, Bihani SC, Banerjee M, Ballal A. Novel molecular insights into the anti-oxidative stress response and structure-function of a salt-inducible cyanobacterial Mn-catalase. PLANT, CELL & ENVIRONMENT 2019; 42:2508-2521. [PMID: 30993731 DOI: 10.1111/pce.13563] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 04/07/2019] [Indexed: 06/09/2023]
Abstract
KatB, a salt-inducible Mn-catalase, protects the cyanobacterium Anabaena from salinity/oxidative stress. In this report, we provide distinctive insights into the biological-biochemical function of KatB at the molecular level. Anabaena overexpressing the wild-type KatB protein (KatBWT) detoxified H2 O2 efficiently, showing reduced burden of reactive oxygen species compared with the strain overproducing KatBF2V (wherein F-2 is replaced by V). Correspondingly, the KatBWT protein also displayed several folds more activity than KatBF2V. Interestingly, the KatB variants with large hydrophobic amino acids (F/W/Y) were more compact, showed enhanced activity, and were resistant to thermal/chemical denaturation than variants with smaller residues (G/A/V) at the second position. X-ray crystallography-based analysis showed that F-2 was required for appropriate interactions between two subunits. These contacts provided stability to the hexamer, making it more compact. F-2, through its interaction with F-66 and W-43, formed the proper hydrophobic pocket that held the active site together. Consequently, only residues that supported activity (i.e., F/Y/W) were selected at the second position in Mn-catalases during evolution. This study (a) demonstrates that modification of nonactive site residues can alter the response of catalases to environmental stress and (b) has expanded the scope of amino acids that can be targeted for rational protein engineering in plants.
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Affiliation(s)
- Dhiman Chakravarty
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Subhash C Bihani
- Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
| | - Manisha Banerjee
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Anand Ballal
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
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27
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Das S, Batra S, Gupta PP, Kumar M, Srivastava VK, Jyoti A, Singh N, Kaushik S. Identification and evaluation of quercetin as a potential inhibitor of naphthoate synthase from Enterococcus faecalis. J Mol Recognit 2019; 32:e2802. [PMID: 31353747 DOI: 10.1002/jmr.2802] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/29/2019] [Accepted: 06/07/2019] [Indexed: 12/31/2022]
Abstract
Enterococcus faecalis is a gram-positive, rod-shape bacteria responsible for around 65% to 80% of all enterococcal nosocomial infections. It is multidrug resistant (MDR) bacterium resistant to most of the first-line antibiotics. Due to the emergence of MDR strains, there is an urgent need to find novel targets to develop new antibacterial drugs against E. faecalis. In this regard, we have identified naphthoate synthase (1,4-dihydroxy-2-naphthoyl-CoA synthase, EC: 4.1.3.36; DHNS) as an anti-E. faecalis target, as it is an essential enzyme for menaquinone (vitamin K2 ) synthetic pathway in the bacterium. Thus, inhibiting naphtholate synthase may consequently inhibit the bacteria's growth. In this regard, we report here cloning, expression, purification, and preliminary structural studies of naphthoate synthase along with in silico modeling, molecular dynamic simulation of the model and docking studies of naphthoate synthase with quercetin, a plant alkaloid. Biochemical studies have indicated quercetin, a plant flavonoid as the potential lead compound to inhibit catalytic activity of EfDHNS. Quercetin binding has also been validated by spectrofluorimetric studies in order to confirm the bindings of the ligand compound with EfDHNS at ultralow concentrations. Reported studies may provide a base for structure-based drug development of antimicrobial compounds against E. faecalis.
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Affiliation(s)
- Satyajeet Das
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Sagar Batra
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Pramodkumar P Gupta
- School of Biotechnology and Bioinformatics, DY Patil Deemed to be University, Navi Mumbai, India
| | - Mukesh Kumar
- School of Medicine, Case Western reserve University, Cleveland, Ohio
| | | | - Anupam Jyoti
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Nagendra Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, India
| | - Sanket Kaushik
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
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28
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Agrawal R, Goyal VD, Kumar A, Gaur NK, Jamdar SN, Kumar A, Makde RD. Two-domain aminopeptidase of M1 family: Structural features for substrate binding and gating in absence of C-terminal domain. J Struct Biol 2019; 208:51-60. [PMID: 31351924 DOI: 10.1016/j.jsb.2019.07.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 07/19/2019] [Accepted: 07/24/2019] [Indexed: 02/08/2023]
Abstract
Zinc metallopeptidases of the M1 family (M1 peptidases) with unique metal binding motif HEXXH(X)18E regulate many important biological processes such as tumor growth, angiogenesis, hormone regulation, and immune cell development. Typically, these enzymes exist in three-domain [N-terminal domain (N-domain), catalytic domain, and C-terminal domain (C-domain)] or four-domain (N-domain, catalytic domain, middle domain, and C-domain) format in which N-domain and catalytic domain are more conserved. The C-domain plays important roles in substrate binding and gating. In this study we report the first structure of a two-domain (N-domain and catalytic domain) M1 peptidase at 2.05 Å resolution. Despite the lack of C-domain, the enzyme is active and prefers peptide substrates with large hydrophobic N-terminal residues. Its substrate-bound structure was determined at 1.9 Å resolution. Structural analyses supported by site directed mutagenesis and molecular dynamics simulations reveal structural features that could compensate for the lack of C-domain. A unique loop insertion (loop A) in the N-domain has important roles in gating and desolvation of active site. Three Arg residues of the catalytic domain are involved in substrate-binding roles typically played by positively charged residues of C-domain in other M1 peptidases. Further, its unique exopeptidase sequence motif, LALET, creates a more hydrophobic environment at the S1 subsite (which binds N-terminal residue of the substrate in aminopeptidases) than the more common GXMEN motif in the family. This leads to high affinity for large hydrophobic residues in the S1 subsite, which contributes towards efficient substrate binding in absence of C-domain.
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Affiliation(s)
- Richa Agrawal
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore 453552, India; High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Venuka Durani Goyal
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Ashwani Kumar
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Neeraj K Gaur
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Sahayog N Jamdar
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore 453552, India.
| | - Ravindra D Makde
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India.
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29
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Sonani RR, Rastogi RP, Patel SN, Chaubey MG, Singh NK, Gupta GD, Kumar V, Madamwar D. Phylogenetic and crystallographic analysis of Nostoc phycocyanin having blue-shifted spectral properties. Sci Rep 2019; 9:9863. [PMID: 31285455 PMCID: PMC6614406 DOI: 10.1038/s41598-019-46288-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 06/26/2019] [Indexed: 01/22/2023] Open
Abstract
The distinct sequence feature and spectral blue-shift (~10 nm) of phycocyanin, isolated from Nostoc sp. R76DM (N-PC), were investigated by phylogenetic and crystallographic analyses. Twelve conserved substitutions in N-PC sequence were found distributed unequally among α- and β-subunit (3 in α- and 9 in β-subunit). The phylogenetic analysis suggested that molecular evolution of α- and β-subunit of Nostoc-phycocyanin is faster than evolution of Nostoc-species. The divergence events seem to have occurred more frequently in β-subunit, compared to α-subunit (relative divergence, 7.38 for α-subunit and 9.66 for β-subunit). Crystal structure of N-PC was solved at 2.35 Å resolution to reasonable R-factors (Rwork/RFree = 0.199/0.248). Substitutions congregate near interface of two αβ-monomer in N-PC trimer and are of compensatory nature. Six of the substitutions in β-subunit may be involved in maintaining topology of β-subunit, one in inter-monomer interaction and one in interaction with linker-protein. The β153Cys-attached chromophore adopts high-energy conformational state resulting due to reduced coplanarity of B- and C-pyrrole rings. Distortion in chromophore conformation can result in blue-shift in N-PC spectral properties. N-PC showed significant in-vitro and in-vivo antioxidant activity comparable with other phycocyanin. Since Nostoc-species constitute a distinct phylogenetic clade, the present structure would provide a better template to build a model for phycocyanins of these species.
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Affiliation(s)
- Ravi R Sonani
- Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India
| | - Rajesh Prasad Rastogi
- Ministry of Environment, Forest & Climate Change, Indira Paryavaran Bhawan, New Delhi, 110003, India
| | - Stuti Nareshkumar Patel
- Post-Graduate Department of Biosciences, Satellite Campus, Sardar Patel University, Bakrol, Anand, 388 315, Gujarat, India
| | - Mukesh Ghanshyam Chaubey
- Shri A. N. Patel P. G. Institute of Science and Research, Sardar Patel University, Anand, Gujarat, 388001, India
| | - Niraj Kumar Singh
- Shri A. N. Patel P. G. Institute of Science and Research, Sardar Patel University, Anand, Gujarat, 388001, India
| | - Gagan D Gupta
- Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India
| | - Vinay Kumar
- Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India.
| | - Datta Madamwar
- Post-Graduate Department of Biosciences, Satellite Campus, Sardar Patel University, Bakrol, Anand, 388 315, Gujarat, India.
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30
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Megta AK, Mishra AK, Palva A, von Ossowski I, Krishnan V. Crystal structure of basal pilin SpaE reveals the molecular basis of its incorporation in the lactobacillar SpaFED pilus. J Struct Biol 2019; 207:74-84. [PMID: 31026587 DOI: 10.1016/j.jsb.2019.04.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 04/15/2019] [Accepted: 04/23/2019] [Indexed: 11/16/2022]
Abstract
For some Gram-positive genera and species, the long-extended and adhesive sortase-dependent pilus plays an essential role during host colonization, biofilm formation, and immune modulation. Lactobacillus rhamnosus GG is a gut-adapted commensal strain that harbors the operonic genes for the SpaCBA and SpaFED pili, both being comprised of three different protein subunits termed the backbone, tip, and basal pilins. Crystal structures of the backbone pilins (SpaA and SpaD) have recently been solved, and here we describe the high-resolution (1.5 Å) structural determination of the SpaE basal pilin. SpaE consists of two immunoglobulin-like CnaB domains, with each displaying a spontaneously formed internal isopeptide bond, though apparently slow forming in the N-terminal domain. Remarkably, SpaE contains an atypically lengthy unstructured C-terminal tail, along with an YPKN pilin motif peptide, which is normally reserved for backbone subunits. Based on our analysis of the crystal structure data, we provide a molecular model for the basal positioning of the SpaE pilin within the SpaFED pilus.
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Affiliation(s)
- Abhin Kumar Megta
- Laboratory of Structural Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana 121 001, India; School of Biotechnology, KIIT University, Odisha 751024, India
| | - Arjun K Mishra
- Laboratory of Structural Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana 121 001, India
| | - Airi Palva
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | | | - Vengadesan Krishnan
- Laboratory of Structural Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana 121 001, India.
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31
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Yadav P, Goyal VD, Chandravanshi K, Kumar A, Gokhale SM, Jamdar SN, Makde RD. Catalytic triad heterogeneity in S51 peptidase family: Structural basis for functional variability. Proteins 2019; 87:679-692. [PMID: 30968972 DOI: 10.1002/prot.25693] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 04/03/2019] [Accepted: 04/05/2019] [Indexed: 11/07/2022]
Abstract
Peptidase E (PepE) is a nonclassical serine peptidase with a Ser-His-Glu catalytic triad. It is specific for dipeptides with an N-terminal aspartate residue (Asp-X dipeptidase activity). Its homolog from Listeria monocytogenes (PepElm) has a Ser-His-Asn "catalytic triad." Based on sequence alignment we predicted that the PepE homolog from Deinococcus radiodurans (PepEdr) would have a Ser-His-Asp "catalytic triad." We confirmed this by solving the crystal structure of PepEdr to 2.7 Å resolution. We show that PepElm and PepEdr lack the Asp-X dipeptidase activity. Our analyses suggest that absence of P1 pocket in the active site could be the main reason for this lack of typical activity. Sequence and structural data reveal that the PepE homologs can be divided into long and short PepEs based on presence or absence of a C-terminal tail which adopts a β-hairpin conformation in the canonical PepE from Salmonella enterica. A long PepE from Bacillus subtilis with Ser-His-Asp catalytic triad exhibits Asp-X dipeptidase activity. Whereas the three long PepEs enzymatically characterized till date have been found to possess the Asp-X dipeptidase activity, the three enzymatically characterized short PepEs lack this activity irrespective of the nature of their catalytic triads. This study illuminates the structural and functional heterogeneity in the S51 family and also provides structural basis for the functional variability among PepE homologs.
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Affiliation(s)
- Pooja Yadav
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India.,School of Biochemistry, Devi Ahilya University, Indore, India
| | - Venuka Durani Goyal
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India
| | - Khileshwari Chandravanshi
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India
| | - Ashwani Kumar
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India
| | | | - Sahayog N Jamdar
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India
| | - Ravindra D Makde
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India
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32
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Agrawal R, Singh R, Kumar A, Kumar A, Makde RD. Crystal structures of pyrrolidone-carboxylate peptidase I from Deinococcus radiodurans reveal the mechanism of L-pyroglutamate recognition. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:308-316. [DOI: 10.1107/s2059798319000676] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 01/14/2019] [Indexed: 11/10/2022]
Abstract
Pyrrolidone-carboxylate peptidase (PCP) catalyzes the removal of an unusual amino acid, L-pyroglutamate (pG), from the N-termini of peptides and proteins. It has implications in the functional regulation of different peptides in both prokaryotes and eukaryotes. However, the pG-recognition mechanism of the PCP enzyme remains largely unknown. Here, crystal structures of PCP I from Deinococcus radiodurans (PCPdr) are reported in pG-free and pG-bound forms at resolutions of 1.73 and 1.55 Å, respectively. Four protomers in PCPdr form a tetrameric structure. The residues responsible for recognizing the pG residue are mostly contributed by a flexible loop (loop A) that is present near the active site. These residues are conserved in all known PCPs I, including those from mammals. Phe9 and Phe12 of loop A form stacking interactions with the pyrrolidone ring of pG, while Asn18 forms a hydrogen bond to OE of pG. The main chain of a nonconserved residue, Leu71, forms two hydrogen bonds to NH and OE of pG. Thus, pG is recognized in the S1 substrate subsite of the enzyme by both van der Waals and polar interactions, which provide specificity for the pG residue of the peptide. In contrast to previously reported PCP I structures, the PCPdr tetramer is in a closed conformation with an inaccessible active site. The structures show that the active site can be accessed by the substrates via disordering of loop A. This disordering could also prevent product inhibition by releasing the bound pG product from the S1 subsite, thus allowing the enzyme to engage a fresh substrate.
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33
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Agarwal S, Dey S, Ghosh B, Biswas M, Dasgupta J. Mechanistic basis of vitamin B12 and cobinamide salvaging by the Vibrio species. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:140-151. [DOI: 10.1016/j.bbapap.2018.11.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 10/31/2018] [Accepted: 11/16/2018] [Indexed: 12/17/2022]
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34
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Singh R, Goyal VD, Kumar A, Sabharwal NS, Makde RD. Crystal structures and biochemical analyses of intermediate cleavage peptidase: role of dynamics in enzymatic function. FEBS Lett 2019; 593:443-454. [PMID: 30582634 DOI: 10.1002/1873-3468.13321] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 12/19/2018] [Accepted: 12/19/2018] [Indexed: 01/20/2023]
Abstract
Intermediate cleavage peptidase (Icp55) processes a subset of mitochondrial matrix proteins by removing a bulky residue at their N termini, leaving behind smaller N-terminal residues (icp activity). This contributes towards the stability of the mitochondrial proteome. We report crystal structures of yeast Icp55 including one bound to the apstatin inhibitor. Apart from icp activity, the enzyme was found to exhibit Xaa-Pro aminopeptidase activity in vitro. Structural and biochemical data suggest that the enzyme exists in a rapid equilibrium between monomer and dimer. Furthermore, the dimer, and not the monomer, was found to be the active species with loop dynamics at the dimer interface playing an important role in activity. Based on the new evidence, we propose a model for binding and processing of cellular targets by Icp55. DATABASE: The atomic coordinates and structure factors for the structures of Icp55 (code 6A9T, 6A9U, 6A9V) have been deposited in the Protein Data Bank (PDB) (http://www.pdb.org/).
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Affiliation(s)
- Rahul Singh
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Venuka Durani Goyal
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Ashwani Kumar
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Naripjeet Singh Sabharwal
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Ravindra D Makde
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India
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35
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Bendre AD, Suresh CG, Shanmugam D, Ramasamy S. Structural insights into the unique inhibitory mechanism of Kunitz type trypsin inhibitor from Cicer arietinum L. J Biomol Struct Dyn 2018; 37:2669-2677. [PMID: 30052127 DOI: 10.1080/07391102.2018.1494633] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Kunitz-type trypsin inhibitors bind to the active pocket of trypsin causing its inhibition. Plant Kunitz-type inhibitors are thought to be important in defense, especially against insect pests. From sequence analysis of various Kunitz-type inhibitors from plants, we identified CaTI2 from chickpea as a unique variant lacking the functionally important arginine residue corresponding to the soybean trypsin inhibitor (STI) and having a distinct and unique inhibitory loop organization. To further explore the implications of these sequence variations, we obtained the crystal structure of recombinant CaTI2 at 2.8Å resolution. It is evident from the structure that the variations in the inhibitory loop facilitates non-substrate like binding of CaTI2 to trypsin, while the canonical inhibitor STI binds to trypsin in substrate like manner. Our results establish the unique mechanism of trypsin inhibition by CaTI2, which warrant further research into its substrate spectrum. Abbreviations BApNA Nα-Benzoyl-L-arginine 4-nitroanilide BPT bovine pancreatic trypsin CaTI2 Cicer arietinum L trypsin inhibitor 2 DrTI Delonix regia Trypsin inhibitor EcTI Enterolobium contortisiliquum trypsin inhibitor ETI Erythrina caffra trypsin inhibitor KTI Kunitz type inhibitor STI soybean trypsin inhibitor TKI Tamarindus indica Kunitz inhibitor Communicated By Ramaswamy H. Sarma.
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Affiliation(s)
- Ameya D Bendre
- a Division of Biochemical Sciences, CSIR-National Chemical Laboratory , Pune , India.,b Academy of Scientific and Innovative Research (AcSIR) , Pune , India
| | - C G Suresh
- a Division of Biochemical Sciences, CSIR-National Chemical Laboratory , Pune , India
| | - Dhanasekaran Shanmugam
- a Division of Biochemical Sciences, CSIR-National Chemical Laboratory , Pune , India.,b Academy of Scientific and Innovative Research (AcSIR) , Pune , India
| | - Sureshkumar Ramasamy
- a Division of Biochemical Sciences, CSIR-National Chemical Laboratory , Pune , India
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36
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Chatterjee S, Nath S, Ghosh B, Sen U. Vibrio cholerae LMWPTP-2 display unique surface charge and grooves around the active site: Indicative of distinctive substrate specificity and scope to design specific inhibitor. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1867:114-124. [PMID: 30447286 DOI: 10.1016/j.bbapap.2018.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 11/08/2018] [Accepted: 11/13/2018] [Indexed: 11/25/2022]
Abstract
Low molecular weight protein tyrosine phosphatases (LMWPTPs) are ubiquitously found as small cytoplasmic enzymes which act on phospho-tyrosine containing proteins that are engaged in various cellular functions. Vibrio cholerae O395 contains two LMWPTPs having widely different sequence. Phylogenetic analysis based on a non redundant set of 124 LMWPTP sequences, designate that LMWPTP-2 from Vibrio choleraeO395 (VcLMWPTP-2) is a single taxon. We have determined the crystal structure of VcLMWPTP-2 at 2.6 Å with MOPS bound in the active site. Tertiary structure analysis indicates that VcLMWPTP-2 forms dimer. Studies in solution state also confirm exclusive presence of a dimeric form. Kinetic studies demonstrate that VcLMWPTP-2 dimer is catalytically active while inactivation through oligomerisation was reported as one of the regulatory mechanism in case of mammalian LMWPTP viz., Bos taurus LMWPTP, BPTP. Kinetic studies using p-nitrophenyl phosphate (p-NPP) as a substrate demonstrate active participation of both the P-loop cysteine in catalysis. Vicinal Cys17, in addition plays a role of protecting the catalytic Cys12 under oxidative stress. Structural analysis and MD simulations allowed us to propose the role of several conserved residues around the active site. Distribution of surface charges and grooves around the active site delineates unique features of VcLMWPTP-2 which could be utilized to design specific inhibitor.
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Affiliation(s)
- Shramana Chatterjee
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, HBNI, 1/AF Bidhan Nagar, Kolkata 700064, India
| | - Seema Nath
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, HBNI, 1/AF Bidhan Nagar, Kolkata 700064, India
| | - Biplab Ghosh
- High Pressure & Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Udayaditya Sen
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, HBNI, 1/AF Bidhan Nagar, Kolkata 700064, India.
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37
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Yadav P, Goyal VD, Gaur NK, Kumar A, Gokhale SM, Jamdar SN, Makde RD. Carboxypeptidase in prolyl oligopeptidase family: Unique enzyme activation and substrate-screening mechanisms. J Biol Chem 2018; 294:89-100. [PMID: 30409909 DOI: 10.1074/jbc.ra118.004254] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 11/02/2018] [Indexed: 02/06/2023] Open
Abstract
Serine peptidases of the prolyl oligopeptidase (POP) family are of substantial therapeutic importance because of their involvement in diseases such as diabetes, cancer, neurological diseases, and autoimmune disorders. Proper annotation and knowledge of substrate specificity mechanisms in this family are highly valuable. Although endopeptidase, dipeptidyl peptidase, tripeptidyl peptidase, and acylaminoacyl peptidase activities have been reported previously, here we report the first instance of carboxypeptidase activity in a POP family member. We determined the crystal structures of this carboxypeptidase, an S9C subfamily member from Deinococcus radiodurans, in its active and inactive states at 2.3-Å resolution, providing an unprecedented view of assembly and disassembly of the active site mediated by an arginine residue. We observed that this residue is poised to bind substrate in the active structure and disrupts the catalytic triad in the inactive structure. The assembly of the active site is accompanied by the ordering of gating loops, which reduces the effective size of the oligomeric pore. This prevents the entry of larger peptides and constitutes a novel mechanism for substrate screening. Furthermore, we observed structural adaptations that enable its carboxypeptidase activity, with a unique loop and two arginine residues in the active site cavity orienting the peptide substrate for catalysis. Using these structural features, we identified homologs of this enzyme in the POP family and confirmed the presence of carboxypeptidase activity in one of them. In conclusion, we have identified a new type within POP enzymes that exhibits not only unique activity but also a novel substrate-screening mechanism.
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Affiliation(s)
- Pooja Yadav
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra 400085, India; School of Biochemistry, Devi Ahilya University, Indore 452001, India
| | - Venuka Durani Goyal
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra 400085, India
| | - Neeraj Kailash Gaur
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra 400085, India
| | - Ashwani Kumar
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra 400085, India
| | | | - Sahayog N Jamdar
- Food Technology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra 400085, India.
| | - Ravindra D Makde
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra 400085, India.
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Structural basis of inactivation of human counterpart of mouse motor neuron degeneration 2 mutant in serine protease HtrA2. Biosci Rep 2018; 38:BSR20181072. [PMID: 30068699 PMCID: PMC6172425 DOI: 10.1042/bsr20181072] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 07/23/2018] [Accepted: 07/31/2018] [Indexed: 02/06/2023] Open
Abstract
Serine protease high temperature requirement protease A2 (HtrA2) is involved in apoptosis and protein quality control. However, one of its murine inactive mutants (S276C aka mnd2) is associated with motor neuron degeneration 2. Similarly, this conserved mutation in human HtrA2 (hHtrA2) also renders the protease inactive, implicating pathogenicity. However, the structural determinants for its inactivation have not yet been elucidated. Here, using multidisciplinary approach, we studied the structural basis of inactivity associated with this mutation in hHtrA2. Characterization of secondary and tertiary structural properties, protein stability, oligomeric properties, and enzyme activity for both wild-type and mutant has been performed using biophysical and functional enzymology studies. The structural comparison at atomic resolution has been carried out using X-ray crystallography. While enzyme kinetics showed inactivity, spectroscopic probes did not identify any significant secondary structural changes in the mutant. X-ray crystallographic analysis of the mutant protein at 2 Å resolution highlighted the significance of a water molecule that plays important role in mediating intermolecular interactions for maintaining the functional ensemble of the protease. Overall, the crystallographic data along with biophysical and enzymology studies helped decipher the structural basis of inactivity of hHtrA2S276C, which might pave way toward further investigating its correlation with aberration of normal cellular functions, hence pathogenicity.
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39
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Yadav P, Goyal VD, Gaur NK, Kumar A, Gokhale SM, Makde RD. Structure of Asp‐bound peptidase E from
Salmonella enterica
: Active site at dimer interface illuminates Asp recognition. FEBS Lett 2018; 592:3346-3354. [DOI: 10.1002/1873-3468.13247] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 08/13/2018] [Accepted: 09/05/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Pooja Yadav
- High Pressure and Synchrotron Radiation Physics Division Bhabha Atomic Research Centre Mumbai India
- School of Biochemistry Devi Ahilya University Indore India
| | - Venuka Durani Goyal
- High Pressure and Synchrotron Radiation Physics Division Bhabha Atomic Research Centre Mumbai India
| | - Neeraj K. Gaur
- High Pressure and Synchrotron Radiation Physics Division Bhabha Atomic Research Centre Mumbai India
| | - Ashwani Kumar
- High Pressure and Synchrotron Radiation Physics Division Bhabha Atomic Research Centre Mumbai India
| | | | - Ravindra D. Makde
- High Pressure and Synchrotron Radiation Physics Division Bhabha Atomic Research Centre Mumbai India
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40
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Saikhedkar NS, Joshi RS, Bhoite AS, Mohandasan R, Yadav AK, Fernandes M, Kulkarni KA, Giri AP. Tripeptides derived from reactive centre loop of potato type II protease inhibitors preferentially inhibit midgut proteases of Helicoverpa armigera. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2018; 95:17-25. [PMID: 29486250 DOI: 10.1016/j.ibmb.2018.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 02/07/2018] [Indexed: 06/08/2023]
Abstract
Potato type II protease inhibitors (Pin-II PIs) impede the growth of lepidopteran insects by inhibiting serine protease-like enzymes in the larval gut. The three amino acid reactive centre loop (RCL) of these proteinaceous inhibitors is crucial for protease binding and is conserved across the Pin-II family. However, the molecular mechanism and inhibitory potential of the RCL tripeptides in isolation of the native protein has remained elusive. In this study, six peptides corresponding to the RCLs of the predominant Pin-II PIs were identified, synthesized and evaluated for in vitro and in vivo inhibitory activity against serine proteases of the polyphagous insect, Helicoverpa armigera. RCL peptides with sequences PRN, PRY and TRE were found to be potent inhibitors that adversely affected the growth and development of H. armigera. The binding mechanism and differential affinity of the RCL peptides with serine proteases was delineated by crystal structures of complexes of the RCL peptides with trypsin. Residues P1 and P2 of the inhibitors play a crucial role in the interaction and specificity of these inhibitors. Important features of RCL peptides like higher inhibition of insect proteases, enhanced efficacy at alkaline gut pH, longer retention and high stability in insect gut make them suitable molecules for the development of sustainable pest management strategies for crop protection.
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Affiliation(s)
- Nidhi S Saikhedkar
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India
| | - Rakesh S Joshi
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India; Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, India
| | - Ashiwini S Bhoite
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India
| | - Radhika Mohandasan
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India
| | - Amit Kumar Yadav
- Division of Organic Chemistry, CSIR-National Chemical Laboratory, Pune 411 008, India
| | - Moneesha Fernandes
- Division of Organic Chemistry, CSIR-National Chemical Laboratory, Pune 411 008, India
| | - Kiran A Kulkarni
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India.
| | - Ashok P Giri
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India.
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41
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Bihani SC, Panicker L, Rajpurohit YS, Misra HS, Kumar V. drFrnE Represents a Hitherto Unknown Class of Eubacterial Cytoplasmic Disulfide Oxido-Reductases. Antioxid Redox Signal 2018; 28:296-310. [PMID: 28899103 DOI: 10.1089/ars.2016.6960] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
AIMS Living cells employ thioredoxin and glutaredoxin disulfide oxido-reductases to protect thiol groups in intracellular proteins. FrnE protein of Deinococcus radiodurans (drFrnE) is a disulfide oxido-reductase that is induced in response to Cd2+ exposure and is involved in cadmium and radiation tolerance. The aim of this study is to probe structure, function, and cellular localization of FrnE class of proteins. RESULTS Here, we show drFrnE as a novel cytoplasmic oxido-reductase that could be functional in eubacteria under conditions where thioredoxin/glutaredoxin systems are inhibited or absent. Crystal structure analysis of drFrnE reveals thioredoxin fold with an alpha helical insertion domain and a unique, flexible, and functionally important C-terminal tail. The C-tail harbors a novel 239-CX4C-244 motif that interacts with the active site 22-CXXC-25 motif. Crystal structures with different active site redox states, including mixed disulfide (Cys22-Cys244), are reported here. The biochemical data show that 239-CX4C-244 motif channels electrons to the active site cysteines. drFrnE is more stable in the oxidized form, compared with the reduced form, supporting its role as a disulfide reductase. Using bioinformatics analysis and fluorescence microscopy, we show cytoplasmic localization of drFrnE. We have found "true" orthologs of drFrnE in several eubacterial phyla and, interestingly, all these groups apparently lack a functional glutaredoxin system. Innovation and Conclusion: We show that drFrnE represents a new class of hitherto unknown intracellular oxido-reductases that are abundantly present in eubacteria. Unlike other well-known oxido-reductases, FrnE harbors an additional dithiol motif that acts as a conduit to channel electrons to the active site during catalytic turnover. Antioxid. Redox Signal. 28, 296-310.
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Affiliation(s)
- Subhash C Bihani
- 1 Protein Crystallography Section, Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre , Mumbai, India
| | - Lata Panicker
- 1 Protein Crystallography Section, Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre , Mumbai, India
| | | | - Hari S Misra
- 2 Molecular Biology Division, Bhabha Atomic Research Centre , Mumbai, India .,3 Life Sciences, Homi Bhabha National Institute , Mumbai, India
| | - Vinay Kumar
- 1 Protein Crystallography Section, Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre , Mumbai, India .,3 Life Sciences, Homi Bhabha National Institute , Mumbai, India
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42
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Structure and function of a highly active Bile Salt Hydrolase (BSH) from Enterococcus faecalis and post-translational processing of BSH enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:507-518. [PMID: 29325872 DOI: 10.1016/j.bbapap.2018.01.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 11/02/2017] [Accepted: 01/04/2018] [Indexed: 12/14/2022]
Abstract
Bile Salt Hydrolase (BSH), a member of Cholylglycine hydrolase family, catalyzes the de-conjugation of bile acids and is evolutionarily related to penicillin V acylase (PVA) that hydrolyses a different substrate such as penicillin V. We report the three-dimensional structure of a BSH enzyme from the Gram-positive bacteria Enterococcus faecalis (EfBSH) which has manifold higher hydrolase activity compared to other known BSHs and displays unique allosteric catalytic property. The structural analysis revealed reduced secondary structure content compared to other known BSH structures, particularly devoid of an anti-parallel β-sheet in the assembly loop and part of a β-strand is converted to increase the length of a substrate binding loop 2. The analysis of the substrate binding pocket showed reduced volume owing to altered loop conformations and increased hydrophobicity contributed by a higher ratio of hydrophobic to hydrophilic groups present. The aromatic residues F18, Y20 and F65 participate in substrate binding. Thus, their mutation affects enzyme activity. Docking and Molecular Dynamics simulation studies showed effective polar complementarity present for the three hydroxyl (-OH) groups of GCA substrate in the binding site contributing to higher substrate specificity and efficient catalysis. These are unique features characteristics of this BSH enzyme and thought to contribute to its higher activity and specificity towards bile salts as well as allosteric effects. Further, mechanism of autocatalytic processing of Cholylglycine Hydrolases by the excision of an N-terminal Pre-peptide was examined by inserting different N-terminal pre-peptides in EfBSH sequence. The results suggest that two serine residues next to nucleophile cysteine are essential for autocalytic processing to remove precursor peptide. Since pre-peptide is absent in EfBSH the mutation of these serines is tolerated. This suggests that an evolution-mediated subordination of the pre-peptide excision site resulted in loss of pre-peptide in EfBSH and other related Cholylglycine hydrolases.
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43
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Bajaj N, Bhatt H, Pandey KK, Poswal HK, Arya A, Ghosh PS, Garg N, Deo MN. Phase transition in metal–organic complex trans-PtCl2(PEt3)2 under pressure: insights into the molecular and crystal structure. CrystEngComm 2018. [DOI: 10.1039/c8ce00433a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Molecular reorientations result in structural phase transition in trans-PtCl2(PEt3)2 under pressure, leading to a hydrogen bond assisted supramolecular architecture.
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Affiliation(s)
- Naini Bajaj
- Homi Bhabha National Institute
- Bhabha Atomic Research Centre
- Mumbai
- India 400085
- High Pressure & Synchrotron Radiation Physics Division
| | - Himal Bhatt
- High Pressure & Synchrotron Radiation Physics Division
- Bhabha Atomic Research Centre
- Mumbai
- India 400085
| | - K. K. Pandey
- High Pressure & Synchrotron Radiation Physics Division
- Bhabha Atomic Research Centre
- Mumbai
- India 400085
| | - H. K. Poswal
- High Pressure & Synchrotron Radiation Physics Division
- Bhabha Atomic Research Centre
- Mumbai
- India 400085
| | - A. Arya
- Materials Science Division
- Bhabha Atomic Research Centre
- Mumbai
- India 400085
| | - P. S. Ghosh
- Materials Science Division
- Bhabha Atomic Research Centre
- Mumbai
- India 400085
| | - N. Garg
- High Pressure & Synchrotron Radiation Physics Division
- Bhabha Atomic Research Centre
- Mumbai
- India 400085
| | - M. N. Deo
- High Pressure & Synchrotron Radiation Physics Division
- Bhabha Atomic Research Centre
- Mumbai
- India 400085
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44
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Vajravijayan S, Nandhagopal N, Gunasekaran K. Crystal structure determination and analysis of 11S coconut allergen: Cocosin. Mol Immunol 2017; 92:132-135. [PMID: 29096167 DOI: 10.1016/j.molimm.2017.10.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 10/16/2017] [Accepted: 10/21/2017] [Indexed: 10/18/2022]
Abstract
Allergy is an abnormal immune response against an innocuous target. Food allergy is an adverse reaction caused by common foods most well-known being those involving peanuts. Apart from mono sensitized food allergy, cross-reactivity with other food allergens is also commonly observed. To understand the phenomenon of cross-reactivity related to immune response, three dimensional structures of the allergens and their antigenic epitopes has to be analysed in detail. The X-ray crystal structure of Cocosin, a common 11S food allergen from coconut, has been determined at 2.2Å resolution using molecular replacement technique. The monomer of 52kDa is composed of two β-jelly roll domains, one with acidic and the other with basic character. The structure shows hexameric association with two trimers facing each other. Though the overall structure of Cocosin is similar to other 11S allergens, the occurrence of experimentally determined epitopes of the peanut allergen Ara h 3 at flexible as well as variable regions could be the reason for the clinically reported result of cross-reactivity that the peanut allergic patients are not sensitized with coconut allergen.
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Affiliation(s)
- S Vajravijayan
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India
| | - N Nandhagopal
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India.
| | - K Gunasekaran
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India.
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45
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Are VN, Jamdar SN, Ghosh B, Goyal VD, Kumar A, Neema S, Gadre R, Makde RD. Crystal structure of a novel prolidase from Deinococcus radiodurans identifies new subfamily of bacterial prolidases. Proteins 2017; 85:2239-2251. [PMID: 28929533 DOI: 10.1002/prot.25389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 08/29/2017] [Accepted: 09/15/2017] [Indexed: 11/10/2022]
Abstract
Xaa-Pro peptidases (XPP) are dinuclear peptidases of MEROPS M24B family that hydrolyze Xaa-Pro iminopeptide bond with a trans-proline at the second position of the peptide substrate. XPPs specific towards dipeptides are called prolidases while those that prefer longer oligopeptides are called aminopeptidases P. Though XPPs are strictly conserved in bacterial and archaeal species, the structural and sequence features that distinguish between prolidases and aminopeptidases P are not always clear. Here, we report 1.4 Å resolution crystal structure of a novel XPP from Deinococcus radiodurans (XPPdr). XPPdr forms a novel dimeric structure via unique dimer stabilization loops of N-terminal domains such that their C-terminal domains are placed far apart from each other. This novel dimerization is also the consequence of a different orientation of N-terminal domain in XPPdr monomer than those in other known prolidases. The enzymatic assays show that it is a prolidase with broad substrate specificity. Our structural, mutational, and molecular dynamics simulation analyses show that the conserved Arg46 of N-terminal domain is important for the dipeptide selectivity. Our BLAST search found XPPdr orthologs with conserved sequence motifs which correspond to unique structural features of XPPdr, thus identify a new subfamily of bacterial prolidases.
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Affiliation(s)
- Venkata N Are
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India.,School of Biochemistry, Devi Ahilya Vishwavidyalaya, Indore, India
| | - Sahayog N Jamdar
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Biplab Ghosh
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Venuka Durani Goyal
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Ashwani Kumar
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Sanchit Neema
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Rekha Gadre
- School of Biochemistry, Devi Ahilya Vishwavidyalaya, Indore, India
| | - Ravindra D Makde
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India
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46
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Shivakumar KI, Swathi K, Goudappagouda, Das TC, Kumar A, Makde RD, Vanka K, Narayan KS, Babu SS, Sanjayan GJ. Mixed-Stack Charge Transfer Crystals of Pillar[5]quinone and Tetrathiafulvalene Exhibiting Ferroelectric Features. Chemistry 2017; 23:12630-12635. [PMID: 28661012 DOI: 10.1002/chem.201702577] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Indexed: 11/11/2022]
Abstract
Ferroelectric materials find extensive applications in the fabrication of compact memory devices and ultra-sensitive multifunctional detectors. Face-to-face alternate stacking of electron donors and acceptors effectuate long-range unidirectional ordering of charge-transfer (CT) dipoles, promising tunable ferroelectricity. Herein we report a new TTF-quinone system-an emerald green CT complex consisting pillar[5]quinone (P5Q) and tetrathiafulvalene (TTF). The CT crystals, as determined by single crystal synchrotron X-ray diffraction, adopt a 1:1 mixed-stack arrangement of donor and acceptor with alternating dimers of TTF and 1,4-dioxane encapsulated P5Q. The TTF-P5Q.dioxane crystal possesses a macroscopic polarization axis giving rise to ferroelectricity at room temperature. The CT complex manifests ferroelectric features such as optical polarization rotation, temperature-dependent phase transition and piezoelectric response in single crystals. Ferroelectric behavior observed in P5Q-based CT complex widens the scope for further work on this structurally intriguing and readily accessible cyclic pentaquinone.
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Affiliation(s)
- Kilingaru I Shivakumar
- Division of Organic Chemistry, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India.,Academy of Scientific and Innovation Research, CSIR-National Chemical Laboratory, Pune, 411008, India
| | - Kadaba Swathi
- Molecular Electronics Lab, Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru, 560064, India
| | - Goudappagouda
- Division of Organic Chemistry, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India.,Academy of Scientific and Innovation Research, CSIR-National Chemical Laboratory, Pune, 411008, India
| | - Tamal C Das
- Inorganic and Computational Group, Division of Physical Chemistry, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India.,Academy of Scientific and Innovation Research, CSIR-National Chemical Laboratory, Pune, 411008, India
| | - Ashwani Kumar
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, 400 085, India
| | - Ravindra D Makde
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, 400 085, India
| | - Kumar Vanka
- Inorganic and Computational Group, Division of Physical Chemistry, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India.,Academy of Scientific and Innovation Research, CSIR-National Chemical Laboratory, Pune, 411008, India
| | - Kavassery S Narayan
- Molecular Electronics Lab, Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru, 560064, India
| | - Sukumaran Santhosh Babu
- Division of Organic Chemistry, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India.,Academy of Scientific and Innovation Research, CSIR-National Chemical Laboratory, Pune, 411008, India
| | - Gangadhar J Sanjayan
- Division of Organic Chemistry, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India.,Academy of Scientific and Innovation Research, CSIR-National Chemical Laboratory, Pune, 411008, India
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47
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Sharma B, Jamdar SN, Ghosh B, Yadav P, Kumar A, Kundu S, Goyal VD, Makde RD. Active site gate of M32 carboxypeptidases illuminated by crystal structure and molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1406-1415. [PMID: 28844748 DOI: 10.1016/j.bbapap.2017.07.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 07/21/2017] [Accepted: 07/24/2017] [Indexed: 01/09/2023]
Abstract
Enzyme gates are important dynamic features that regulate function. Study of these features is critical for understanding of enzyme mechanism. In this study, the active-site gate of M32 carboxypeptidases (M32CP) is illuminated. Only a handful of members of this family have been structurally and functionally characterized and various aspects of their activity and mechanism are yet not clarified. Here, crystal structure of putative M32CP from Deinococcus radiodurans (M32dr) was solved to 2.4Å resolution. Enzymatic assays confirmed its identity as a carboxypeptidase. Open and relatively closed conformations observed in the structure provided supporting evidence for previously hypothesized hinge motion in this family of enzymes. Molecular dynamics simulations of 1.5μs displayed distinct open and closed conformations revealing amplitude of the motion to be beyond what was observed in the crystal structure. Hinge region and anchoring region of this shell-type gate were identified. A small displacement of 3Å and a helical tilt of 9° propagated by the hinge region translates into a 10Å motion at the top of the gate. The dynamics of the gate was supported by our mutagenesis experiment involving formation of disulphide bond across helices of the gate. The nearly inactive mutant enzyme showed 65-fold increase in the enzymatic activity in presence of reducing agent. Further, while a previously proposed structural basis would have led to its classification in subfamily II, experimentally observed substrate length restriction places M32dr in subfamily I of M32CPs.
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Affiliation(s)
- Bhaskar Sharma
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India; Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Sahayog N Jamdar
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Biplab Ghosh
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Pooja Yadav
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Ashwani Kumar
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Suman Kundu
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Venuka Durani Goyal
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India.
| | - Ravindra D Makde
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India.
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48
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Singh R, Jamdar SN, Goyal VD, Kumar A, Ghosh B, Makde RD. Structure of the human aminopeptidase XPNPEP3 and comparison of its in vitro activity with Icp55 orthologs: Insights into diverse cellular processes. J Biol Chem 2017; 292:10035-10047. [PMID: 28476889 DOI: 10.1074/jbc.m117.783357] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 05/04/2017] [Indexed: 11/06/2022] Open
Abstract
The human aminopeptidase XPNPEP3 is associated with cystic kidney disease and TNF-TNFR2 cellular signaling. Its yeast and plant homolog Icp55 processes several imported mitochondrial matrix proteins leading to their stabilization. However, the molecular basis for the diverse roles of these enzymes in the cell is unknown. Here, we report the crystal structure of human XPNPEP3 with bound apstatin product at 1.65 Å resolution, and we compare its in vitro substrate specificity with those of fungal Icp55 enzymes. In contrast to the suggestions by earlier in vivo studies of mitochondrial processing, we found that these enzymes are genuine Xaa-Pro aminopeptidases, which hydrolyze peptides with proline at the second position (P1'). The mitochondrial processing activity involving cleavage of peptides lacking P1' proline was also detected in the purified enzymes. A wide proline pocket as well as molecular complementarity and capping at the S1 substrate site of XPNPEP3 provide the necessary structural features for processing the mitochondrial substrates. However, this activity was found to be significantly lower as compared with Xaa-Pro aminopeptidase activity. Because of similar activity profiles of Icp55 and XPNPEP3, we propose that XPNPEP3 plays the same mitochondrial role in humans as Icp55 does in yeast. Both Xaa-Pro aminopeptidase and mitochondrial processing activities of XPNPEP3 have implications toward mitochondrial fitness and cystic kidney disease. Furthermore, the presence of both these activities in Icp55 elucidates the unexplained processing of the mitochondrial cysteine desulfurase Nfs1 in yeast. The enzymatic and structural analyses reported here provide a valuable molecular framework for understanding the diverse cellular roles of XPNPEP3.
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Affiliation(s)
- Rahul Singh
- From the High Pressure and Synchrotron Radiation Physics Division and
| | - Sahayog N Jamdar
- Food Technology Division, Bhabha Atomic Research Centre, 400085 Mumbai, India
| | | | - Ashwani Kumar
- From the High Pressure and Synchrotron Radiation Physics Division and
| | - Biplab Ghosh
- From the High Pressure and Synchrotron Radiation Physics Division and
| | - Ravindra D Makde
- From the High Pressure and Synchrotron Radiation Physics Division and
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49
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Agarwal S, Dey S, Ghosh B, Biswas M, Dasgupta J. Structure and dynamics of Type III periplasmic proteins VcFhuD and VcHutB reveal molecular basis of their distinctive ligand binding properties. Sci Rep 2017; 7:42812. [PMID: 28216648 PMCID: PMC5316997 DOI: 10.1038/srep42812] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 01/13/2017] [Indexed: 12/20/2022] Open
Abstract
Molecular mechanisms of xenosiderophore and heme acquisitions using periplasmic binding protein (PBP) dependent ATP-binding cassette transporters to scavenge the essential nutrient iron are elusive yet in Vibrio cholerae. Our current study delineates the structures, dynamics and ligand binding properties of two Type III PBPs of V. cholerae, VcFhuD and VcHutB. Through crystal structures and fluorescence quenching studies we demonstrate unique features of VcFhuD to bind both hydroxamate and catecholate type xenosiderophores. Like E. coli FhuD, VcFhuD binds ferrichrome and ferri-desferal using conserved Tryptophans and R102. However, unlike EcFhuD, slightly basic ligand binding pocket of VcFhuD could favour ferri-enterobactin binding with plausible participation of R203, along with R102, like it happens in catecholate binding PBPs. Structural studies coupled with spectrophotometric and native PAGE analysis indicated parallel binding of two heme molecules to VcHutB in a pH dependent manner, while mutational analysis established the relative importance of Y65 and H164 in heme binding. MD simulation studies exhibited an unforeseen inter-lobe swinging motion in Type III PBPs, magnitude of which is inversely related to the packing of the linker helix with its neighboring helices. Small inter-lobe movement in VcFhuD or dramatic twisting in VcHutB is found to influence ligand binding.
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Affiliation(s)
- Shubhangi Agarwal
- Department of Biotechnology, St. Xavier's College, 30 Park Street, Kolkata 700016, India
| | - Sanjay Dey
- Department of Biotechnology, St. Xavier's College, 30 Park Street, Kolkata 700016, India
| | - Biplab Ghosh
- High Pressure &Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Maitree Biswas
- Department of Biotechnology, St. Xavier's College, 30 Park Street, Kolkata 700016, India
| | - Jhimli Dasgupta
- Department of Biotechnology, St. Xavier's College, 30 Park Street, Kolkata 700016, India
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50
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Crystal structure and biochemical investigations reveal novel mode of substrate selectivity and illuminate substrate inhibition and allostericity in a subfamily of Xaa-Pro dipeptidases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:153-164. [PMID: 27816563 DOI: 10.1016/j.bbapap.2016.10.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 10/27/2016] [Accepted: 10/31/2016] [Indexed: 12/13/2022]
Abstract
Xaa-Pro dipeptidase (XPD) catalyzes hydrolysis of iminopeptide bond in dipeptides containing trans-proline as a second residue. XPDs are found in all living organisms and are believed to play an essential role in proline metabolism. Here, we report crystal structures and extensive enzymatic studies of XPD from Xanthomonas campestris (XPDxc), the first such comprehensive study of a bacterial XPD. We also report enzymatic activities of its ortholog from Mycobacterium tuberculosis (XPDmt). These enzymes are strictly dipeptidases with broad substrate specificities. They exhibit substrate inhibition and allostericity, as described earlier for XPD from Lactococcus lactis (XPDll). The structural, mutational and comparative data have revealed a novel mechanism of dipeptide selectivity and substrate binding in these enzymes. Moreover, we have identified conserved sequence motifs that distinguish these enzymes from other prolidases, thus defining a new subfamily. This study provides a suitable structural template for explaining unique properties of this XPDxc subfamily. In addition, we report unique structural features of XPDxc protein like an extended N-terminal tail region and absence of a conserved Tyr residue near the active site.
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