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Xu S, Grochulski P, Tanaka T. Structural basis for the allosteric behaviour and substrate specificity of Lactococcus lactis Prolidase. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:141000. [PMID: 38224826 DOI: 10.1016/j.bbapap.2024.141000] [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: 08/18/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/17/2024]
Abstract
Prolidase (EC 3.4.13.9) is an enzyme that specifically hydrolyzes Xaa-Pro dipeptides into free amino acids. We previously studied kinetic behaviours and solved the crystal structure of wild-type (WT) Lactococcus lactis prolidase (Llprol), showing that this homodimeric enzyme has unique characteristics: allosteric behaviour and substrate inhibition. In this study, we focused on solving the crystal structures of three Llprol mutants (D36S, H38S, and R293S) which behave differently in v-S plots. The D36S and R293S Llprol mutants do not show allosteric behaviour, and the Llprol mutant H38S has allosteric behaviour comparable to the WT enzyme (Hill constant 1.52 and 1.58, respectively). The crystal structures of Llprol variants suggest that the active site of Llprol formed with amino acid residues from both monomers, i.e., located in an interfacial area of dimer. The comparison between the structure models of Llprol indicated that the two monomers in the dimers of Llprol variants have different relative positions among Llprol variants. They showed different interatomic distances between the amino acid residues bridging the two monomers and varied sizes of the solvent-accessible interface areas in each Llprol variant. These observations indicated that Llprol could adapt to different conformational states with distinctive substrate affinities. It is strongly speculated that the domain movements required for productive substrate binding are restrained in allosteric Llprol (WT and H38S). At low substrate concentrations, only one out of the two active sites at the dimer interface could accept substrate; as a result, the asymmetrical activated dimer leads to allosteric behaviour.
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Affiliation(s)
- Shangyi Xu
- Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Pawel Grochulski
- Canadian Light Source, Saskatoon, SK, Canada; College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, SK, Canada
| | - Takuji Tanaka
- Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK, Canada.
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Dong Z, Yang S, Lee BH. Bioinformatic mapping of a more precise Aspergillus niger degradome. Sci Rep 2021; 11:693. [PMID: 33436802 PMCID: PMC7804941 DOI: 10.1038/s41598-020-80028-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/15/2020] [Indexed: 11/21/2022] Open
Abstract
Aspergillus niger has the ability to produce a large variety of proteases, which are of particular importance for protein digestion, intracellular protein turnover, cell signaling, flavour development, extracellular matrix remodeling and microbial defense. However, the A. niger degradome (the full repertoire of peptidases encoded by the A. niger genome) available is not accurate and comprehensive. Herein, we have utilized annotations of A. niger proteases in AspGD, JGI, and version 12.2 MEROPS database to compile an index of at least 232 putative proteases that are distributed into the 71 families/subfamilies and 26 clans of the 6 known catalytic classes, which represents ~ 1.64% of the 14,165 putative A. niger protein content. The composition of the A. niger degradome comprises ~ 7.3% aspartic, ~ 2.2% glutamic, ~ 6.0% threonine, ~ 17.7% cysteine, ~ 31.0% serine, and ~ 35.8% metallopeptidases. One hundred and two proteases have been reassigned into the above six classes, while the active sites and/or metal-binding residues of 110 proteases were recharacterized. The probable physiological functions and active site architectures of these peptidases were also investigated. This work provides a more precise overview of the complete degradome of A. niger, which will no doubt constitute a valuable resource and starting point for further experimental studies on the biochemical characterization and physiological roles of these proteases.
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Affiliation(s)
- Zixing Dong
- Henan Provincial Engineering Laboratory of Insect Bio-Reactor and Henan Key Laboratory of Ecological Security for Water Region of Mid-Line of South-To-North, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, People's Republic of China.
| | - Shuangshuang Yang
- College of Physical Education, Nanyang Normal University, Nanyang, 473061, People's Republic of China
| | - Byong H Lee
- Department of Microbiology/Immunology, McGill University, Montreal, QC, Canada
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Wilk P, Wątor E, Weiss MS. Prolidase - A protein with many faces. Biochimie 2020; 183:3-12. [PMID: 33045291 DOI: 10.1016/j.biochi.2020.09.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/31/2020] [Accepted: 09/15/2020] [Indexed: 12/21/2022]
Abstract
Prolidase is a metal-dependent peptidase specialized in the cleavage of dipeptides containing proline or hydroxyproline on their C-termini. Prolidase homologues are found in all kingdoms of life. The importance of prolidase in human health is underlined by a rare hereditary syndrome referred to as Prolidase Deficiency. A growing number of studies highlight the importance of prolidase in various other human conditions, including cancer. Some recent studies link prolidase's activity-independent regulatory role to tumorigenesis. Furthermore, the enzyme or engineered variants have some applications in biotechnology. In this short review, we aim to highlight different aspects of the protein the importance of which is increasingly recognized over the last years.
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Affiliation(s)
- Piotr Wilk
- Malopolska Centre of Biotechnology, Jagiellonian University, ul. Gronostajowa 7a, 30-387 Krakow, Poland.
| | - Elżbieta Wątor
- Malopolska Centre of Biotechnology, Jagiellonian University, ul. Gronostajowa 7a, 30-387 Krakow, Poland
| | - Manfred S Weiss
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Str. 15, 12489, Berlin, Germany
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Wang TF, Chi MC, Lai KL, Lin MG, Chen YY, Lo HF, Lin LL. High-level expression and molecular characterization of a recombinant prolidase from Escherichia coli NovaBlue. PeerJ 2018; 6:e5863. [PMID: 30402354 PMCID: PMC6215446 DOI: 10.7717/peerj.5863] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 10/03/2018] [Indexed: 12/21/2022] Open
Abstract
Long-term use of organophosphorus (OP) compounds has become an increasing global problem and a major threat to sustainability and human health. Prolidase is a proline-specific metallopeptidase that can offer an efficient option for the degradation of OP compounds. In this study, a full-length gene from Escherichia coli NovaBlue encoding a prolidase (EcPepQ) was amplified and cloned into the commercially-available vector pQE-30 to yield pQE-EcPepQ. The overexpressed enzyme was purified from the cell-free extract of isopropyl thio-β-D-galactoside IPTG-induced E. coli M15 (pQE-EcPepQ) cells by nickel-chelate chromatography. The molecular mass of EcPepQ was determined to be about 57 kDa by 12% sodium dodecyl sulfate–polyacrylamide gel electrophoresis and the result of size-exclusion chromatography demonstrated that the enzyme was mainly present in 25 mM Tris–HCl buffer (pH 8.0) as a dimeric form. The optimal conditions for EcPepQ activity were 60 °C, pH 8.0, and 0.1 mM Mn2+ ion. Kinetic analysis with Ala-Pro as the substrate showed that the Km and kcat values of EcPepQ were 8.8 mM and 926.5 ± 2.0 s−1, respectively. The thermal unfolding of EcPepQ followed a two-state process with one well-defined unfolding transition of 64.2 °C. Analysis of guanidine hydrochloride (GdnHCl)-induced denaturation by tryptophan emission fluorescence spectroscopy revealed that the enzyme had a [GdnHCl]0.5,N-U value of 1.98 M. The purified enzyme also exhibited some degree of tolerance to various water/organic co-solvents. Isopropanol and tetrahydrofuran were very detrimental to the enzymatic activity of EcPepQ; however, other more hydrophilic co-solvents, such as formamide, methanol, and ethylene glycol, were better tolerated. Eventually, the non-negative influence of some co-solvents on both catalytic activity and structural stability of EcPepQ allows to adjust the reaction conditions more suitable for EcPepQ-catalyzed bioprocess.
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Affiliation(s)
- Tzu-Fan Wang
- Department of Applied Chemistry, National Chiayi University, Chiayi, Taiwan
| | - Meng-Chun Chi
- Department of Applied Chemistry, National Chiayi University, Chiayi, Taiwan
| | - Kuan-Ling Lai
- Department of Applied Chemistry, National Chiayi University, Chiayi, Taiwan.,Department of Food Science and Technology, Hungkuang University, Taichung, Taiwan
| | - Min-Guan Lin
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Yi-Yu Chen
- Department of Applied Chemistry, National Chiayi University, Chiayi, Taiwan
| | - Huei-Fen Lo
- Department of Food Science and Technology, Hungkuang University, Taichung, Taiwan
| | - Long-Liu Lin
- Department of Applied Chemistry, National Chiayi University, Chiayi, Taiwan
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Wilk P, Uehlein M, Piwowarczyk R, Dobbek H, Mueller U, Weiss MS. Structural basis for prolidase deficiency disease mechanisms. FEBS J 2018; 285:3422-3441. [DOI: 10.1111/febs.14620] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 07/18/2018] [Accepted: 07/30/2018] [Indexed: 01/06/2023]
Affiliation(s)
- Piotr Wilk
- Helmholtz‐Zentrum Berlin, Macromolecular Crystallography (HZB‐MX) Germany
- Institut für Biologie, Strukturbiologie/Biochemie Humboldt‐Universität zu Berlin Germany
| | - Monika Uehlein
- Helmholtz‐Zentrum Berlin, Macromolecular Crystallography (HZB‐MX) Germany
| | - Rafal Piwowarczyk
- Helmholtz‐Zentrum Berlin, Macromolecular Crystallography (HZB‐MX) Germany
| | - Holger Dobbek
- Institut für Biologie, Strukturbiologie/Biochemie Humboldt‐Universität zu Berlin Germany
| | - Uwe Mueller
- Helmholtz‐Zentrum Berlin, Macromolecular Crystallography (HZB‐MX) Germany
| | - Manfred S. Weiss
- Helmholtz‐Zentrum Berlin, Macromolecular Crystallography (HZB‐MX) Germany
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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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