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Jeong KH, Son SB, Ko JH, Lee M, Lee JY. Structural insights into BirA from Haemophilus influenzae, a bifunctional protein as a biotin protein ligase and a transcriptional repressor. Biochem Biophys Res Commun 2024; 733:150601. [PMID: 39213703 DOI: 10.1016/j.bbrc.2024.150601] [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: 08/22/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024]
Abstract
Biotin is an essential coenzyme involved in various metabolic processes across all known organisms, with biotinylation being crucial for the activity of carboxylases. BirA from Haemophilus influenzae is a bifunctional protein that acts as a biotin protein ligase and a transcriptional repressor. This study reveals the crystal structures of Hin BirA in both its apo- and holo-(biotinyl-5'-AMP bound) forms. As a class II BirA, it consists of three domains: N-terminal DNA binding domain, central catalytic domain, and C-terminal SH3-like domain. The structural analysis shows that the biotin-binding loop forms an ordered structure upon biotinyl-5'-AMP binding. This facilitates its interaction with the ligand and promotes protein dimerization. Comparative studies with other BirA homologs from different organisms indicate that the residues responsible for binding biotinyl-5'-AMP are highly conserved. This study also utilized AlphaFold2 to model the potential heterodimeric interaction between Hin BirA and biotin carboxyl carrier protein, thereby providing insights into the structural basis for biotinylation. These findings enhance our understanding of the structural and functional characteristics of Hin BirA, highlighting its potential as a target for novel antibiotics that disrupt the bacterial biotin synthesis pathways.
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Affiliation(s)
- Kang Hwa Jeong
- Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggi-do, 10326, Republic of Korea
| | - Su Bin Son
- Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggi-do, 10326, Republic of Korea
| | - Ji Hyuk Ko
- Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggi-do, 10326, Republic of Korea
| | - Minho Lee
- Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggi-do, 10326, Republic of Korea.
| | - Jae Young Lee
- Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggi-do, 10326, Republic of Korea.
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2
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Hu F, Chang F, Tao L, Sun X, Liu L, Zhao Y, Han Z, Li C. Prediction of Protein Allosteric Sites with Transfer Entropy and Spatial Neighbor-Based Evolutionary Information Learned by an Ensemble Model. J Chem Inf Model 2024; 64:6197-6204. [PMID: 39075972 DOI: 10.1021/acs.jcim.4c00544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
Allostery is one of the most direct and efficient ways to regulate protein functions. The diverse allosteric sites make it possible to design allosteric modulators of differential selectivity and improved safety compared with those of orthosteric drugs targeting conserved orthosteric sites. Here, we develop an ensemble machine learning method AllosES to predict protein allosteric sites in which the new and effective features are utilized, including the entropy transfer-based dynamic property, secondary structure features, and our previously proposed spatial neighbor-based evolutionary information besides the traditional physicochemical properties. To overcome the class imbalance problem, the multiple grouping strategy is proposed, which is applied to feature selection and model construction. The ensemble model is constructed where multiple submodels are trained on multiple training subsets, respectively, and their results are then integrated to be the final output. AllosES achieves a prediction performance of 0.556 MCC on the independent test set D24, and additionally, AllosES can rank the real allosteric sites in the top three for 83.3/89.3% of allosteric proteins from the test set D24/D28, outperforming the state-of-the-art peer methods. The comprehensive results demonstrate that AllosES is a promising method for protein allosteric site prediction. The source code is available at https://github.com/ChunhuaLab/AllosES.
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Affiliation(s)
- Fangrui Hu
- College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Fubin Chang
- College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Lianci Tao
- College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Xiaohan Sun
- College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Lamei Liu
- College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Yingchun Zhao
- College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Zhongjie Han
- College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Chunhua Li
- College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
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3
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Cronan JE. Biotin protein ligase as you like it: Either extraordinarily specific or promiscuous protein biotinylation. Proteins 2024; 92:435-448. [PMID: 37997490 PMCID: PMC10932917 DOI: 10.1002/prot.26642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023]
Abstract
Biotin (vitamin H or B7) is a coenzyme essential for all forms of life. Biotin has biological activity only when covalently attached to a few key metabolic enzyme proteins. Most organisms have only one attachment enzyme, biotin protein ligase (BPL), which attaches biotin to all target proteins. The sequences of these proteins and their substrate proteins are strongly conserved throughout biology. Structures of both the biotin ligase- and biotin-acceptor domains of mammals, plants, several bacterial species, and archaea have been determined. These, together with mutational analyses of ligases and their protein substrates, illustrate the exceptional specificity of this protein modification. For example, the Escherichia coli BPL biotinylates only one of the >4000 cellular proteins. Several bifunctional bacterial biotin ligases transcriptionally regulate biotin synthesis and/or transport in concert with biotinylation. The human BPL has been demonstrated to play an important role in that mutations in the BPL encoding gene cause one form of the disease, biotin-responsive multiple carboxylase deficiency. Promiscuous mutant versions of several BPL enzymes release biotinoyl-AMP, the active intermediate of the ligase reaction, to solvent. The released biotinoyl-AMP acts as a chemical biotinylation reagent that modifies lysine residues of neighboring proteins in vivo. This proximity-dependent biotinylation (called BioID) approach has been heavily utilized in cell biology.
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Affiliation(s)
- John E Cronan
- Department of Microbiology, University of Illinois, Urbana, Illinois, USA
- Department of Biochemistry, University of Illinois, Urbana, Illinois, USA
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4
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Abstract
A survey of protein databases indicates that the majority of enzymes exist in oligomeric forms, with about half of those found in the UniProt database being homodimeric. Understanding why many enzymes are in their dimeric form is imperative. Recent developments in experimental and computational techniques have allowed for a deeper comprehension of the cooperative interactions between the subunits of dimeric enzymes. This review aims to succinctly summarize these recent advancements by providing an overview of experimental and theoretical methods, as well as an understanding of cooperativity in substrate binding and the molecular mechanisms of cooperative catalysis within homodimeric enzymes. Focus is set upon the beneficial effects of dimerization and cooperative catalysis. These advancements not only provide essential case studies and theoretical support for comprehending dimeric enzyme catalysis but also serve as a foundation for designing highly efficient catalysts, such as dimeric organic catalysts. Moreover, these developments have significant implications for drug design, as exemplified by Paxlovid, which was designed for the homodimeric main protease of SARS-CoV-2.
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Affiliation(s)
- Ke-Wei Chen
- Lab of Computional Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Tian-Yu Sun
- Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Yun-Dong Wu
- Lab of Computional Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Shenzhen Bay Laboratory, Shenzhen 518132, China
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5
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Samanta R, Sanghvi N, Beckett D, Matysiak S. Emergence of allostery through reorganization of protein residue network architecture. J Chem Phys 2023; 158:085104. [PMID: 36859102 PMCID: PMC9974213 DOI: 10.1063/5.0136010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 02/03/2023] [Indexed: 02/09/2023] Open
Abstract
Despite more than a century of study, consensus on the molecular basis of allostery remains elusive. A comparison of allosteric and non-allosteric members of a protein family can shed light on this important regulatory mechanism, and the bacterial biotin protein ligases, which catalyze post-translational biotin addition, provide an ideal system for such comparison. While the Class I bacterial ligases only function as enzymes, the bifunctional Class II ligases use the same structural architecture for an additional transcription repression function. This additional function depends on allosterically activated homodimerization followed by DNA binding. In this work, we used experimental, computational network, and bioinformatics analyses to uncover distinguishing features that enable allostery in the Class II biotin protein ligases. Experimental studies of the Class II Escherichia coli protein indicate that catalytic site residues are critical for both catalysis and allostery. However, allostery also depends on amino acids that are more broadly distributed throughout the protein structure. Energy-based community network analysis of representative Class I and Class II proteins reveals distinct residue community architectures, interactions among the communities, and responses of the network to allosteric effector binding. Bioinformatics mutual information analyses of multiple sequence alignments indicate distinct networks of coevolving residues in the two protein families. The results support the role of divergent local residue community network structures both inside and outside of the conserved enzyme active site combined with distinct inter-community interactions as keys to the emergence of allostery in the Class II biotin protein ligases.
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Affiliation(s)
- Riya Samanta
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, USA
| | - Neel Sanghvi
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, USA
| | - Dorothy Beckett
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
| | - Silvina Matysiak
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, USA
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Rajak MK, Bhatnagar S, Pandey S, Kumar S, Verma S, Patel AK, Sundd M. Leishmania major biotin protein ligase forms a unique cross-handshake dimer. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2021; 77:510-521. [PMID: 33825711 DOI: 10.1107/s2059798321001418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/08/2021] [Indexed: 11/10/2022]
Abstract
Biotin protein ligase catalyses the post-translational modification of biotin carboxyl carrier protein (BCCP) domains, a modification that is crucial for the function of several carboxylases. It is a two-step process that results in the covalent attachment of biotin to the ϵ-amino group of a conserved lysine of the BCCP domain of a carboxylase in an ATP-dependent manner. In Leishmania, three mitochondrial enzymes, acetyl-CoA carboxylase, methylcrotonyl-CoA carboxylase and propionyl-CoA carboxylase, depend on biotinylation for activity. In view of the indispensable role of the biotinylating enzyme in the activation of these carboxylases, crystal structures of L. major biotin protein ligase complexed with biotin and with biotinyl-5'-AMP have been solved. L. major biotin protein ligase crystallizes as a unique dimer formed by cross-handshake interactions of the hinge region of the two monomers formed by partial unfolding of the C-terminal domain. Interestingly, the substrate (BCCP domain)-binding site of each monomer is occupied by its own C-terminal domain in the dimer structure. This was observed in all of the crystals that were obtained, suggesting a closed/inactive conformation of the enzyme. Size-exclusion chromatography studies carried out using high protein concentrations (0.5 mM) suggest the formation of a concentration-dependent dimer that exists in equilibrium with the monomer.
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Affiliation(s)
- Manoj Kumar Rajak
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Sonika Bhatnagar
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Shubhant Pandey
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar 752 050, India
| | - Sunil Kumar
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi 110 016, India
| | - Shalini Verma
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Ashok Kumar Patel
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi 110 016, India
| | - Monica Sundd
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
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7
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Sirithanakorn C, Cronan JE. Biotin, a universal and essential cofactor: Synthesis, ligation and regulation. FEMS Microbiol Rev 2021; 45:6081095. [PMID: 33428728 DOI: 10.1093/femsre/fuab003] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/08/2021] [Indexed: 12/22/2022] Open
Abstract
Biotin is a covalently attached enzyme cofactor required for intermediary metabolism in all three domains of life. Several important human pathogens (e.g. Mycobacterium tuberculosis) require biotin synthesis for pathogenesis. Humans lack a biotin synthetic pathway hence bacterial biotin synthesis is a prime target for new therapeutic agents. The biotin synthetic pathway is readily divided into early and late segments. Although pimelate, a seven carbon α,ω-dicarboxylic acid that contributes seven of the ten biotin carbons atoms, was long known to be a biotin precursor, its biosynthetic pathway was a mystery until the E. coli pathway was discovered in 2010. Since then, diverse bacteria encode evolutionarily distinct enzymes that replace enzymes in the E. coli pathway. Two new bacterial pimelate synthesis pathways have been elucidated. In contrast to the early pathway the late pathway, assembly of the fused rings of the cofactor, was long thought settled. However, a new enzyme that bypasses a canonical enzyme was recently discovered as well as homologs of another canonical enzyme that functions in synthesis of another protein-bound coenzyme, lipoic acid. Most bacteria tightly regulate transcription of the biotin synthetic genes in a biotin-responsive manner. The bifunctional biotin ligases which catalyze attachment of biotin to its cognate enzymes and repress biotin gene transcription are best understood regulatory system.
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Affiliation(s)
- Chaiyos Sirithanakorn
- Faculty of Medicine, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand.,Department of Microbiology, University of Illinois, Urbana, IL 61801, USA
| | - John E Cronan
- Department of Microbiology, University of Illinois, Urbana, IL 61801, USA.,Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA
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8
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Sternicki LM, Nguyen S, Pacholarz KJ, Barran P, Pendini NR, Booker GW, Huet Y, Baltz R, Wegener KL, Pukala TL, Polyak SW. Biochemical characterisation of class III biotin protein ligases from Botrytis cinerea and Zymoseptoria tritici. Arch Biochem Biophys 2020; 691:108509. [PMID: 32717225 DOI: 10.1016/j.abb.2020.108509] [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: 06/17/2020] [Revised: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 10/23/2022]
Abstract
Biotin protein ligase (BPL) is an essential enzyme in all kingdoms of life, making it a potential target for novel anti-infective agents. Whilst bacteria and archaea have simple BPL structures (class I and II), the homologues from certain eukaryotes such as mammals, insects and yeast (class III) have evolved a more complex structure with a large extension on the N-terminus of the protein in addition to the conserved catalytic domain. The absence of atomic resolution structures of any class III BPL hinders structural and functional analysis of these enzymes. Here, two new class III BPLs from agriculturally important moulds Botrytis cinerea and Zymoseptoria tritici were characterised alongside the homologue from the prototypical yeast Saccharomyces cerevisiae. Circular dichroism and ion mobility-mass spectrometry analysis revealed conservation of the overall tertiary and secondary structures of all three BPLs, corresponding with the high sequence similarity. Subtle structural differences were implied by the different thermal stabilities of the enzymes and their varied Michaelis constants for their interactions with ligands biotin, MgATP, and biotin-accepting substrates from different species. The three BPLs displayed different preferences for fungal versus bacterial protein substrates, providing further evidence that class III BPLs have a 'substrate validation' activity for selecting only appropriate proteins for biotinylation. Selective, potent inhibition of these three BPLs was demonstrated despite sequence and structural homology. This highlights the potential for targeting BPL for novel, selective antifungal therapies against B. cinerea, Z. tritici and other fungal species.
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Affiliation(s)
- Louise M Sternicki
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia
| | - Stephanie Nguyen
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia; Institute for Photonics and Advanced Sensing (IPAS), The University of Adelaide, South Australia, 5005, Australia
| | - Kamila J Pacholarz
- Michael Barber Centre for Collaborative Mass Spectrometry, Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Perdita Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Nicole R Pendini
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia
| | - Grant W Booker
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia
| | - Yoann Huet
- Bayer SAS CropScience, La Dargoire Research Centre, Lyon, 69263 Cedex 09, France
| | - Rachel Baltz
- Bayer SAS CropScience, La Dargoire Research Centre, Lyon, 69263 Cedex 09, France
| | - Kate L Wegener
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia; Institute for Photonics and Advanced Sensing (IPAS), The University of Adelaide, South Australia, 5005, Australia
| | - Tara L Pukala
- School of Physical Sciences, The University of Adelaide, South Australia, 5005, Australia
| | - Steven W Polyak
- School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia; Institute for Photonics and Advanced Sensing (IPAS), The University of Adelaide, South Australia, 5005, Australia.
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9
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Bockman MR, Mishra N, Aldrich CC. The Biotin Biosynthetic Pathway in Mycobacterium tuberculosis is a Validated Target for the Development of Antibacterial Agents. Curr Med Chem 2020; 27:4194-4232. [PMID: 30663561 DOI: 10.2174/0929867326666190119161551] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 12/14/2018] [Accepted: 01/12/2019] [Indexed: 12/11/2022]
Abstract
Mycobacterium tuberculosis, responsible for Tuberculosis (TB), remains the leading cause of mortality among infectious diseases worldwide from a single infectious agent, with an estimated 1.7 million deaths in 2016. Biotin is an essential cofactor in M. tuberculosis that is required for lipid biosynthesis and gluconeogenesis. M. tuberculosis relies on de novo biotin biosynthesis to obtain this vital cofactor since it cannot scavenge sufficient biotin from a mammalian host. The biotin biosynthetic pathway in M. tuberculosis has been well studied and rigorously genetically validated providing a solid foundation for medicinal chemistry efforts. This review examines the mechanism and structure of the enzymes involved in biotin biosynthesis and ligation, summarizes the reported genetic validation studies of the pathway, and then analyzes the most promising inhibitors and natural products obtained from structure-based drug design and phenotypic screening.
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Affiliation(s)
- Matthew R Bockman
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, United States
| | - Neeraj Mishra
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, United States
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, United States
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10
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Lee KJ, Tieu W, Blanco-Rodriguez B, Paparella AS, Yu J, Hayes A, Feng J, Marshall AC, Noll B, Milne R, Cini D, Wilce MCJ, Booker GW, Bruning JB, Polyak SW, Abell AD. Sulfonamide-Based Inhibitors of Biotin Protein Ligase as New Antibiotic Leads. ACS Chem Biol 2019; 14:1990-1997. [PMID: 31407891 DOI: 10.1021/acschembio.9b00463] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Here, we report the design, synthesis, and evaluation of a series of inhibitors of Staphylococcus aureus BPL (SaBPL), where the central acyl phosphate of the natural intermediate biotinyl-5'-AMP (1) is replaced by a sulfonamide isostere. Acylsulfamide (6) and amino sulfonylurea (7) showed potent in vitro inhibitory activity (Ki = 0.007 ± 0.003 and 0.065 ± 0.03 μM, respectively) and antibacterial activity against S. aureus ATCC49775 with minimum inhibitory concentrations of 0.25 and 4 μg/mL, respectively. Additionally, the bimolecular interactions between the BPL and inhibitors 6 and 7 were defined by X-ray crystallography and molecular dynamics simulations. The high acidity of the sulfonamide linkers of 6 and 7 likely contributes to the enhanced in vitro inhibitory activities by promoting interaction with SaBPL Lys187. Analogues with alkylsulfamide (8), β-ketosulfonamide (9), and β-hydroxysulfonamide (10) isosteres were devoid of significant activity. Binding free energy estimation using computational methods suggests deprotonated 6 and 7 to be the best binders, which is consistent with enzyme assay results. Compound 6 was unstable in whole blood, leading to poor pharmacokinetics. Importantly, 7 has a vastly improved pharmacokinetic profile compared to that of 6 presumably due to the enhanced metabolic stability of the sulfonamide linker moiety.
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Affiliation(s)
- Kwang Jun Lee
- Department of Chemistry, School of Physical Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
- Centre for Nanoscale BioPhotonics (CNBP), University of Adelaide, Adelaide, South Australia 5005, Australia
| | - William Tieu
- Department of Chemistry, School of Physical Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Beatriz Blanco-Rodriguez
- Department of Chemistry, School of Physical Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Ashleigh S. Paparella
- Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Jingxian Yu
- Department of Chemistry, School of Physical Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
- Centre for Nanoscale BioPhotonics (CNBP), University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Andrew Hayes
- Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Jiage Feng
- Department of Chemistry, School of Physical Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Andrew C. Marshall
- Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Benjamin Noll
- School of Pharmacy & Medical Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
| | - Robert Milne
- School of Pharmacy & Medical Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
| | - Danielle Cini
- Department of Biochemistry, School of Biomedical Science, Monash University, Clayton, Victoria 3800, Australia
| | - Matthew C. J. Wilce
- Department of Biochemistry, School of Biomedical Science, Monash University, Clayton, Victoria 3800, Australia
| | - Grant W. Booker
- Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - John B. Bruning
- Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Steven W. Polyak
- Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Andrew D. Abell
- Department of Chemistry, School of Physical Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
- Centre for Nanoscale BioPhotonics (CNBP), University of Adelaide, Adelaide, South Australia 5005, Australia
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11
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A green fluorescent protein-based assay for high-throughput ligand-binding studies of a mycobacterial biotin protein ligase. Microbiol Res 2017; 205:35-39. [PMID: 28942842 DOI: 10.1016/j.micres.2017.08.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 08/23/2017] [Accepted: 08/24/2017] [Indexed: 01/06/2023]
Abstract
Biotin protein ligase (BirA) has been identified as an emerging drug target in Mycobacterium tuberculosis due to its essential metabolic role. Indeed, it is the only enzyme capable of covalently attaching biotin onto the biotin carboxyl carrier protein subunit of the acetyl-CoA carboxylase. Despite recent interest in this protein, there is still a gap in cost-effective high-throughput screening assays for rapid identification of mycobacterial BirA-targeting inhibitors. We present for the first time the cloning, expression, purification of mycobacterial GFP-tagged BirA and its application for the development of a high-throughput assay building on the principle of differential scanning fluorimetry of GFP-tagged proteins. The data obtained in this study reveal how biotin and ATP significantly increase the thermal stability (ΔTm=+16.5°C) of M. tuberculosis BirA and lead to formation of a high affinity holoenzyme complex (Kobs=7.7nM). The new findings and mycobacterial BirA high-throughput assay presented in this work could provide an efficient platform for future anti-tubercular drug discovery campaigns.
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12
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Mechanisms Governing Precise Protein Biotinylation. Trends Biochem Sci 2017; 42:383-394. [DOI: 10.1016/j.tibs.2017.02.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/25/2017] [Accepted: 02/03/2017] [Indexed: 12/26/2022]
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13
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Bond TEH, Sorenson AE, Schaeffer PM. Functional characterisation of Burkholderia pseudomallei biotin protein ligase: A toolkit for anti-melioidosis drug development. Microbiol Res 2017; 199:40-48. [PMID: 28454708 DOI: 10.1016/j.micres.2017.03.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 03/06/2017] [Accepted: 03/15/2017] [Indexed: 01/17/2023]
Abstract
Burkholderia pseudomallei (Bp) is the causative agent of melioidosis. The bacterium is responsible for 20% of community-acquired sepsis cases and 40% of sepsis-related mortalities in northeast Thailand, and is intrinsically resistant to aminoglycosides, macrolides, rifamycins, cephalosporins, and nonureidopenicillins. There is no vaccine and its diagnosis is problematic. Biotin protein ligase (BirA) which is essential for fatty acid synthesis has been proposed as a drug target in bacteria. Very few bacterial BirA have been characterized, and a better understanding of these enzymes is necessary to further assess their value as drug targets. BirA within the Burkholderia genus have not yet been investigated. We present for the first time the cloning, expression, purification and functional characterisation of the putative Bp BirA and orthologous B. thailandensis (Bt) biotin carboxyl carrier protein (BCCP) substrate. A GFP-tagged Bp BirA was produced and applied for the development of a high-throughput (HT) assay based on our differential scanning fluorimetry of GFP-tagged proteins (DSF-GTP) principle as well as an electrophoretic mobility shift assay. Our biochemical data in combination with the new HT DSF-GTP and biotinylation activity assay could facilitate future drug screening efforts against this drug-resistant organism.
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Affiliation(s)
- Thomas E H Bond
- Comparative Genomics Centre, James Cook University, DB21, James Cook Drive, Townsville, QLD 4811, Australia
| | - Alanna E Sorenson
- Comparative Genomics Centre, James Cook University, DB21, James Cook Drive, Townsville, QLD 4811, Australia
| | - Patrick M Schaeffer
- Comparative Genomics Centre, James Cook University, DB21, James Cook Drive, Townsville, QLD 4811, Australia.
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Biotin Protein Ligase Is a Target for New Antibacterials. Antibiotics (Basel) 2016; 5:antibiotics5030026. [PMID: 27463729 PMCID: PMC5039522 DOI: 10.3390/antibiotics5030026] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 07/18/2016] [Accepted: 07/19/2016] [Indexed: 12/02/2022] Open
Abstract
There is a desperate need for novel antibiotic classes to combat the rise of drug resistant pathogenic bacteria, such as Staphylococcus aureus. Inhibitors of the essential metabolic enzyme biotin protein ligase (BPL) represent a promising drug target for new antibacterials. Structural and biochemical studies on the BPL from S. aureus have paved the way for the design and development of new antibacterial chemotherapeutics. BPL employs an ordered ligand binding mechanism for the synthesis of the reaction intermediate biotinyl-5′-AMP from substrates biotin and ATP. Here we review the structure and catalytic mechanism of the target enzyme, along with an overview of chemical analogues of biotin and biotinyl-5′-AMP as BPL inhibitors reported to date. Of particular promise are studies to replace the labile phosphoroanhydride linker present in biotinyl-5′-AMP with alternative bioisosteres. A novel in situ click approach using a mutant of S. aureus BPL as a template for the synthesis of triazole-based inhibitors is also presented. These approaches can be widely applied to BPLs from other bacteria, as well as other closely related metabolic enzymes and antibacterial drug targets.
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15
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Mechanisms of biotin-regulated gene expression in microbes. Synth Syst Biotechnol 2016; 1:17-24. [PMID: 29062923 PMCID: PMC5640590 DOI: 10.1016/j.synbio.2016.01.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 01/08/2016] [Accepted: 01/10/2016] [Indexed: 12/23/2022] Open
Abstract
Biotin is an essential micronutrient that acts as a co-factor for biotin-dependent metabolic enzymes. In bacteria, the supply of biotin can be achieved by de novo synthesis or import from exogenous sources. Certain bacteria are able to obtain biotin through both mechanisms while others can only fulfill their biotin requirement through de novo synthesis. Inability to fulfill their cellular demand for biotin can have detrimental consequences on cell viability and virulence. Therefore understanding the transcriptional mechanisms that regulate biotin biosynthesis and transport will extend our knowledge about bacterial survival and metabolic adaptation during pathogenesis when the supply of biotin is limited. The most extensively characterized protein that regulates biotin synthesis and uptake is BirA. In certain bacteria, such as Escherichia coli and Staphylococcus aureus, BirA is a bi-functional protein that serves as a transcriptional repressor to regulate biotin biosynthesis genes, as well as acting as a ligase to catalyze the biotinylation of biotin-dependent enzymes. Recent studies have identified two other proteins that also regulate biotin synthesis and transport, namely BioQ and BioR. This review summarizes the different transcriptional repressors and their mechanism of action. Moreover, the ability to regulate the expression of target genes through the activity of a vitamin, such as biotin, may have biotechnological applications in synthetic biology.
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16
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Ma Q, Akhter Y, Wilmanns M, Ehebauer MT. Active site conformational changes upon reaction intermediate biotinyl-5'-AMP binding in biotin protein ligase from Mycobacterium tuberculosis. Protein Sci 2014; 23:932-9. [PMID: 24723382 DOI: 10.1002/pro.2475] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 03/25/2014] [Accepted: 03/28/2014] [Indexed: 11/07/2022]
Abstract
Protein biotinylation, a rare form of post-translational modification, is found in enzymes required for lipid biosynthesis. In mycobacteria, this process is essential for the formation of their complex and distinct cell wall and has become a focal point of drug discovery approaches. The enzyme responsible for this process, biotin protein ligase, substantially varies in different species in terms of overall structural organization, regulation of function and substrate specificity. To advance the understanding of the molecular mechanism of biotinylation in Mycobacterium tuberculosis we have biochemically and structurally characterized the corresponding enzyme. We report the high-resolution crystal structures of the apo-form and reaction intermediate biotinyl-5'-AMP-bound form of M. tuberculosis biotin protein ligase. Binding of the reaction intermediate leads to clear disorder-to-order transitions. We show that a conserved lysine, Lys138, in the active site is essential for biotinylation.
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Affiliation(s)
- Qingjun Ma
- European Molecular Biology Laboratory, EMBL-Hamburg, c/o DESY, Building 25A, Notkestrasse 85, 22603, Hamburg, Germany
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17
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Pendini NR, Yap MY, Traore DAK, Polyak SW, Cowieson NP, Abell A, Booker GW, Wallace JC, Wilce JA, Wilce MCJ. Structural characterization of Staphylococcus aureus biotin protein ligase and interaction partners: an antibiotic target. Protein Sci 2013; 22:762-73. [PMID: 23559560 DOI: 10.1002/pro.2262] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 03/26/2013] [Accepted: 03/26/2013] [Indexed: 11/06/2022]
Abstract
The essential metabolic enzyme biotin protein ligase (BPL) is a potential target for the development of new antibiotics required to combat drug-resistant pathogens. Staphylococcus aureus BPL (SaBPL) is a bifunctional protein, possessing both biotin ligase and transcription repressor activities. This positions BPL as a key regulator of several important metabolic pathways. Here, we report the structural analysis of both holo- and apo-forms of SaBPL using X-ray crystallography. We also present small-angle X-ray scattering data of SaBPL in complex with its biotin-carboxyl carrier protein substrate as well as the SaBPL:DNA complex that underlies repression. This has revealed the molecular basis of ligand (biotinyl-5'-AMP) binding and conformational changes associated with catalysis and repressor function. These data provide new information to better understand the bifunctional activities of SaBPL and to inform future strategies for antibiotic discovery.
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Affiliation(s)
- Nicole R Pendini
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Victoria, Australia
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18
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Soares da Costa TP, Yap MY, Perugini MA, Wallace JC, Abell AD, Wilce MCJ, Polyak SW, Booker GW. Dual roles of F123 in protein homodimerization and inhibitor binding to biotin protein ligase fromStaphylococcus aureus. Mol Microbiol 2013; 91:110-20. [DOI: 10.1111/mmi.12446] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2013] [Indexed: 12/17/2022]
Affiliation(s)
| | - Min Y. Yap
- School of Biomedical Science; Monash University; Victoria 3800 Australia
| | - Matthew A. Perugini
- Department of Biochemistry; La Trobe Institute for Molecular Science; La Trobe University; Victoria 3086 Australia
| | - John C. Wallace
- School of Molecular and Biomedical Science; University of Adelaide; South Australia 5005 Australia
| | - Andrew D. Abell
- School of Chemistry and Physics; University of Adelaide; South Australia 5005 Australia
- Centre for Molecular Pathology; University of Adelaide; South Australia 5005 Australia
| | | | - Steven W. Polyak
- School of Molecular and Biomedical Science; University of Adelaide; South Australia 5005 Australia
- Centre for Molecular Pathology; University of Adelaide; South Australia 5005 Australia
| | - Grant W. Booker
- School of Molecular and Biomedical Science; University of Adelaide; South Australia 5005 Australia
- Centre for Molecular Pathology; University of Adelaide; South Australia 5005 Australia
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19
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Saracino GAA, Gelain F. Modelling and analysis of early aggregation events of BMHP1-derived self-assembling peptides. J Biomol Struct Dyn 2013; 32:759-75. [PMID: 23730849 DOI: 10.1080/07391102.2013.790848] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Despite the increasing use and development of peptide-based scaffolds in different fields including that of regenerative medicine, the understanding of the factors governing the self-assembly process and the relationship between sequence and properties have not yet been fully understood. BMHP1-derived self-assembling peptides (SAPs) have been developed and characterized showing that biotinylation at the N-terminal cap corresponds to better performing assembly and scaffold biomechanics. In this study, the effects of biotinylation on the self-assembly dynamics of seven BMHP1-derived SAPs have been investigated by molecular dynamics simulations. We confirmed that these SAPs self-assemble into β-structures and that proline acts as a β-breaker of the assembled aggregates. In biotinylated peptides, the formation of ordered β-structured aggregates is triggered by both the establishment of a dense and dynamic H-bonds network and the formation of a 'hydrophobic wall' available to interact with other peptides. Such conditions result from the peculiar chemical composition of the biotinyl-cap, given by the synergic cooperation of the uracil function of the ureido ring with the high hydrophobic portion consisting of the thiophenyl ring and valeryl chain. The inbuilt propensity of biotinylated peptides towards the formation of ordered small aggregates makes them ideal precursors of higher hierarchically organized self-assembled nanostructures as experimentally observed.
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Affiliation(s)
- Gloria Anna Ada Saracino
- a Center of Nanomedicine and Tissue Engineering A. O. Ospedale Niguarda Ca' Granda , Milan , 20162 Italy
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Altaf M, Stoeckli-Evans H. Chiral one- and two-dimensional silver(I)-biotin coordination polymers. Acta Crystallogr C 2013; 69:127-37. [PMID: 23377677 DOI: 10.1107/s0108270113000322] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 01/04/2013] [Indexed: 11/10/2022] Open
Abstract
Reaction of biotin {C(10)H(16)N(2)O(3)S, HL; systematic name: 5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid} with silver acetate and a few drops of aqueous ammonia leads to the deprotonation of the carboxylic acid group and the formation of a neutral chiral two-dimensional polymer network, poly[[{μ(3)-5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoato}silver(I)] trihydrate], {[Ag(C(10)H(15)N(2)O(3)S)]·3H(2)O}(n) or {[Ag(L)]·3H(2)O}(n), (I). Here, the Ag(I) cations are pentacoordinate, coordinated by four biotin anions via two S atoms and a ureido O atom, and by two carboxylate O atoms of the same molecule. The reaction of biotin with silver salts of potentially coordinating anions, viz. nitrate and perchlorate, leads to the formation of the chiral one-dimensional coordination polymers catena-poly[[bis[nitratosilver(I)]-bis{μ(3)-5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoato}] monohydrate], {[Ag(2)(NO(3))(2)(C(10)H(16)N(2)O(3)S)(2)]·H(2)O}(n) or {[Ag(2)(NO(3))(2)(HL)(2)]·H(2)O}(n), (II), and catena-poly[bis[perchloratosilver(I)]-bis{μ(3)-5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoato}], [Ag(2)(ClO(4))(2)(C(10)H(16)N(2)O(3)S)(2)](n) or [Ag(2)(ClO(4))(2)(HL)(2)](n), (III), respectively. In (II), the Ag(I) cations are again pentacoordinated by three biotin molecules via two S atoms and a ureido O atom, and by two O atoms of a nitrate anion. In (I), (II) and (III), the Ag(I) cations are bridged by an S atom and are coordinated by the ureido O atom and the O atoms of the anions. The reaction of biotin with silver salts of noncoordinating anions, viz. hexafluoridophosphate (PF(6)(-)) and hexafluoridoantimonate (SbF(6)(-)), gave the chiral double-stranded helical structures catena-poly[[silver(I)-bis{μ(2)-5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoato}] hexafluoridophosphate], {[Ag(C(10)H(16)N(2)O(3)S)(2)](PF(6))}(n) or {[Ag(HL)(2)](PF(6))}(n), (IV), and catena-poly[[[{5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoato}silver(I)]-μ(2)-{5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoato}] hexafluoridoantimonate], {[Ag(C(10)H(16)N(2)O(3)S)(2)](SbF(6))}(n) or {[Ag(HL)(2)](SbF(6))}(n), (V), respectively. In (IV), the Ag(I) cations have a tetrahedral coordination environment, coordinated by four biotin molecules via two S atoms, and by two carboxy O atoms of two different molecules. In (V), however, the Ag(I) cations have a trigonal coordination environment, coordinated by three biotin molecules via two S atoms and one carboxy O atom. In (IV) and (V), neither the ureido O atom nor the F atoms of the anion are involved in coordination. Hence, the coordination environment of the Ag(I) cations varies from AgS(2)O trigonal to AgS(2)O(2) tetrahedral to AgS(2)O(3) square-pyramidal. The conformation of the valeric acid side chain varies from extended to twisted and this, together with the various anions present, has an influence on the solid-state structures of the resulting compounds. The various O-H···O and N-H···O hydrogen bonds present result in the formation of chiral two- and three-dimensional networks, which are further stabilized by C-H···X (X = O, F, S) interactions, and by N-H···F interactions for (IV) and (V). Biotin itself has a twisted valeric acid side chain which is involved in an intramolecular C-H···S hydrogen bond. The tetrahydrothiophene ring has an envelope conformation with the S atom as the flap. It is displaced from the mean plane of the four C atoms (plane B) by 0.8789 (6) Å, towards the ureido ring (plane A). Planes A and B are inclined to one another by 58.89 (14)°. In the crystal, molecules are linked via O-H···O and N-H···O hydrogen bonds, enclosing R(2)(2)(8) loops, forming zigzag chains propagating along [001]. These chains are linked via N-H···O hydrogen bonds, and C-H···S and C-H···O interactions forming a three-dimensional network. The absolute configurations of biotin and complexes (I), (II), (IV) and (V) were confirmed crystallographically by resonant scattering.
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Affiliation(s)
- Muhammad Altaf
- Institute of Physics, University of Neuchâtel, Rue Emile-Argand 11, CH-2000 Neuchâtel, Switzerland.
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21
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Tieu W, Soares da Costa TP, Yap MY, Keeling KL, Wilce MCJ, Wallace JC, Booker GW, Polyak SW, Abell AD. Optimising in situ click chemistry: the screening and identification of biotin protein ligase inhibitors. Chem Sci 2013. [DOI: 10.1039/c3sc51127h] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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22
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Böttcher C, Dennis EG, Booker GW, Polyak SW, Boss PK, Davies C. A novel tool for studying auxin-metabolism: the inhibition of grapevine indole-3-acetic acid-amido synthetases by a reaction intermediate analogue. PLoS One 2012; 7:e37632. [PMID: 22649546 PMCID: PMC3359377 DOI: 10.1371/journal.pone.0037632] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 04/27/2012] [Indexed: 02/03/2023] Open
Abstract
An important process for the regulation of auxin levels in plants is the inactivation of indole-3-acetic acid (IAA) by conjugation to amino acids. The conjugation reaction is catalysed by IAA-amido synthetases belonging to the family of GH3 proteins. Genetic approaches to study the biological significance of these enzymes have been hampered by large gene numbers and a high degree of functional redundancy. To overcome these difficulties a chemical approach based on the reaction mechanism of GH3 proteins was employed to design a small molecule inhibitor of IAA-amido synthetase activity. Adenosine-5'-[2-(1H-indol-3-yl)ethyl]phosphate (AIEP) mimics the adenylated intermediate of the IAA-conjugation reaction and was therefore proposed to compete with the binding of MgATP and IAA in the initial stages of catalysis. Two grapevine IAA-amido synthetases with different catalytic properties were chosen to test the inhibitory effects of AIEP in vitro. GH3-1 has previously been implicated in the grape berry ripening process and is restricted to two amino acid substrates, whereas GH3-6 conjugated IAA to 13 amino acids. AIEP is the most potent inhibitor of GH3 enzymes so far described and was shown to be competitive against MgATP and IAA binding to both enzymes with K(i)-values 17-68-fold lower than the respective K(m)-values. AIEP also exhibited in vivo activity in an ex planta test system using young grape berries. Exposure to 5-20 µM of the inhibitor led to decreased levels of the common conjugate IAA-Asp and reduced the accumulation of the corresponding Asp-conjugate upon treatment with a synthetic auxin. AIEP therefore represents a novel chemical probe with which to study IAA-amido synthetase function.
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23
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Bisubstrate adenylation inhibitors of biotin protein ligase from Mycobacterium tuberculosis. ACTA ACUST UNITED AC 2012; 18:1432-41. [PMID: 22118677 DOI: 10.1016/j.chembiol.2011.08.013] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Revised: 08/05/2011] [Accepted: 08/24/2011] [Indexed: 10/15/2022]
Abstract
The mycobacterial biotin protein ligase (MtBPL) globally regulates lipid metabolism in Mtb through the posttranslational biotinylation of acyl coenzyme A carboxylases involved in lipid biosynthesis that catalyze the first step in fatty acid biosynthesis and pyruvate coenzyme A carboxylase, a gluconeogenic enzyme vital for lipid catabolism. Here we describe the design, development, and evaluation of a rationally designed bisubstrate inhibitor of MtBPL. This inhibitor displays potent subnanomolar enzyme inhibition and antitubercular activity against multidrug resistant and extensively drug resistant Mtb strains. We show that the inhibitor decreases in vivo protein biotinylation of key enzymes involved in fatty acid biosynthesis and that the antibacterial activity is MtBPL dependent. Additionally, the gene encoding BPL was found to be essential in M. smegmatis. Finally, the X-ray cocrystal structure of inhibitor bound MtBPL was solved providing detailed insight for further structure-activity analysis. Collectively, these data suggest that MtBPL is a promising target for further antitubercular therapeutic development.
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Soares da Costa TP, Tieu W, Yap MY, Pendini NR, Polyak SW, Sejer Pedersen D, Morona R, Turnidge JD, Wallace JC, Wilce MCJ, Booker GW, Abell AD. Selective inhibition of biotin protein ligase from Staphylococcus aureus. J Biol Chem 2012; 287:17823-17832. [PMID: 22437830 DOI: 10.1074/jbc.m112.356576] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
There is a well documented need to replenish the antibiotic pipeline with new agents to combat the rise of drug resistant bacteria. One strategy to combat resistance is to discover new chemical classes immune to current resistance mechanisms that inhibit essential metabolic enzymes. Many of the obvious drug targets that have no homologous isozyme in the human host have now been investigated. Bacterial drug targets that have a closely related human homologue represent a new frontier in antibiotic discovery. However, to avoid potential toxicity to the host, these inhibitors must have very high selectivity for the bacterial enzyme over the human homolog. We have demonstrated that the essential enzyme biotin protein ligase (BPL) from the clinically important pathogen Staphylococcus aureus could be selectively inhibited. Linking biotin to adenosine via a 1,2,3 triazole yielded the first BPL inhibitor selective for S. aureus BPL over the human equivalent. The synthesis of new biotin 1,2,3-triazole analogues using click chemistry yielded our most potent structure (K(i) 90 nM) with a >1100-fold selectivity for the S. aureus BPL over the human homologue. X-ray crystallography confirmed the mechanism of inhibitor binding. Importantly, the inhibitor showed cytotoxicity against S. aureus but not cultured mammalian cells. The biotin 1,2,3-triazole provides a novel pharmacophore for future medicinal chemistry programs to develop this new antibiotic class.
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Affiliation(s)
- Tatiana P Soares da Costa
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - William Tieu
- School of Chemistry and Physics, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Min Y Yap
- School of Biomedical Science, Monash University, Victoria 3800, Australia
| | - Nicole R Pendini
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia; School of Biomedical Science, Monash University, Victoria 3800, Australia
| | - Steven W Polyak
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia.
| | - Daniel Sejer Pedersen
- School of Chemistry and Physics, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Renato Morona
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - John D Turnidge
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia; SA Pathology at Women's and Children's Hospital, South Australia 5006, Australia
| | - John C Wallace
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Matthew C J Wilce
- School of Biomedical Science, Monash University, Victoria 3800, Australia
| | - Grant W Booker
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Andrew D Abell
- School of Chemistry and Physics, University of Adelaide, Adelaide, South Australia 5005, Australia
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Peters-Wendisch P, Stansen KC, Götker S, Wendisch VF. Biotin protein ligase from Corynebacterium glutamicum: role for growth and L: -lysine production. Appl Microbiol Biotechnol 2011; 93:2493-502. [PMID: 22159614 DOI: 10.1007/s00253-011-3771-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2011] [Revised: 11/16/2011] [Accepted: 11/17/2011] [Indexed: 01/08/2023]
Abstract
Corynebacterium glutamicum is a biotin auxotrophic Gram-positive bacterium that is used for large-scale production of amino acids, especially of L-glutamate and L-lysine. It is known that biotin limitation triggers L-glutamate production and that L-lysine production can be increased by enhancing the activity of pyruvate carboxylase, one of two biotin-dependent proteins of C. glutamicum. The gene cg0814 (accession number YP_225000) has been annotated to code for putative biotin protein ligase BirA, but the protein has not yet been characterized. A discontinuous enzyme assay of biotin protein ligase activity was established using a 105aa peptide corresponding to the carboxyterminus of the biotin carboxylase/biotin carboxyl carrier protein subunit AccBC of the acetyl CoA carboxylase from C. glutamicum as acceptor substrate. Biotinylation of this biotin acceptor peptide was revealed with crude extracts of a strain overexpressing the birA gene and was shown to be ATP dependent. Thus, birA from C. glutamicum codes for a functional biotin protein ligase (EC 6.3.4.15). The gene birA from C. glutamicum was overexpressed and the transcriptome was compared with the control strain revealing no significant gene expression changes of the bio-genes. However, biotin protein ligase overproduction increased the level of the biotin-containing protein pyruvate carboxylase and entailed a significant growth advantage in glucose minimal medium. Moreover, birA overexpression resulted in a twofold higher L-lysine yield on glucose as compared with the control strain.
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Affiliation(s)
- P Peters-Wendisch
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Bielefeld, Germany.
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A novel molecular mechanism to explain biotin-unresponsive holocarboxylase synthetase deficiency. J Mol Med (Berl) 2011; 90:81-8. [DOI: 10.1007/s00109-011-0811-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Revised: 07/26/2011] [Accepted: 08/18/2011] [Indexed: 10/17/2022]
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Lombard J, Moreira D. Early evolution of the biotin-dependent carboxylase family. BMC Evol Biol 2011; 11:232. [PMID: 21827699 PMCID: PMC3199775 DOI: 10.1186/1471-2148-11-232] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Accepted: 08/09/2011] [Indexed: 01/15/2023] Open
Abstract
Background Biotin-dependent carboxylases are a diverse family of carboxylating enzymes widespread in the three domains of life, and thus thought to be very ancient. This family includes enzymes that carboxylate acetyl-CoA, propionyl-CoA, methylcrotonyl-CoA, geranyl-CoA, acyl-CoA, pyruvate and urea. They share a common catalytic mechanism involving a biotin carboxylase domain, which fixes a CO2 molecule on a biotin carboxyl carrier peptide, and a carboxyl transferase domain, which transfers the CO2 moiety to the specific substrate of each enzyme. Despite this overall similarity, biotin-dependent carboxylases from the three domains of life carrying their reaction on different substrates adopt very diverse protein domain arrangements. This has made difficult the resolution of their evolutionary history up to now. Results Taking advantage of the availability of a large amount of genomic data, we have carried out phylogenomic analyses to get new insights on the ancient evolution of the biotin-dependent carboxylases. This allowed us to infer the set of enzymes present in the last common ancestor of each domain of life and in the last common ancestor of all living organisms (the cenancestor). Our results suggest that the last common archaeal ancestor had two biotin-dependent carboxylases, whereas the last common bacterial ancestor had three. One of these biotin-dependent carboxylases ancestral to Bacteria most likely belonged to a large family, the CoA-bearing-substrate carboxylases, that we define here according to protein domain composition and phylogenetic analysis. Eukaryotes most likely acquired their biotin-dependent carboxylases through the mitochondrial and plastid endosymbioses as well as from other unknown bacterial donors. Finally, phylogenetic analyses support previous suggestions about the existence of an ancient bifunctional biotin-protein ligase bound to a regulatory transcription factor. Conclusions The most parsimonious scenario for the early evolution of the biotin-dependent carboxylases, supported by the study of protein domain composition and phylogenomic analyses, entails that the cenancestor possessed two different carboxylases able to carry out the specific carboxylation of pyruvate and the non-specific carboxylation of several CoA-bearing substrates, respectively. These enzymes may have been able to participate in very diverse metabolic pathways in the cenancestor, such as in ancestral versions of fatty acid biosynthesis, anaplerosis, gluconeogenesis and the autotrophic fixation of CO2.
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Affiliation(s)
- Jonathan Lombard
- Unité d'Ecologie, Systématique et Evolution, UMR CNRS 8079, Univ, Paris-Sud, 91405 Orsay Cedex, France
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Purushothaman S, Annamalai K, Tyagi AK, Surolia A. Diversity in functional organization of class I and class II biotin protein ligase. PLoS One 2011; 6:e16850. [PMID: 21390227 PMCID: PMC3048393 DOI: 10.1371/journal.pone.0016850] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2010] [Accepted: 01/16/2011] [Indexed: 11/28/2022] Open
Abstract
The cell envelope of Mycobacterium tuberculosis
(M.tuberculosis) is composed of a variety of lipids
including mycolic acids, sulpholipids, lipoarabinomannans, etc., which impart
rigidity crucial for its survival and pathogenesis. Acyl CoA carboxylase (ACC)
provides malonyl-CoA and methylmalonyl-CoA, committed precursors for fatty acid
and essential for mycolic acid synthesis respectively. Biotin Protein Ligase
(BPL/BirA) activates apo-biotin carboxyl carrier protein (BCCP) by biotinylating
it to an active holo-BCCP. A minimal peptide (Schatz), an efficient substrate
for Escherichia coli BirA, failed to serve as substrate for
M. tuberculosis Biotin Protein Ligase
(MtBPL). MtBPL specifically biotinylates
homologous BCCP domain, MtBCCP87, but not
EcBCCP87. This is a unique feature of
MtBPL as EcBirA lacks such a stringent
substrate specificity. This feature is also reflected in the lack of
self/promiscuous biotinylation by MtBPL. The N-terminus/HTH
domain of EcBirA has the self-biotinable lysine residue that is
inhibited in the presence of Schatz peptide, a peptide designed to act as a
universal acceptor for EcBirA. This suggests that when biotin
is limiting, EcBirA preferentially catalyzes, biotinylation of
BCCP over self-biotinylation. R118G mutant of EcBirA showed
enhanced self and promiscuous biotinylation but its homologue, R69A
MtBPL did not exhibit these properties. The catalytic
domain of MtBPL was characterized further by limited
proteolysis. Holo-MtBPL is protected from proteolysis by
biotinyl-5′ AMP, an intermediate of MtBPL catalyzed
reaction. In contrast, apo-MtBPL is completely digested by
trypsin within 20 min of co-incubation. Substrate selectivity and inability to
promote self biotinylation are exquisite features of MtBPL and
are a consequence of the unique molecular mechanism of an enzyme adapted for the
high turnover of fatty acid biosynthesis.
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Affiliation(s)
| | | | - Anil K. Tyagi
- Department of Biochemistry, University of
Delhi South Campus, New Delhi, India
| | - Avadhesha Surolia
- Molecular Biophysics Unit, Indian Institute of
Science, Bangalore, India
- National Institute of Immunology, Aruna Asaf
Ali Marg, New Delhi, India
- * E-mail:
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29
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Ingaramo M, Beckett D. Biotinylation, a post-translational modification controlled by the rate of protein-protein association. J Biol Chem 2011; 286:13071-8. [PMID: 21343300 DOI: 10.1074/jbc.m110.183624] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Biotin protein ligases catalyze specific covalent linkage of the coenzyme biotin to biotin-dependent carboxylases. The reaction proceeds in two steps, including synthesis of an adenylated intermediate followed by biotin transfer to the carboxylase substrate. In this work specificity in the transfer reaction was investigated using single turnover stopped-flow and quench-flow assays. Cognate and noncognate reactions were measured using the enzymes and minimal biotin acceptor substrates from Escherichia coli, Pyrococcus horikoshii, and Homo sapiens. The kinetic analysis demonstrates that for all enzyme-substrate pairs the bimolecular rate of association of enzyme with substrate limits post-translational biotinylation. In addition, in noncognate reactions the three enzymes displayed a range of selectivities. These results highlight the importance of protein-protein binding kinetics for specific biotin addition to carboxylases and provide one mechanism for determining biotin distribution in metabolism.
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Affiliation(s)
- Maria Ingaramo
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland 20742, USA
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30
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Daniels KG, Beckett D. Biochemical properties and biological function of a monofunctional microbial biotin protein ligase. Biochemistry 2010; 49:5358-65. [PMID: 20499837 DOI: 10.1021/bi1003958] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biotin protein ligases constitute a family of enzymes that catalyze the linkage of biotin to biotin-dependent carboxylases. In bacteria, these enzymes are functionally divided into two classes: the monofunctional enzymes that catalyze only biotin addition and the bifunctional enzymes that also bind to DNA to regulate transcription initiation. Biochemical and biophysical studies of the bifunctional Escherichia coli ligase suggest that several properties of the enzyme have evolved to support its additional regulatory role. Included among these properties are the order of substrate binding and linkage between the oligomeric state and ligand binding. To test this hypothesized relationship between functionality and biochemical properties in ligases, we have conducted studies of the monofunctional ligase from Pyrococcus horikoshii. Sedimentation equilibrium measurements to determine the effect of ligand binding on oligomerization indicate that the enzyme exists as a dimer regardless of liganded state. Measurements performed using isothermal titration calorimetry and fluorescence spectroscopy indicate that, in contrast to the bifunctional E. coli enzyme, substrate binding does not occur by an obligatorily ordered mechanism. Finally, thermodynamic signatures of ligand binding to the monofunctional enzyme differ significantly from those measured for the bifunctional enzyme. These results indicate a correlation between the functional complexity of biotin protein ligases and their detailed biochemical characteristics.
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Affiliation(s)
- Kyle G Daniels
- Department of Chemistry and Biochemistry, Center for Biological Structure and Organization, University of Maryland, College Park, Maryland 20742, usa
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31
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Fujiwara K, Maita N, Hosaka H, Okamura-Ikeda K, Nakagawa A, Taniguchi H. Global conformational change associated with the two-step reaction catalyzed by Escherichia coli lipoate-protein ligase A. J Biol Chem 2010; 285:9971-9980. [PMID: 20089862 PMCID: PMC2843243 DOI: 10.1074/jbc.m109.078717] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Revised: 12/28/2009] [Indexed: 11/06/2022] Open
Abstract
Lipoate-protein ligase A (LplA) catalyzes the attachment of lipoic acid to lipoate-dependent enzymes by a two-step reaction: first the lipoate adenylation reaction and, second, the lipoate transfer reaction. We previously determined the crystal structure of Escherichia coli LplA in its unliganded form and a binary complex with lipoic acid (Fujiwara, K., Toma, S., Okamura-Ikeda, K., Motokawa, Y., Nakagawa, A., and Taniguchi, H. (2005) J Biol. Chem. 280, 33645-33651). Here, we report two new LplA structures, LplA.lipoyl-5'-AMP and LplA.octyl-5'-AMP.apoH-protein complexes, which represent the post-lipoate adenylation intermediate state and the pre-lipoate transfer intermediate state, respectively. These structures demonstrate three large scale conformational changes upon completion of the lipoate adenylation reaction: movements of the adenylate-binding and lipoate-binding loops to maintain the lipoyl-5'-AMP reaction intermediate and rotation of the C-terminal domain by about 180 degrees . These changes are prerequisites for LplA to accommodate apoprotein for the second reaction. The Lys(133) residue plays essential roles in both lipoate adenylation and lipoate transfer reactions. Based on structural and kinetic data, we propose a reaction mechanism driven by conformational changes.
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Affiliation(s)
- Kazuko Fujiwara
- Institute for Enzyme Research, University of Tokushima, Kuramotocho 3-chome, Tokushima 770-8503.
| | - Nobuo Maita
- Institute for Enzyme Research, University of Tokushima, Kuramotocho 3-chome, Tokushima 770-8503
| | - Harumi Hosaka
- Institute for Protein Research, Osaka University, Suita 565-0871, Japan
| | - Kazuko Okamura-Ikeda
- Institute for Enzyme Research, University of Tokushima, Kuramotocho 3-chome, Tokushima 770-8503
| | - Atsushi Nakagawa
- Institute for Protein Research, Osaka University, Suita 565-0871, Japan
| | - Hisaaki Taniguchi
- Institute for Enzyme Research, University of Tokushima, Kuramotocho 3-chome, Tokushima 770-8503
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32
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Gupta V, Gupta RK, Khare G, Salunke DM, Surolia A, Tyagi AK. Structural ordering of disordered ligand-binding loops of biotin protein ligase into active conformations as a consequence of dehydration. PLoS One 2010; 5:e9222. [PMID: 20169168 PMCID: PMC2821413 DOI: 10.1371/journal.pone.0009222] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2009] [Accepted: 01/23/2010] [Indexed: 11/19/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb), a dreaded pathogen, has a unique cell envelope composed of high fatty acid content that plays a crucial role in its pathogenesis. Acetyl Coenzyme A Carboxylase (ACC), an important enzyme that catalyzes the first reaction of fatty acid biosynthesis, is biotinylated by biotin acetyl-CoA carboxylase ligase (BirA). The ligand-binding loops in all known apo BirAs to date are disordered and attain an ordered structure only after undergoing a conformational change upon ligand-binding. Here, we report that dehydration of Mtb-BirA crystals traps both the apo and active conformations in its asymmetric unit, and for the first time provides structural evidence of such transformation. Recombinant Mtb-BirA was crystallized at room temperature, and diffraction data was collected at 295 K as well as at 120 K. Transfer of crystals to paraffin and paratone-N oil (cryoprotectants) prior to flash-freezing induced lattice shrinkage and enhancement in the resolution of the X-ray diffraction data. Intriguingly, the crystal lattice rearrangement due to shrinkage in the dehydrated Mtb-BirA crystals ensued structural order of otherwise flexible ligand-binding loops L4 and L8 in apo BirA. In addition, crystal dehydration resulted in a shift of approximately 3.5 A in the flexible loop L6, a proline-rich loop unique to Mtb complex as well as around the L11 region. The shift in loop L11 in the C-terminal domain on dehydration emulates the action responsible for the complex formation with its protein ligand biotin carboxyl carrier protein (BCCP) domain of ACCA3. This is contrary to the involvement of loop L14 observed in Pyrococcus horikoshii BirA-BCCP complex. Another interesting feature that emerges from this dehydrated structure is that the two subunits A and B, though related by a noncrystallographic twofold symmetry, assemble into an asymmetric dimer representing the ligand-bound and ligand-free states of the protein, respectively. In-depth analyses of the sequence and the structure also provide answers to the reported lower affinities of Mtb-BirA toward ATP and biotin substrates. This dehydrated crystal structure not only provides key leads to the understanding of the structure/function relationships in the protein in the absence of any ligand-bound structure, but also demonstrates the merit of dehydration of crystals as an inimitable technique to have a glance at proteins in action.
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Affiliation(s)
- Vibha Gupta
- Department of Biochemistry, University of Delhi, New Delhi, India
| | - Rakesh K. Gupta
- Department of Biochemistry, University of Delhi, New Delhi, India
- Department of Microbiology, University of Delhi, New Delhi, India
| | - Garima Khare
- Department of Biochemistry, University of Delhi, New Delhi, India
| | | | | | - Anil K. Tyagi
- Department of Biochemistry, University of Delhi, New Delhi, India
- * E-mail:
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33
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Tron CM, McNae IW, Nutley M, Clarke DJ, Cooper A, Walkinshaw MD, Baxter RL, Campopiano DJ. Structural and functional studies of the biotin protein ligase from Aquifex aeolicus reveal a critical role for a conserved residue in target specificity. J Mol Biol 2009; 387:129-46. [PMID: 19385043 DOI: 10.1016/j.jmb.2008.12.086] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Biotin protein ligase (BPL; EC 6.3.4.15) catalyses the formation of biotinyl-5'-AMP from biotin and ATP, and the succeeding biotinylation of the biotin carboxyl carrier protein. We describe the crystal structures, at 2.4 A resolution, of the class I BPL from the hyperthermophilic bacteria Aquifex aeolicus (AaBPL) in its ligand-free form and in complex with biotin and ATP. The solvent-exposed beta- and gamma-phosphates of ATP are located in the inter-subunit cavity formed by the N- and C-terminal domains. The Arg40 residue from the conserved GXGRXG motif is shown to interact with the carboxyl group of biotin and to stabilise the alpha- and beta-phosphates of the nucleotide. The structure of the mutant AaBPL R40G in both the ligand-free and biotin-bound forms reveals that the mutated loop has collapsed, thus hindering ATP binding. Isothermal titration calorimetry indicated that the presence of biotin is not required for ATP binding to wild-type AaBPL in the absence of Mg(2+), and the binding of biotin and ATP has been determined to occur via a random but cooperative process. The affinity for biotin is relatively unaffected by the R40G mutation. In contrast, the thermodynamic data indicate that binding of ATP to AaBPL R40G is very weak in the absence or in the presence of biotin. The AaBPL R40G mutant remains catalytically active but shows poor substrate specificity; mass spectrometry and Western blot studies revealed that the mutant biotinylates both the target A. aeolicus BCCPDelta67 fragment and BSA, and is subject to self-biotinylation.
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Affiliation(s)
- Cecile M Tron
- School of Chemistry, EaStCHEM, The University of Edinburgh, West Mains Road, King's Buildings, Edinburgh, Scotland, UK
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34
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Sugahara M, Asada Y, Shimizu K, Yamamoto H, Lokanath NK, Mizutani H, Bagautdinov B, Matsuura Y, Taketa M, Kageyama Y, Ono N, Morikawa Y, Tanaka Y, Shimada H, Nakamoto T, Sugahara M, Yamamoto M, Kunishima N. High-throughput crystallization-to-structure pipeline at RIKEN SPring-8 Center. ACTA ACUST UNITED AC 2008; 9:21-8. [PMID: 18677553 DOI: 10.1007/s10969-008-9042-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2007] [Accepted: 07/11/2008] [Indexed: 10/21/2022]
Abstract
A high-throughput crystallization-to-structure pipeline for structural genomics was recently developed at the Advanced Protein Crystallography Research Group of the RIKEN SPring-8 Center in Japan. The structure determination pipeline includes three newly developed technologies for automating X-ray protein crystallography: the automated crystallization and observation robot system "TERA", the SPring-8 Precise Automatic Cryosample Exchanger "SPACE" for automated data collection, and the Package of Expert Researcher's Operation Network "PERON" for automated crystallographic computation from phasing to model checking. During the 5 years following April, 2002, this pipeline was used by seven researchers to determine 138 independent crystal structures (resulting from 437 purified proteins, 234 cryoloop-mountable crystals, and 175 diffraction data sets). The protocols used in the high-throughput pipeline are described in this paper.
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Affiliation(s)
- Michihiro Sugahara
- Advanced Protein Crystallography Research Group, RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
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35
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Pendini NR, Bailey LM, Booker GW, Wilce MC, Wallace JC, Polyak SW. Microbial biotin protein ligases aid in understanding holocarboxylase synthetase deficiency. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:973-82. [DOI: 10.1016/j.bbapap.2008.03.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2008] [Revised: 03/16/2008] [Accepted: 03/26/2008] [Indexed: 11/16/2022]
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36
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Pendini NR, Polyak SW, Booker GW, Wallace JC, Wilce MCJ. Purification, crystallization and preliminary crystallographic analysis of biotin protein ligase from Staphylococcus aureus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:520-3. [PMID: 18540065 PMCID: PMC2496860 DOI: 10.1107/s1744309108012244] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2008] [Accepted: 04/28/2008] [Indexed: 11/10/2022]
Abstract
Biotin protein ligase from Staphylococcus aureus catalyses the biotinylation of acetyl-CoA carboxylase and pyruvate carboxylase. Recombinant biotin protein ligase from S. aureus has been cloned, expressed and purified. Crystals were grown using the hanging-drop vapour-diffusion method using PEG 8000 as the precipitant at 295 K. X-ray diffraction data were collected to 2.3 A resolution from crystals using synchrotron X-ray radiation at 100 K. The diffraction was consistent with the tetragonal space group P4(2)2(1)2, with unit-cell parameters a = b = 93.665, c = 131.95.
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Affiliation(s)
- Nicole R. Pendini
- School of Molecular and Biomedical Sciences, University of Adelaide, North Terrace, Adelaide SA 5005, Australia
- Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton VIC 3800, Australia
| | - Steve W. Polyak
- School of Molecular and Biomedical Sciences, University of Adelaide, North Terrace, Adelaide SA 5005, Australia
| | - Grant W. Booker
- School of Molecular and Biomedical Sciences, University of Adelaide, North Terrace, Adelaide SA 5005, Australia
| | - John C. Wallace
- School of Molecular and Biomedical Sciences, University of Adelaide, North Terrace, Adelaide SA 5005, Australia
| | - Matthew C. J. Wilce
- Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton VIC 3800, Australia
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37
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Purushothaman S, Gupta G, Srivastava R, Ramu VG, Surolia A. Ligand specificity of group I biotin protein ligase of Mycobacterium tuberculosis. PLoS One 2008; 3:e2320. [PMID: 18509457 PMCID: PMC2384007 DOI: 10.1371/journal.pone.0002320] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2008] [Accepted: 03/25/2008] [Indexed: 11/19/2022] Open
Abstract
Background Fatty acids are indispensable constituents of mycolic acids that impart toughness & permeability barrier to the cell envelope of M. tuberculosis. Biotin is an essential co-factor for acetyl-CoA carboxylase (ACC) the enzyme involved in the synthesis of malonyl-CoA, a committed precursor, needed for fatty acid synthesis. Biotin carboxyl carrier protein (BCCP) provides the co-factor for catalytic activity of ACC. Methodology/Principal Findings BPL/BirA (Biotin Protein Ligase), and its substrate, biotin carboxyl carrier protein (BCCP) of Mycobacterium tuberculosis (Mt) were cloned and expressed in E. coli BL21. In contrast to EcBirA and PhBPL, the ∼29.5 kDa MtBPL exists as a monomer in native, biotin and bio-5′AMP liganded forms. This was confirmed by molecular weight profiling by gel filtration on Superdex S-200 and Dynamic Light Scattering (DLS). Computational docking of biotin and bio-5′AMP to MtBPL show that adenylation alters the contact residues for biotin. MtBPL forms 11 H-bonds with biotin, relative to 35 with bio-5′AMP. Docking simulations also suggest that bio-5′AMP hydrogen bonds to the conserved ‘GRGRRG’ sequence but not biotin. The enzyme catalyzed transfer of biotin to BCCP was confirmed by incorporation of radioactive biotin and by Avidin blot. The Km for BCCP was ∼5.2 µM and ∼420 nM for biotin. MtBPL has low affinity (Kb = 1.06×10−6 M) for biotin relative to EcBirA but their Km are almost comparable suggesting that while the major function of MtBPL is biotinylation of BCCP, tight binding of biotin/bio-5′AMP by EcBirA is channeled for its repressor activity. Conclusions/Significance These studies thus open up avenues for understanding the unique features of MtBPL and the role it plays in biotin utilization in M. tuberculosis.
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Affiliation(s)
| | - Garima Gupta
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Richa Srivastava
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | | | - Avadhesha Surolia
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
- * E-mail:
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38
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Kim DJ, Lee SJ, Kim HS, Kim KH, Lee HH, Yoon HJ, Suh SW. Structural basis of octanoic acid recognition by lipoate-protein ligase B. Proteins 2008; 70:1620-5. [PMID: 18076036 DOI: 10.1002/prot.21843] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Do Jin Kim
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Korea
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39
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Bagautdinov B, Matsuura Y, Bagautdinova S, Kunishima N. Protein biotinylation visualized by a complex structure of biotin protein ligase with a substrate. J Biol Chem 2008; 283:14739-50. [PMID: 18372281 DOI: 10.1074/jbc.m709116200] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Biotin protein ligase (BPL) catalyzes the biotinylation of the biotin carboxyl carrier protein (BCCP) only at a special lysine residue. Here we report the first structure of BPL.BCCP complex crystals, which are prepared using two BPL mutants: R48A and R48A/K111A. From a detailed structural characterization, it is likely that the mutants retain functionality as enzymes but have a reduced activity to produce the reaction intermediate biotinyl-5'-AMP. The observed biotin and partly disordered ATP in the mutant structures may act as a non-reactive analog of the substrates or biotinyl-5'-AMP, thereby providing the complex crystals. The four crystallographically independent BPL.BCCP complexes obtained can be classified structurally into three groups: the formation stages 1 and 2 with apo-BCCP and the product stage with biotinylated holo-BCCP. Residues responsible for the complex formation as well as for the biotinylation reaction have been identified. The C-terminal domain of BPL shows especially large conformational changes to accommodate BCCP, suggesting its functional importance. The formation stage 1 complex shows the closest distance between the carboxyl carbon of biotin and the special lysine of BCCP, suggesting its relevance to the unobserved reaction stage. Interestingly, bound ATP and biotin are also seen in the product stage, indicating that the substrates may be recruited into the product stage complex before the release of holo-BCCP, probably for the next reaction cycle. The existence of formation and product stages before and after the reaction stage would be favorable to ensure both the reaction efficiency and the extreme substrate specificity of the biotinylation reaction.
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40
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Slavoff SA, Chen I, Ting AY. Expanding the substrate tolerance of biotin ligase through exploration of enzymes from diverse species. J Am Chem Soc 2008; 130:1160-2. [PMID: 18171066 PMCID: PMC3501195 DOI: 10.1021/ja076655i] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sarah A. Slavoff
- Contribution from the Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139,
| | - Irwin Chen
- Contribution from the Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139,
| | - Alice Y. Ting
- Contribution from the Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139,
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41
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Pindolia K, Jensen K, Wolf B. Three dimensional structure of human biotinidase: computer modeling and functional correlations. Mol Genet Metab 2007; 92:13-22. [PMID: 17629531 DOI: 10.1016/j.ymgme.2007.04.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2007] [Revised: 04/23/2007] [Accepted: 04/23/2007] [Indexed: 11/20/2022]
Abstract
Untreated individuals with deficient activity of biotinidase, the enzyme responsible for recycling the vitamin biotin, usually exhibit neurological and cutaneous findings. To better understand the variability in expression of the disorder it is important to understand the structure of the enzyme and the putative effects of various mutations on its activity. Past attempts to express and purify sufficient quantities of the enzyme by us and others have failed. Therefore, we have resorted to computer modeling using homologous related, crystallized nitrilases/amidases to predict the 3-dimensional structure of biotinidase. The resultant structure is a two domain protein with the catalytic triad consisting of glutamate, lysine and cysteine, within the larger domain. The model predicts multiple glycosylation sites at the surface of the enzyme and multiple disulfide bonds. The precise location of the biotin-binding site could not be determined. Characteristics of 45 missense mutations known to cause profound and partial biotinidase deficiency were examined, including their location, their distance from the catalytic triad, and their potential effect on the structure of the enzyme. Although there are obviously short-comings in predicting the 3-dimensional structure of a protein without crystallographic data, because of the marked homology between biotinidase and specific crystallized amidases/nitrilases, the predicted 3-dimensional structure of biotinidase is probable and should be useful providing clues to structure-function relationships and ultimately the effect of mutations on altering the enzyme's hydrolase and transferase activities.
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Affiliation(s)
- Kirit Pindolia
- Department of Medical Genetics, Henry Ford Hospital, and Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48202, USA
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42
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Naganathan S, Beckett D. Nucleation of an allosteric response via ligand-induced loop folding. J Mol Biol 2007; 373:96-111. [PMID: 17765263 PMCID: PMC2792881 DOI: 10.1016/j.jmb.2007.07.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2007] [Revised: 06/30/2007] [Accepted: 07/12/2007] [Indexed: 10/23/2022]
Abstract
The Escherichia coli biotin repressor BirA is an allosteric transcription regulatory protein to which binding of the small ligand corepressor biotinyl-5'-AMP promotes homodimerization and subsequent DNA binding. Structural data indicate that the apo or unliganded repressor is characterized by four partially disordered loops that are ordered in the ligand-bound dimer. While three of these loops participate directly in the dimerization, the fourth, consisting of residues 212-234 is distal to the interface. This loop, which is ordered around the adenine ring of the adenylate moiety in the BirA.adenylate structure, is referred to as the adenylate-binding loop (ABL). Although residues in the loop do not interact directly with the ligand, a hydrophobic cluster consisting of a tryptophan and two valine side-chains assembles over the adenine base. Results of previous measurements suggest that folding of the ABL is integral to the allosteric response. This idea and the role of the hydrophobic cluster in the process were investigated by systematic replacement of each side-chain in the cluster with alanine and analysis of the mutant proteins for small ligand binding and dimerization. Isothermal titration calorimetry measurements indicate defects in adenylate binding for all ABL variants. Additionally, sedimentation equilibrium measurements reveal that coupling between adenylate binding and dimerization is compromised in each mutant. Partial proteolysis measurements indicate that the mutants are defective in ligand-linked folding of the ABL. These results indicate that the hydrophobic cluster is critical to the ligand-induced disorder-to-order transition in the ABL and that this transition is integral to the allosteric response in the biotin repressor.
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43
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Fujiwara K, Hosaka H, Matsuda M, Okamura-Ikeda K, Motokawa Y, Suzuki M, Nakagawa A, Taniguchi H. Crystal structure of bovine lipoyltransferase in complex with lipoyl-AMP. J Mol Biol 2007; 371:222-34. [PMID: 17570395 DOI: 10.1016/j.jmb.2007.05.059] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2007] [Revised: 05/21/2007] [Accepted: 05/22/2007] [Indexed: 11/22/2022]
Abstract
Lipoic acid is an essential cofactor of the alpha-ketoacid dehydrogenase complexes and the glycine cleavage system. It is covalently attached to a specific lysine residue of the subunit of the complexes. The bovine lipoyltransferase (bLT) catalyzes the lipoic acid attachment reaction using lipoyl-AMP as a substrate, forming a lipoylated protein and AMP. To gain insights into the reaction mechanism at the atomic level, we have determined the crystal structure of bLT at 2.10 A resolution. Unexpectedly, the purified recombinant bLT contains endogenous lipoyl-AMP. The structure of bLT consists of N-terminal and C-terminal domains, and lipoyl-AMP is bound to the active site in the N-terminal domain, adopting a U-shaped conformation. The lipoyl moiety is buried in the hydrophobic pocket, forming van der Waals interactions, and the AMP moiety forms numerous hydrogen bonds with bLT in another tunnel-like cavity. These interactions work together to expose the C10 atom of lipoyl-AMP to the surface of the bLT molecule. The carbonyl oxygen atom of lipoyl-AMP interacts with the invariant Lys135. The interaction might stimulate the positive charge of the C10 atom of lipoyl-AMP, and consequently facilitate the nucleophilic attack by the lysine residue of the lipoate-acceptor protein, accompanying the bond cleavage between the carbonyl group and the phosphate group. We discuss the structural differences between bLT and the lipoate-protein ligase A from Escherichia coli and Thermoplasma acidophilum. We further demonstrate that bLT in mitochondria also contains endogenous lipoylmononucleotide, being ready for the lipoylation of apoproteins.
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Affiliation(s)
- Kazuko Fujiwara
- Institute for Enzyme Research, the University of Tokushima, Tokushima 770-8503, Japan.
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Bagautdinov B, Matsuura Y, Bagautdinova S, Kunishima N. Crystallization and preliminary X-ray crystallographic studies of the biotin carboxyl carrier protein and biotin protein ligase complex from Pyrococcus horikoshii OT3. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:334-7. [PMID: 17401210 PMCID: PMC2330208 DOI: 10.1107/s1744309107011967] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2007] [Accepted: 03/14/2007] [Indexed: 11/10/2022]
Abstract
Biotin protein ligase (BPL) catalyses the biotinylation of the biotin carboxyl carrier protein (BCCP) subunit of acetyl-CoA carboxylase. To elucidate the exact details of the protein-protein interactions in the biotinylation function, the C-terminal half fragment of BCCP (BCCPDeltaN76), the R48A mutant of BPL (BPL*) and the R48A K111A double mutant of BPL (BPL**), all of which are from Pyrococcus horikoshii OT3, have been expressed, purified and successfully cocrystallized. Cocrystals of the BPL*-BCCPDeltaN76 and BPL**-BCCPDeltaN76 complexes as well as crystals of BPL*, BPL** and BCCPDeltaN76 were obtained by the oil-microbatch method using PEG 20 000 as a precipitant at 295 K. Complete X-ray diffraction data sets for BPL*-BCCPDeltaN76 and BPL**-BCCPDeltaN76 crystals were collected at 100 K to 2.7 and 2.0 A resolution, respectively, using synchrotron radiation. They belong to the monoclinic space group P2(1), with similar unit-cell parameters a = 69.85, b = 63.12, c = 75.64 A, beta = 95.9 degrees . Assuming two subunits of the complex per asymmetric unit gives a V(M) value of 2.45 A(3) Da(-1) and a solvent content of 50%.
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Affiliation(s)
- Bagautdin Bagautdinov
- Advanced Protein Crystallography Research Group, RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yoshinori Matsuura
- Advanced Protein Crystallography Research Group, RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Svetlana Bagautdinova
- Advanced Protein Crystallography Research Group, RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Naoki Kunishima
- Advanced Protein Crystallography Research Group, RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Correspondence e-mail:
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Müller S, Kappes B. Vitamin and cofactor biosynthesis pathways in Plasmodium and other apicomplexan parasites. Trends Parasitol 2007; 23:112-21. [PMID: 17276140 PMCID: PMC2330093 DOI: 10.1016/j.pt.2007.01.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2006] [Revised: 12/13/2006] [Accepted: 01/18/2007] [Indexed: 10/23/2022]
Abstract
Vitamins are essential components of the human diet. By contrast, the malaria parasite Plasmodium falciparum and related apicomplexan parasites synthesize certain vitamins de novo, either completely or in parts. The various biosynthesis pathways are specific to different apicomplexan parasites and emphasize the distinct requirements of these parasites for nutrients and growth factors. The absence of vitamin biosynthesis in humans implies that inhibition of the parasite pathways might be a way to interfere specifically with parasite development. However, the roles of biosynthesis and uptake of vitamins in the regulation of vitamin homeostasis in parasites needs to be established first. In this article, the procurement of vitamins B(1), B(5) and B(6) by Plasmodium and other apicomplexan parasites is discussed.
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Affiliation(s)
- Sylke Müller
- University of Glasgow, Glasgow Biomedical Research Centre, Division of Infection and Immunity, Wellcome Centre for Molecular Parasitology, 120 University Place, Glasgow G12 8TA, UK.
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Ma Q, Zhao X, Eddine AN, Geerlof A, Li X, Cronan JE, Kaufmann SHE, Wilmanns M. The Mycobacterium tuberculosis LipB enzyme functions as a cysteine/lysine dyad acyltransferase. Proc Natl Acad Sci U S A 2006; 103:8662-7. [PMID: 16735476 PMCID: PMC1472244 DOI: 10.1073/pnas.0510436103] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Lipoic acid is essential for the activation of a number of protein complexes involved in key metabolic processes. Growth of Mycobacterium tuberculosis relies on a pathway in which the lipoate attachment group is synthesized from an endogenously produced octanoic acid moiety. In patients with multiple-drug-resistant M. tuberculosis, expression of one gene from this pathway, lipB, encoding for octanoyl-[acyl carrier protein]-protein acyltransferase is considerably up-regulated, thus making it a potential target in the search for novel antiinfectives against tuberculosis. Here we present the crystal structure of the M. tuberculosis LipB protein at atomic resolution, showing an unexpected thioether-linked active-site complex with decanoic acid. We provide evidence that the transferase functions as a cysteine/lysine dyad acyltransferase, in which two invariant residues (Lys-142 and Cys-176) are likely to function as acid/base catalysts. Analysis by MS reveals that the LipB catalytic reaction proceeds by means of an internal thioesteracyl intermediate. Structural comparison of LipB with lipoate protein ligase A indicates that, despite conserved structural and sequence active-site features in the two enzymes, 4'-phosphopantetheine-bound octanoic acid recognition is a specific property of LipB.
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Affiliation(s)
- Qingjun Ma
- *EMBL–Hamburg Unit, European Molecular Biology Laboratory, Notkestrasse 85, 22603 Hamburg, Germany
| | - Xin Zhao
- Departments of Microbiology and Biochemistry, University of Illinois, Urbana, IL 61801
| | - Ali Nasser Eddine
- Department of Immunology, Max Planck Institute for Infection Biology, Schumannstrasse 21/22, 10117 Berlin, Germany; and
| | - Arie Geerlof
- *EMBL–Hamburg Unit, European Molecular Biology Laboratory, Notkestrasse 85, 22603 Hamburg, Germany
| | - Xinping Li
- Proteomics Core Facility, European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
| | - John E. Cronan
- Departments of Microbiology and Biochemistry, University of Illinois, Urbana, IL 61801
| | - Stefan H. E. Kaufmann
- Department of Immunology, Max Planck Institute for Infection Biology, Schumannstrasse 21/22, 10117 Berlin, Germany; and
| | - Matthias Wilmanns
- *EMBL–Hamburg Unit, European Molecular Biology Laboratory, Notkestrasse 85, 22603 Hamburg, Germany
- To whom correspondence should be addressed. E-mail:
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Sueda S, Li YQ, Kondo H, Kawarabayasi Y. Substrate specificity of archaeon Sulfolobus tokodaii biotin protein ligase. Biochem Biophys Res Commun 2006; 344:155-9. [PMID: 16616010 DOI: 10.1016/j.bbrc.2006.03.118] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2006] [Accepted: 03/21/2006] [Indexed: 11/21/2022]
Abstract
Biotin protein ligase (BPL) is an enzyme mediating biotinylation of a specific lysine residue of the carboxyl carrier protein (BCCP) of biotin-dependent enzymes. We recently found that the substrate specificity of BPL from archaeon Sulfolobus tokodaii is totally different from those of many other organisms, in reflection of a difference in the local sequence of BCCP surrounding the canonical lysine residue. There is a conserved glycine residue in the biotin-binding site of Escherichia coli BPL, but this residue is replaced with alanine in S. tokodaii BPL. To test the notion that this substitution dictates the substrate specificity of the latter enzyme, this residue, Ala-43, was converted to glycine. The K(m) values of the resulting mutant, A43G, for substrates, were smaller than those of the wild type, suggesting that the residue in position 43 of BPL plays an important role in substrate binding.
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Affiliation(s)
- Shinji Sueda
- Department of Biochemical Engineering and Science, Kyushu Institute of Technology, Kawazu 680-4, Iizuka 820-8502, Japan.
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48
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Li YQ, Sueda S, Kondo H, Kawarabayasi Y. A unique biotin carboxyl carrier protein in archaeonSulfolobus tokodaii. FEBS Lett 2006; 580:1536-40. [PMID: 16480719 DOI: 10.1016/j.febslet.2006.01.083] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2005] [Revised: 01/26/2006] [Accepted: 01/27/2006] [Indexed: 11/19/2022]
Abstract
Biotin carboxyl carrier protein (BCCP) is one subunit or domain of biotin-dependent enzymes. BCCP becomes an active substrate for carboxylation and carboxyl transfer, after biotinylation of its canonical lysine residue by biotin protein ligase (BPL). BCCP carries a characteristic local sequence surrounding the canonical lysine residue, typically -M-K-M-. Archaeon Sulfolobus tokodaii is unique in that its BCCP has serine replaced for the methionine C-terminal to the lysine. This BCCP is biotinylated by its own BPL, but not by Escherichia coli BPL. Likewise, E. coli BCCP is not biotinylated by S. tokodaii BPL, indicating that the substrate specificity is different between the two organisms.
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Affiliation(s)
- Yan-Qiu Li
- Department of Biochemical Engineering and Science, Kyushu Institute of Technology, Kawazu 680-4, Iizuka 820-8502, Japan
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Wood ZA, Weaver LH, Brown PH, Beckett D, Matthews BW. Co-repressor induced order and biotin repressor dimerization: a case for divergent followed by convergent evolution. J Mol Biol 2006; 357:509-23. [PMID: 16438984 DOI: 10.1016/j.jmb.2005.12.066] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2005] [Revised: 12/15/2005] [Accepted: 12/18/2005] [Indexed: 11/19/2022]
Abstract
BirA catalyzes the adenylation and subsequent covalent attachment of biotin to the biotin carboxyl carrier protein (BCCP). In the absence of apo-BCCP, biotin-5'-AMP acts as a co-repressor that induces BirA dimerization and binding to the bio operator to repress biotin biosynthesis. The crystal structures of apo-BirA, and BirA in complex with biotin have been reported. We here describe the 2.8A resolution crystal structure of BirA in complex with the co-repressor analog biotinol-5'-AMP. It was previously shown that the structure of apo-BirA is monomeric and that binding of biotin weakly induces a dimeric structure in which three disordered surface loops become organized to form the dimer interface. The structure of the co-repressor complex is also a dimer, clearly related to the BirA.biotin structure, but with several significant conformational changes. A hitherto disordered "adenylate binding loop" forms a well-defined structure covering the co-repressor. The co-repressor buttresses the dimer interface, resulting in improved packing and a 12 degrees change in the hinge-bending angle along the dimer interface relative to the BirA.biotin structure. This helps explain why the binding of the co-repressor is necessary to optimize the binding of BirA to the bioO operator. The structure reveals an unexpected use of the nucleotide-binding motif GXGXXG in binding adenylate and controlling the repressor function. Finally, based on structural analysis we propose that the class of adenylating enzymes represented by BirA, lipoate protein ligase and class II tRNA synthetases diverged early and were selected based on their ability to sequester co-factors or amino acid residues, and adenylation activity arose independently through functional convergence.
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Affiliation(s)
- Zachary A Wood
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403-1229, USA
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