1
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Nirwan S, Chahal V, Kakkar R. A comparative study of different docking methodologies to assess the protein-ligand interaction for the E. coli MurB enzyme. J Biomol Struct Dyn 2022; 40:11229-11238. [PMID: 34323658 DOI: 10.1080/07391102.2021.1957019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
We have investigated the active site of E. coli MurB using the Quantum Mechanics/Molecular Mechanics (QM/MM) methodology. The docking of three novel series of 4-thiazolidinone derivatives has been performed using two methods: rigid docking and flexible docking (Induced Fit Docking: IFD). The results have been compared to understand the conformational aspects of the enzyme. The docking results from rigid docking show that the ligands with highly negative ΔGbind have poor docking scores. In addition, the value of the regression coefficient (R) obtained on correlating the ΔGbind and the experimental pMIC values is insignificant. On keeping the protein flexible, there is a remarkable improvement in both the docking score and ΔGbind, along with a good value of R (0.64). Two important residues, Tyr254 and Try190 are found to be highly displaced during the flexible docking and hence their role in effective ligand binding has been confirmed. Thus, comparing the two methodologies, IFD has emerged as the more appropriate one for studying the E. coli MurB enzyme. To further substantiate the findings, MD studies over a time period of 20 ns have been performed on the IFD-LIII j and Rigid/XP-LIII j complexes and the results shows the former complex to be more stable, with lower average RMSD and higher average ΔGbind.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sonam Nirwan
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Varun Chahal
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Rita Kakkar
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi, Delhi, India
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2
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Puthran D, Poojary B, Nayak SG, Purushotham N, Rasheed MS, Hegde H. Design, synthesis, molecular docking, and biological evaluation of novel selenium containing lumefantrine analogues. J Heterocycl Chem 2020. [DOI: 10.1002/jhet.3868] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Divyaraj Puthran
- Department of Studies in ChemistryMangalore University Mangalagangotri Karnataka India
- Process Development Laboratory, Solara Active Pharma Sciences, Ltd Mangaluru Karnataka India
| | - Boja Poojary
- Department of Studies in ChemistryMangalore University Mangalagangotri Karnataka India
| | | | - Nikil Purushotham
- Department of Studies in ChemistryMangalore University Mangalagangotri Karnataka India
| | | | - Hemant Hegde
- Department of ChemistryManipal Academy of Higher Education Manipal Karnataka India
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3
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Abboud MI, Chowdhury R, Leung IKH, Lippl K, Loenarz C, Claridge TDW, Schofield CJ. Studies on the Substrate Selectivity of the Hypoxia-Inducible Factor Prolyl Hydroxylase 2 Catalytic Domain. Chembiochem 2018; 19:2262-2267. [PMID: 30144273 DOI: 10.1002/cbic.201800246] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Indexed: 12/19/2022]
Abstract
In animals, the response to chronic hypoxia is mediated by upregulation of the α,β-heterodimeric hypoxia-inducible factors (HIFs). Levels of HIFα isoforms, but not HIFβ, are regulated by their post-translational modification as catalysed by prolyl hydroxylase domain enzymes (PHDs). Different roles for the human HIF-1/2α isoforms and their two oxygen-dependent degradation domains (ODDs) are proposed. We report kinetic and NMR analyses of the ODD selectivity of the catalytic domain of wild-type PHD2 (which is conserved in nearly all animals) and clinically observed variants. Studies using Ala scanning and "hybrid" ODD peptides imply that the relatively rigid conformation of the (hydroxylated) proline plays an important role in ODD binding. They also reveal differential roles in binding for the residues on the N- and C-terminal sides of the substrate proline. The overall results indicate how the PHDs achieve selectivity for HIFα ODDs and might be of use in identifying substrate-selective PHD inhibitors.
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Affiliation(s)
- Martine I Abboud
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Rasheduzzaman Chowdhury
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK.,Present address: Department of Molecular and Cellular Physiology, University of Stanford, Stanford, CA, 94305-5345, USA
| | - Ivanhoe K H Leung
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK.,Present address: School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Kerstin Lippl
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK.,Present address: Roche Innovation Center Munich, Roche Diagnostics GmbH, Nonnenwald 2, 82377, Penzberg, Germany
| | - Christoph Loenarz
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK.,Present address: Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, 79104, Freiburg, Germany
| | - Timothy D W Claridge
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
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4
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Ahmed S, Zayed MF, El-Messery SM, Al-Agamy MH, Abdel-Rahman HM. Design, Synthesis, Antimicrobial Evaluation and Molecular Modeling Study of 1,2,4-Triazole-Based 4-Thiazolidinones. Molecules 2016; 21:molecules21050568. [PMID: 27144547 PMCID: PMC6272934 DOI: 10.3390/molecules21050568] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 04/17/2016] [Accepted: 04/22/2016] [Indexed: 11/16/2022] Open
Abstract
A series of 3-(2H-1,2,4-triazol-5-yl)-1,3-thiazolidin-4-one derivatives (7c–l) was designed and synthesized. Their structures have been elucidated based on analytical and spectral data. They were evaluated for their antibacterial and antifungal activities. Compound 7h showed the highest activity against all tested strains, except P. vulgaris, with MIC 8 μg/mL and 4 μg/mL against S. aureus and C. albicans, respectively. Furthermore, Compounds 7c, 7h, and 7j demonstrated moderate anti-mycobacterium activity. The binding mode of the synthesized thiazolidinones to bacterial MurB enzyme was also studied. Good interactions between the docked compounds to the MurB active site were observed primarily with Asn83, Arg310, Arg188 and Ser82 amino acid residues.
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Affiliation(s)
- Sahar Ahmed
- Department of Pharmacognosy and Pharmaceutical Chemistry, College of Pharmacy, Taibah University, Al-Madinah, Al-Munawarah 30001, Saudi Arabia.
- Department of Medicinal Chemistry, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt.
| | - Mohamed F Zayed
- Department of Pharmacognosy and Pharmaceutical Chemistry, College of Pharmacy, Taibah University, Al-Madinah, Al-Munawarah 30001, Saudi Arabia.
- Pharmaceutical Chemistry, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Azhar University, Cairo 11884, Egypt.
| | - Shahenda M El-Messery
- Department of Pharmacognosy and Pharmaceutical Chemistry, College of Pharmacy, Taibah University, Al-Madinah, Al-Munawarah 30001, Saudi Arabia.
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt.
| | - Mohamed H Al-Agamy
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P. O. Box 2457, Riyadh 11451, Saudi Arabia.
- Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Nasr City, Cairo 11884, Egypt.
| | - Hamdy M Abdel-Rahman
- Department of Medicinal Chemistry, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt.
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5
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Andersson M, Chen G, Otikovs M, Landreh M, Nordling K, Kronqvist N, Westermark P, Jörnvall H, Knight S, Ridderstråle Y, Holm L, Meng Q, Jaudzems K, Chesler M, Johansson J, Rising A. Carbonic anhydrase generates CO2 and H+ that drive spider silk formation via opposite effects on the terminal domains. PLoS Biol 2014; 12:e1001921. [PMID: 25093327 PMCID: PMC4122339 DOI: 10.1371/journal.pbio.1001921] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 06/26/2014] [Indexed: 11/18/2022] Open
Abstract
Spider silk fibers are produced from soluble proteins (spidroins) under ambient conditions in a complex but poorly understood process. Spidroins are highly repetitive in sequence but capped by nonrepetitive N- and C-terminal domains (NT and CT) that are suggested to regulate fiber conversion in similar manners. By using ion selective microelectrodes we found that the pH gradient in the silk gland is much broader than previously known. Surprisingly, the terminal domains respond in opposite ways when pH is decreased from 7 to 5: Urea denaturation and temperature stability assays show that NT dimers get significantly stabilized and then lock the spidroins into multimers, whereas CT on the other hand is destabilized and unfolds into ThT-positive β-sheet amyloid fibrils, which can trigger fiber formation. There is a high carbon dioxide pressure (pCO2) in distal parts of the gland, and a CO2 analogue interacts with buried regions in CT as determined by nuclear magnetic resonance (NMR) spectroscopy. Activity staining of histological sections and inhibition experiments reveal that the pH gradient is created by carbonic anhydrase. Carbonic anhydrase activity emerges in the same region of the gland as the opposite effects on NT and CT stability occur. These synchronous events suggest a novel CO2 and proton-dependent lock and trigger mechanism of spider silk formation.
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Affiliation(s)
- Marlene Andersson
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Gefei Chen
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, People's Republic of China
| | - Martins Otikovs
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Michael Landreh
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Kerstin Nordling
- Department of Neurobiology, Care Sciences and Society (NVS), Karolinska Institutet, Stockholm, Sweden
| | - Nina Kronqvist
- Department of Neurobiology, Care Sciences and Society (NVS), Karolinska Institutet, Stockholm, Sweden
| | - Per Westermark
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Hans Jörnvall
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Stefan Knight
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Yvonne Ridderstråle
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Lena Holm
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Qing Meng
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, People's Republic of China
- * E-mail: (J.J.); (Q.M.); (A.R.)
| | - Kristaps Jaudzems
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Mitchell Chesler
- Departments of Neurosurgery, Physiology and Neuroscience, New York University School of Medicine, New York, New York, United States of America
| | - Jan Johansson
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Department of Neurobiology, Care Sciences and Society (NVS), Karolinska Institutet, Stockholm, Sweden
- Institute of Mathematics and Natural Sciences, Tallinn University, Tallinn, Estonia
- * E-mail: (J.J.); (Q.M.); (A.R.)
| | - Anna Rising
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Department of Neurobiology, Care Sciences and Society (NVS), Karolinska Institutet, Stockholm, Sweden
- * E-mail: (J.J.); (Q.M.); (A.R.)
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6
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Chen MW, Lohkamp B, Schnell R, Lescar J, Schneider G. Substrate Channel Flexibility in Pseudomonas aeruginosa MurB Accommodates Two Distinct Substrates. PLoS One 2013; 8:e66936. [PMID: 23805286 PMCID: PMC3689657 DOI: 10.1371/journal.pone.0066936] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 05/10/2013] [Indexed: 12/03/2022] Open
Abstract
Biosynthesis of UDP-N-acetylmuramic acid in bacteria is a committed step towards peptidoglycan production. In an NADPH- and FAD-dependent reaction, the UDP-N-acetylglucosamine-enolpyruvate reductase (MurB) reduces UDP-N-acetylglucosamine-enolpyruvate to UDP-N-acetylmuramic acid. We determined the three-dimensional structures of the ternary complex of Pseudomonas aeruginosa MurB with FAD and NADP+ in two crystal forms to resolutions of 2.2 and 2.1 Å, respectively, to investigate the structural basis of the first half-reaction, hydride transfer from NADPH to FAD. The nicotinamide ring of NADP+ stacks against the si face of the isoalloxazine ring of FAD, suggesting an unusual mode of hydride transfer to flavin. Comparison with the structure of the Escherichia coli MurB complex with UDP-N-acetylglucosamine-enolpyruvate shows that both substrates share the binding site located between two lobes of the substrate-binding domain III, consistent with a ping pong mechanism with sequential substrate binding. The nicotinamide and the enolpyruvyl moieties are strikingly well-aligned upon superimposition, both positioned for hydride transfer to and from FAD. However, flexibility of the substrate channel allows the non-reactive parts of the two substrates to bind in different conformations. A potassium ion in the active site may assist in substrate orientation and binding. These structural models should help in structure-aided drug design against MurB, which is essential for cell wall biogenesis and hence bacterial survival.
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Affiliation(s)
- Ming Wei Chen
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Bernhard Lohkamp
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Robert Schnell
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Gunter Schneider
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
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7
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Oktaviani NA, Pool TJ, Kamikubo H, Slager J, Scheek RM, Kataoka M, Mulder FAA. Comprehensive determination of protein tyrosine pKa values for photoactive yellow protein using indirect 13C NMR spectroscopy. Biophys J 2012; 102:579-86. [PMID: 22325281 DOI: 10.1016/j.bpj.2011.12.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 11/23/2011] [Accepted: 12/05/2011] [Indexed: 10/14/2022] Open
Abstract
Upon blue-light irradiation, the bacterium Halorhodospira halophila is able to modulate the activity of its flagellar motor and thereby evade potentially harmful UV radiation. The 14 kDa soluble cytosolic photoactive yellow protein (PYP) is believed to be the primary mediator of this photophobic response, and yields a UV/Vis absorption spectrum that closely matches the bacterium's motility spectrum. In the electronic ground state, the para-coumaric acid (pCA) chromophore of PYP is negatively charged and forms two short hydrogen bonds to the side chains of Glu-46 and Tyr-42. The resulting acid triad is central to the marked pH dependence of the optical-absorption relaxation kinetics of PYP. Here, we describe an NMR approach to sequence-specifically follow all tyrosine side-chain protonation states in PYP from pH 3.41 to 11.24. The indirect observation of the nonprotonated (13)C(γ) resonances in sensitive and well-resolved two-dimensional (13)C-(1)H spectra proved to be pivotal in this effort, as observation of other ring-system resonances was hampered by spectral congestion and line-broadening due to ring flips. We observe three classes of tyrosine residues in PYP that exhibit very different pK(a) values depending on whether the phenolic side chain is solvent-exposed, buried, or hydrogen-bonded. In particular, our data show that Tyr-42 remains fully protonated in the pH range of 3.41-11.24, and that pH-induced changes observed in the photocycle kinetics of PYP cannot be caused by changes in the charge state of Tyr-42. It is therefore very unlikely that the pCA chromophore undergoes changes in its electrostatic interactions in the electronic ground state.
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Affiliation(s)
- Nur Alia Oktaviani
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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8
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Setiyaputra S, Mackay JP, Patrick WM. The structure of a truncated phosphoribosylanthranilate isomerase suggests a unified model for evolution of the (βα)8 barrel fold. J Mol Biol 2011; 408:291-303. [PMID: 21354426 DOI: 10.1016/j.jmb.2011.02.048] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Revised: 02/16/2011] [Accepted: 02/18/2011] [Indexed: 11/18/2022]
Abstract
The (βα)(8) barrel is one of the most common protein folds, and enzymes with this architecture display a remarkable range of catalytic activities. Many of these functions are associated with ancient metabolic pathways, and phylogenetic reconstructions suggest that the (βα)(8) barrel was one of the very first protein folds to emerge. Consequently, there is considerable interest in understanding the evolutionary processes that gave rise to this fold. In particular, much attention has been focused on the plausibility of (βα)(8) barrel evolution from homodimers of half barrels. However, we previously isolated a three-quarter-barrel-sized fragment of a (βα)(8) barrel, termed truncated phosphoribosylanthranilate isomerase (trPRAI), that is soluble and almost as thermostable as full-length N-(5'-phosphoribosyl)anthranilate isomerase (PRAI). Here, we report the NMR-derived structure of trPRAI. The subdomain is monomeric, is well ordered and adopts a native-like structure in solution. Side chains from strands β(1) (Glu3 and Lys5), β(2) (Tyr25) and β(6) (Lys122) of trPRAI repack to shield the hydrophobic core from the solvent. This result demonstrates that three-quarter barrels were viable intermediates in the evolution of the (βα)(8) barrel fold. We propose a unified model for (βα)(8) barrel evolution that combines our data, previously published work and plausible scenarios for the emergence of (initially error-prone) genetic systems. In this model, the earliest proto-cells contained diverse pools of part-barrel subdomains. Combinatorial assembly of these subdomains gave rise to many distinct lineages of (βα)(8) barrel proteins, that is, our model excludes the possibility that there was a single (βα)(8) barrel from which all present examples are descended.
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Affiliation(s)
- Surya Setiyaputra
- School of Molecular Bioscience, Darlington Campus, The University of Sydney, NSW 2006, Australia
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9
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Constantine KL, Mueller L, Metzler WJ, McDonnell PA, Todderud G, Goldfarb V, Fan Y, Newitt JA, Kiefer SE, Gao M, Tortolani D, Vaccaro W, Tokarski J. Multiple and Single Binding Modes of Fragment-Like Kinase Inhibitors Revealed by Molecular Modeling, Residue Type-Selective Protonation, and Nuclear Overhauser Effects. J Med Chem 2008; 51:6225-9. [DOI: 10.1021/jm800747w] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Keith L. Constantine
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543
| | - Luciano Mueller
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543
| | - William J. Metzler
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543
| | - Patricia A. McDonnell
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543
| | - Gordon Todderud
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543
| | - Valentina Goldfarb
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543
| | - Yi Fan
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543
| | - John A. Newitt
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543
| | - Susan E. Kiefer
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543
| | - Mian Gao
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543
| | - David Tortolani
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543
| | - Wayne Vaccaro
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543
| | - John Tokarski
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543
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10
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Barreteau H, Kovac A, Boniface A, Sova M, Gobec S, Blanot D. Cytoplasmic steps of peptidoglycan biosynthesis. FEMS Microbiol Rev 2008; 32:168-207. [PMID: 18266853 DOI: 10.1111/j.1574-6976.2008.00104.x] [Citation(s) in RCA: 479] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The biosynthesis of bacterial cell wall peptidoglycan is a complex process that involves enzyme reactions that take place in the cytoplasm (synthesis of the nucleotide precursors) and on the inner side (synthesis of lipid-linked intermediates) and outer side (polymerization reactions) of the cytoplasmic membrane. This review deals with the cytoplasmic steps of peptidoglycan biosynthesis, which can be divided into four sets of reactions that lead to the syntheses of (1) UDP-N-acetylglucosamine from fructose 6-phosphate, (2) UDP-N-acetylmuramic acid from UDP-N-acetylglucosamine, (3) UDP-N-acetylmuramyl-pentapeptide from UDP-N-acetylmuramic acid and (4) D-glutamic acid and dipeptide D-alanyl-D-alanine. Recent data concerning the different enzymes involved are presented. Moreover, special attention is given to (1) the chemical and enzymatic synthesis of the nucleotide precursor substrates that are not commercially available and (2) the search for specific inhibitors that could act as antibacterial compounds.
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Affiliation(s)
- Hélène Barreteau
- Laboratoire des Enveloppes Bactériennes et Antibiotiques, Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Univ Paris-Sud, Orsay, France
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11
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McDonnell PA, Constantine KL, Goldfarb V, Johnson SR, Sulsky R, Magnin DR, Robl JA, Caulfield TJ, Parker RA, Taylor DS, Adam LP, Metzler WJ, Mueller L, Farmer BT. NMR Structure of a Potent Small Molecule Inhibitor Bound to Human Keratinocyte Fatty Acid-Binding Protein. J Med Chem 2006; 49:5013-7. [PMID: 16884313 DOI: 10.1021/jm060360i] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The NMR structure is presented for compound 1 (BMS-480404) (Ki = 33 (+/-2) nM) bound to keratinocyte fatty acid-binding protein. This article describes interactions between a high affinity drug-like compound and a member of the fatty acid-binding protein family. A benzyl group ortho to the mandelic acid in 1 occupies an area of the protein that fatty acids do not normally contact. Similar to that in the kFABP-palmitic acid structure, the acid moiety in 1 is proximal to R129 and Y131. Computational modeling indicates that the acid moiety in 1 interacts indirectly via a modeled water molecule to R109.
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Affiliation(s)
- Patricia A McDonnell
- Bristol-Myers Squibb Pharmaceutical Research Institute, P.O. Box 4000, Princeton, New Jersey 08543, USA.
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12
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Nishida S, Kurokawa K, Matsuo M, Sakamoto K, Ueno K, Kita K, Sekimizu K. Identification and characterization of amino acid residues essential for the active site of UDP-N-acetylenolpyruvylglucosamine reductase (MurB) from Staphylococcus aureus. J Biol Chem 2005; 281:1714-24. [PMID: 16236703 DOI: 10.1074/jbc.m509277200] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The enzymes essential for bacterial peptidoglycan biosynthesis are attractive targets for antimicrobial drug development. One of these is MurB, which contains FAD as a cofactor and catalyzes the NADPH-dependent reduction of UDP-N-acetylenolpyruvylglucosamine (UDP-GlcNAcEP) to UDP-N-acetylmuramic acid. This study examined the roles of the conserved amino acid residues of Staphylococcus aureus MurB, which are located near the active site in x-ray crystal structures. Seven of 11 site-directed mutated murB genes lost the ability to complement a temperature-sensitive S. aureus murB mutant. Biochemical characterization of the seven mutated MurB proteins revealed that they cannot carry out the reduction of UDP-GlcNAcEP, although they can all catalyze the intramolecular reduction of FAD via NADPH. Spectrometric analyses of the oxidized form of the mutated proteins in the presence and absence of NADP+ or UDP-GlcNAcEP revealed that these essential amino acid residues play four distinct roles in substrate interactions: Arg213 is essential for maintenance of the electronic state of FAD; Arg176 is required for interaction with UDP-GlcNAcEP; His259 is required for interaction with both UDP-GlcNAcEP and NADP+; and Asn71, Tyr175, Ser226, and Glu296 are not apparently required for interaction with either ligand. The results presented here identify for the first time the amino acid residues of MurB that are required for the interaction with UDP-Glc-NAcEP and NADP+.
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Affiliation(s)
- Satoshi Nishida
- Laboratory of Developmental Biochemistry, Graduate School of Pharmaceutical Sciences, University of Tokyo, Japan
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13
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Constantine KL, Krystek SR, Healy MD, Doyle ML, Siemers NO, Thanassi J, Yan N, Xie D, Goldfarb V, Yanchunas J, Tao L, Dougherty BA, Farmer BT. Structural and functional characterization of CFE88: evidence that a conserved and essential bacterial protein is a methyltransferase. Protein Sci 2005; 14:1472-84. [PMID: 15929997 PMCID: PMC2253378 DOI: 10.1110/ps.051389605] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2005] [Revised: 03/11/2005] [Accepted: 03/12/2005] [Indexed: 10/25/2022]
Abstract
CFE88 is a conserved essential gene product from Streptococcus pneumoniae. This 227-residue protein has minimal sequence similarity to proteins of known 3D structure. Sequence alignment models and computational protein threading studies suggest that CFE88 is a methyltransferase. Characterization of the conformation and function of CFE88 has been performed by using several techniques. Backbone atom and limited side-chain atom NMR resonance assignments have been obtained. The data indicate that CFE88 has two domains: an N-terminal domain with 163 residues and a C-terminal domain with 64 residues. The C-terminal domain is primarily helical, while the N-terminal domain has a mixed helical/extended (Rossmann) fold. By aligning the experimentally observed elements of secondary structure, an initial unrefined model of CFE88 has been constructed based on the X-ray structure of ErmC' methyltransferase (Protein Data Bank entry 1QAN). NMR and biophysical studies demonstrate binding of S-adenosyl-L-homocysteine (SAH) to CFE88; these interactions have been localized by NMR to the predicted active site in the N-terminal domain. Mutants that target this predicted active site (H26W, E46R, and E46W) have been constructed and characterized. Overall, our results both indicate that CFE88 is a methyltransferase and further suggest that the methyltransferase activity is essential for bacterial survival.
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Affiliation(s)
- Keith L Constantine
- Bristol-Myers Squibb Pharmaceutical Research Institute, P.O. Box 4000, Princeton, NJ 08543.
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Thapar R, Mueller GA, Marzluff WF. The N-terminal domain of the Drosophila histone mRNA binding protein, SLBP, is intrinsically disordered with nascent helical structure. Biochemistry 2004; 43:9390-400. [PMID: 15260482 DOI: 10.1021/bi036314r] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Stem-loop binding protein (SLBP) is a 31 kDa protein that is central to the regulation of histone mRNAs and is highly conserved in metazoans. In vertebrates, the N-terminal domain of SLBP has sequence determinants necessary for histone mRNA translation, SLBP degradation, cyclin binding, and histone mRNA import. We have used high-resolution NMR spectroscopy and circular dichroism to characterize the structural and dynamic features of this domain of SLBP from Drosophila (dSLBP). We report that the N-terminal domain of dSLBP is stably unfolded but has nascent helical structure at physiological pH and native-like solution conditions. The conformational and dynamic properties of the isolated domain are mimicked in a longer 175-residue region of the N-terminus, as well as in the full-length protein. Complete resonance assignments, secondary structure propensity, and motional properties of a 91-residue N-terminal domain (G17-K108) of dSLBP are reported here. The deviation of (1)H(alpha), (13)C(alpha), and (13)C(beta) chemical shifts from random coil reveals that there are four regions between residues I28-A45, S50-L57, S66-G75, and F91-N96 that have helical propensity. These regions also have small but positive heteronuclear NOEs, interresidue d(NN) NOEs, and small but significant protection from solvent exchange. However the lack of medium- and long-range NOEs in 3D (15)N- and (13)C-edited spectra, fast amide proton exchange rates (all greater than 1 s(-1)), and long (15)N relaxation (T(1), T(2)) times suggest that the domain from dSLBP does not adopt a well-defined tertiary fold. The backbone residual dipolar couplings (RDCs) for this domain are small and lie close to 0 Hz (+/-2 Hz) for most residues with no well-defined periodicity. The implications of this unfolded state for the function of dSLBP in regulating histone metabolism are discussed.
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Affiliation(s)
- Roopa Thapar
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA.
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15
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Matsuo M, Kurokawa K, Nishida S, Li Y, Takimura H, Kaito C, Fukuhara N, Maki H, Miura K, Murakami K, Sekimizu K. Isolation and mutation site determination of the temperature-sensitive murB mutants of Staphylococcus aureus. FEMS Microbiol Lett 2003; 222:107-13. [PMID: 12757953 DOI: 10.1016/s0378-1097(03)00260-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The murB gene encodes UDP-N-acetylenolpyruvylglucosamine reductase and functions in bacterial peptidoglycan biosynthesis. A plasmid carrying the murB gene restored the temperature-sensitive growth of six Staphylococcus aureus mutants, in which peptidoglycan biosynthesis stopped at a restrictive temperature. Specific activity of UDP-N-acetylenolpyruvylglucosamine reductase in extracts from the mutants was lower than that from wild-type cells. Nucleotide sequence determination revealed that each mutant had a single amino acid substitution in the murB gene and five of six mutations were located within domain 3, where the proposed substrate binding site is located. These results suggest that the murB gene is essential for growth of S. aureus and that domain 3 is important for the MurB activity.
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Affiliation(s)
- Miki Matsuo
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 3-1, 7-Chome, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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16
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Yi Q, Rajagopal P, Klevit RE, Baker D. Structural and kinetic characterization of the simplified SH3 domain FP1. Protein Sci 2003; 12:776-83. [PMID: 12649436 PMCID: PMC2323857 DOI: 10.1110/ps.0238603] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The simplified SH3 domain sequence, FP1, obtained in phage display selection experiments has an amino acid composition that is 95% Ile, Lys, Glu, Ala, Gly. Here we use NMR to investigate the tertiary structure of FP1. We find that the overall topology of FP1 resembles that of the src SH3 domain, the hydrogen-deuterium exchange and chemical shift perturbation profiles are similar to those of naturally occurring SH3 domains, and the (15)N relaxation rates are in the range of naturally occurring small proteins. Guided by the structure, we further simplify the FP1 sequence and compare the effects on folding kinetics of point mutations in FP1 and the wild-type src SH3 domain. The results suggest that the folding transition state of FP1 is similar to but somewhat less polarized than that of the wild-type src SH3 domain.
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Affiliation(s)
- Qian Yi
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
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17
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Bronson JJ, DenBleyker KL, Falk PJ, Mate RA, Ho HT, Pucci MJ, Snyder LB. Discovery of the first antibacterial small molecule inhibitors of MurB. Bioorg Med Chem Lett 2003; 13:873-5. [PMID: 12617911 DOI: 10.1016/s0960-894x(02)01076-4] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A series of imidazolinone analogues was synthesized and shown to possess potent MurB inhibitory as well as good antibacterial activity.
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Affiliation(s)
- Joanne J Bronson
- Bristol-Myers Squibb Pharmaceutical Research Institute, 5 Research Parkway, Wallingford, CT 06492, USA
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18
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El Zoeiby A, Sanschagrin F, Levesque RC. Structure and function of the Mur enzymes: development of novel inhibitors. Mol Microbiol 2003; 47:1-12. [PMID: 12492849 DOI: 10.1046/j.1365-2958.2003.03289.x] [Citation(s) in RCA: 258] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
One of the biggest challenges for recent medical research is the continuous development of new antibiotics interacting with bacterial essential mechanisms. The machinery for peptidoglycan biosynthesis is a rich source of crucial targets for antibacterial chemotherapy. The cytoplasmic steps of the biosynthesis of peptidoglycan precursor, catalysed by a series of Mur enzymes, are excellent candidates for drug development. There has been growing interest in these bacterial enzymes over the last decade. Many studies attempted to understand the detailed mechanisms and structural features of the key enzymes MurA to MurF. Only MurA is inhibited by a known antibiotic, fosfomycin. Several attempts made to develop novel inhibitors of this pathway are discussed in this review. Three novel inhibitors of MurA were identified recently. 4-Thiazolidinone compounds were designed as MurB inhibitors. Many phosphinic acid derivatives and substrate analogues were identified as inhibitors of the MurC to MurF amino acid ligases.
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Affiliation(s)
- Ahmed El Zoeiby
- Centre de Recherche sur la Fonction, Structure et Ingénierie des Protéines, Faculté de Médecine, Pavillon Charles-Eugène Marchand, Université Laval, Ste-Foy, Québec, Canada, G1K 7P4
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19
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Löhr F, Rüterjans H. Correlation of backbone amide and side-chain (13)C resonances in perdeuterated proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2002; 156:10-18. [PMID: 12081438 DOI: 10.1006/jmre.2002.2539] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Side-chain carbon resonance assignments are difficult to obtain for larger proteins. While standard methods require protons for excitation and detection of magnetization, their presence is often unacceptable and often leads to unacceptable relaxation losses at the directly bound carbon sites. In this paper, pulse sequences are presented which provide connectivities between aliphatic side-chain (13)C and amide (1)H and (15)N chemical shifts in fully deuterated, (13)C/(15)N-enriched proteins. Magnetization either starts off from carbons or from both nitrogens and protons and is passed along the side-chain via (13)C-(13)C isotropic mixing. Direct rather than (13)CO-relayed (15)N-->(13)C(alpha) or (13)C(alpha)-->(15)N transfer steps allow the detection of intraresidual as well as sequential correlations. To avoid ambiguities between these two types in the three-dimensional version of the experiments, a fourth dimension can be introduced to achieve their separation along a (13)C(alpha) frequency axis. The novel methods are demonstrated with the uniformly (2)H/(13)C/(15)N labeled 35-kDa protein diisopropylfluorophosphatase from Loligo vulgaris.
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Affiliation(s)
- Frank Löhr
- Institut für Biophysikalische Chemie, Johann Wolfgang Goethe-Universität Frankfurt, Biozentrum N230, Marie Curie-Strasse 9, Frankfurt am Main, 60439, Germany.
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20
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21
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22
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Song J, Chen Z, Xu P, Gingras R, Ng A, Leberer E, Thomas DY, Ni F. Molecular interactions of the Gbeta binding domain of the Ste20p/PAK family of protein kinases. An isolated but fully functional Gbeta binding domain from Ste20p is only partially folded as shown by heteronuclear NMR spectroscopy. J Biol Chem 2001; 276:41205-12. [PMID: 11509560 DOI: 10.1074/jbc.m103449200] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The transmission of the mating signal of the budding yeast Saccharomyces cerevisiae requires Ste20p, a member of the serine/threonine protein kinases of the Ste20p/PAK family, to link the Gbeta subunit of the heterotrimeric G protein to the mitogen-activated protein kinase cascades. The binding site of Ste20p to the Gbeta subunit was mapped to a consensus sequence of SSLphiPLI/VXphiphibeta (X for any residue; phi for A, I, L, S or T; beta for basic residues), which was shown to be a novel Gbeta binding (GBB) motif present only in the noncatalytic C-terminal domains of the Ste20p/PAK family of protein kinases (Leeuw, T., Wu, C., Schrag, J. D., Whiteway, M., Thomas, D. Y., and Leberer, E. (1998) Nature 391, 191-195; Leberer, E., Dignard, D., Thomas, D. Y., and Leeuw, T. (2000) Biol. Chem. 381, 427-431). Here, we report the results of an NMR study on two GBB motif peptides and the entire C-terminal domain derived from Ste20p. The NMR data show that the two peptide fragments are not uniquely structured in aqueous solution, but in the presence of 40% trifluoroethanol, the longer 37-residue peptide exhibited two well defined, but flexibly linked helical structure elements. Heteronuclear NMR data indicate that the fully functional 86-residue C-terminal domain of Ste20p is again unfolded in aqueous solution but has helical secondary structure preferences similar to those of the two peptide fragments. The NMR results on the two GBB peptides and the entire GBB domain all indicate that the two important binding residues, Ser(879) and Ser(880), are located at the junction between two helical segments. These experimental observations with the prototype GBB domain of a novel family of Gbeta-controlled effectors may have important implications in understanding the molecular mechanisms of the signal transduction from the heterotrimeric G protein to the mitogen-activated protein kinase cascade.
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Affiliation(s)
- J Song
- Biomolecular NMR Laboratory and the Montréal Joint Centre for Structural Biology, Biotechnology Research Institute, National Research Council of Canada, Montréal, Québec H4P 2R2, Canada
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23
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Sylvester DR, Alvarez E, Patel A, Ratnam K, Kallender H, Wallis NG. Identification and characterization of UDP-N-acetylenolpyruvylglucosamine reductase (MurB) from the Gram-positive pathogen Streptococcus pneumoniae. Biochem J 2001; 355:431-5. [PMID: 11284731 PMCID: PMC1221755 DOI: 10.1042/0264-6021:3550431] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The UDP-N-acetylenolpyruvylglucosamine reductase (MurB) from a Gram-positive pathogen, Streptococcus pneumoniae, was identified and characterized. The enzyme from S. pneumoniae shows 31% identity with the MurB protein from Escherichia coli, and contains the catalytic residues, substrate-binding residues and FAD-binding motif identified previously in the E. coli protein. The gene was cloned into the pET28a+ expression vector, and the 34.5 kDa protein that it encodes was overexpressed in E. coli strain BL21(DE3) to 30% of total cell protein. The majority of the protein was found to be insoluble. A variety of methods were used to increase the amount of soluble protein to 10%. This was then purified to near homogeneity in a two-step process. The absorption spectrum of the purified protein indicated it to be a flavoprotein, like its E. coli homologue, with a characteristic absorption at 463 nm. The enzyme was shown to be active, reducing UDP-N-acetylglucosamine enolpyruvate with the concomitant oxidation of NADPH, and was characterized kinetically with respect to its two substrates. The enzyme showed properties similar to those of its E. coli counterpart, being activated by univalent cations and being subject to substrate inhibition. The characterization of an important cell wall biosynthesis enzyme from a Gram-positive pathogen provides a good starting point for the discovery of antibacterial agents against MurB.
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Affiliation(s)
- D R Sylvester
- Department of Anti-Infective Research, SmithKline Beecham Pharmaceuticals, 1250 South Collegeville Road, Collegeville, PA 19426, USA
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24
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Benson TE, Harris MS, Choi GH, Cialdella JI, Herberg JT, Martin JP, Baldwin ET. A structural variation for MurB: X-ray crystal structure of Staphylococcus aureus UDP-N-acetylenolpyruvylglucosamine reductase (MurB). Biochemistry 2001; 40:2340-50. [PMID: 11327854 DOI: 10.1021/bi002162d] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The X-ray crystal structure of the substrate free form of Staphylococcus aureus UDP-N-acetylenolpyruvylglucosamine reductase (MurB) has been solved to 2.3 A resolution with an R-factor of 20.3% and a free R-factor of 22.3%. While the overall fold of the S. aureus enzyme is similar to that of the homologous Escherichia coli MurB X-ray crystal structure, notable distinctions between the S. aureus and E. coli MurB protein structures occur in residues involved in substrate binding. Analysis of available MurB sequences from other bacteria suggest that the S. aureus MurB structure is representative of a distinct structural class of UDP-N-acetylenolpyruvylglucosamine reductases including Bacillus subtilis and Helicobacter pylori that are characterized by a modified mechanism for substrate binding.
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Affiliation(s)
- T E Benson
- Structural, Analytical, and Medicinal Chemistry, Biology, and Protein Science, Pharmacia Corporation, 301 Henrietta Street, Kalamazoo, Michigan 49007, USA.
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25
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Andres CJ, Bronson JJ, D'Andrea SV, Deshpande MS, Falk PJ, Grant-Young KA, Harte WE, Ho HT, Misco PF, Robertson JG, Stock D, Sun Y, Walsh AW. 4-Thiazolidinones: novel inhibitors of the bacterial enzyme MurB. Bioorg Med Chem Lett 2000; 10:715-7. [PMID: 10782671 DOI: 10.1016/s0960-894x(00)00073-1] [Citation(s) in RCA: 169] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
4-Thiazolidinones were synthesized and evaluated for their ability to inhibit the bacterial enzyme MurB. Selected 4-thiazolidinones displayed activity against the enzyme in vitro. This activity, coupled with the design principles of the thiazolidinones, supports the postulate that 4-thiazolidinones may be recognized as diphosphate mimics by a biological selector.
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Affiliation(s)
- C J Andres
- Bristol-Myers Squibb Pharmaceutical Research Institute, Wallingford, CT 06492, USA
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26
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Buchko GW, Daughdrill GW, de Lorimier R, K. SRB, Isern NG, Lingbeck JM, Taylor JS, Wold MS, Gochin M, Spicer LD, Lowry DF, Kennedy MA. Interactions of human nucleotide excision repair protein XPA with DNA and RPA70 Delta C327: chemical shift mapping and 15N NMR relaxation studies. Biochemistry 1999; 38:15116-28. [PMID: 10563794 PMCID: PMC4251892 DOI: 10.1021/bi991755p] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human XPA is an essential component in the multienzyme nucleotide excision repair (NER) pathway. The solution structure of the minimal DNA binding domain of XPA (XPA-MBD: M98-F219) was recently determined [Buchko et al. (1998) Nucleic Acids Res. 26, 2779-2788, Ikegami et al. (1998) Nat. Struct. Biol. 5, 701-706] and shown to consist of a compact zinc-binding core and a loop-rich C-terminal subdomain connected by a linker sequence. Here, the solution structure of XPA-MBD was further refined using an entirely new class of restraints based on pseudocontact shifts measured in cobalt-substituted XPA-MBD. Using this structure, the surface of XPA-MBD which interacts with DNA and a fragment of the largest subunit of replication protein A (RPA70 Delta C327: M1-Y326) was determined using chemical shift mapping. DNA binding in XPA-MBD was highly localized in the loop-rich subdomain for DNA with or without a lesion [dihydrothymidine (dhT) or 6-4-thymidine-cytidine (64TC)], or with DNA in single- or double-stranded form, indicating that the character of the lesion itself is not the driving force for XPA binding DNA. RPA70 Delta C327 was found to contact regions in both the zinc-binding and loop-rich subdomains. Some overlap of the DNA and RPA70 Delta C327 binding regions was observed in the loop-rich subdomain, indicating a possible cooperative DNA-binding mode between XPA and RPA70 Delta C327. To complement the chemical shift mapping data, the backbone dynamics of free XPA-MBD and XPA-MBD bound to DNA oligomers containing dhT or 64TC lesions were investigated using 15N NMR relaxation data. The dynamic analyses for the XPA-MBD complexes with DNA revealed localized increases and decreases in S2 and an increase in the global correlation time. Regions of XPA-MBD with the largest increases in S2 overlapped regions having the largest chemical shifts changes upon binding DNA, indicating that the loop-rich subdomain becomes more rigid upon binding DNA. Interestingly, S2 decreased for some residues in the zinc-binding core upon DNA association, indicating a possible concerted structural rearrangement on binding DNA.
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Affiliation(s)
- Garry W. Buchko
- Pacific Northwest National Laboratories, Environmental Molecular Sciences Laboratory, Richland, Washington 99352
- Departments of Biochemistry and Radiology, Duke University Medical Center, Durham, North Carolina 27710
| | - Gary W. Daughdrill
- Pacific Northwest National Laboratories, Environmental Molecular Sciences Laboratory, Richland, Washington 99352
| | - Robert de Lorimier
- Departments of Biochemistry and Radiology, Duke University Medical Center, Durham, North Carolina 27710
| | - Sudha Rao B. K.
- Pacific Northwest National Laboratories, Environmental Molecular Sciences Laboratory, Richland, Washington 99352
| | - Nancy G. Isern
- Pacific Northwest National Laboratories, Environmental Molecular Sciences Laboratory, Richland, Washington 99352
| | - Jody M. Lingbeck
- Department of Chemistry, Washington University, St. Louis, Missouri 63130
| | | | - Marc S. Wold
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, Iowa 52240
| | - Miriam Gochin
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143
| | - Leonard D. Spicer
- Departments of Biochemistry and Radiology, Duke University Medical Center, Durham, North Carolina 27710
| | - David F. Lowry
- Pacific Northwest National Laboratories, Environmental Molecular Sciences Laboratory, Richland, Washington 99352
| | - Michael A. Kennedy
- Pacific Northwest National Laboratories, Environmental Molecular Sciences Laboratory, Richland, Washington 99352
- To whom correspondence should be addressed. Phone: (509) 372-2168. Fax: (509) 376-2303.
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27
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Ha S, Chang E, Lo MC, Men H, Park P, Ge M, Walker S. The Kinetic Characterization of Escherichia coli MurG Using Synthetic Substrate Analogues. J Am Chem Soc 1999. [DOI: 10.1021/ja991556t] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sha Ha
- Contribution from the Department of Chemistry, Princeton University, Princeton, New Jersey 08544
| | - Emmanuel Chang
- Contribution from the Department of Chemistry, Princeton University, Princeton, New Jersey 08544
| | - Mei-Chu Lo
- Contribution from the Department of Chemistry, Princeton University, Princeton, New Jersey 08544
| | - Hongbin Men
- Contribution from the Department of Chemistry, Princeton University, Princeton, New Jersey 08544
| | - Peter Park
- Contribution from the Department of Chemistry, Princeton University, Princeton, New Jersey 08544
| | - Min Ge
- Contribution from the Department of Chemistry, Princeton University, Princeton, New Jersey 08544
| | - Suzanne Walker
- Contribution from the Department of Chemistry, Princeton University, Princeton, New Jersey 08544
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28
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Shekhtman A, McNaughton L, Cunningham RP, Baxter SM. Identification of the Archaeoglobus fulgidus endonuclease III DNA interaction surface using heteronuclear NMR methods. Structure 1999; 7:919-30. [PMID: 10467137 DOI: 10.1016/s0969-2126(99)80119-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Endonuclease III is the prototype for a family of DNA-repair enzymes that recognize and remove damaged and mismatched bases from DNA via cleavage of the N-glycosidic bond. Crystal structures for endonuclease III, which removes damaged pyrimidines, and MutY, which removes mismatched adenines, show a highly conserved structure. Although there are several models for DNA binding by this family of enzymes, no experimental structures with bound DNA exist for any member of the family. RESULTS Nuclear magnetic resonance (NMR) spectroscopy chemical-shift perturbation of backbone nuclei (1H, 15N, 13CO) has been used to map the DNA-binding site on Archaeoglobus fulgidus endonuclease III. The experimentally determined interaction surface includes five structural elements: the helix-hairpin-helix (HhH) motif, the iron-sulfur cluster loop (FCL) motif, the pseudo helix-hairpin-helix motif, the helix B-helix C loop, and helix H. The elements form a continuous surface that spans the active site of the enzyme. CONCLUSIONS The enzyme-DNA interaction surface for endonuclease III contains five elements of the protein structure and suggests that DNA damage recognition may require several specific interactions between the enzyme and the DNA substrate. Because the target DNA used in this study contained a generic apurinic/apyrimidinic (AP) site, the binding interactions we observed for A. fulgidus endonuclease III should apply to all members of the endonuclease III family and several interactions could apply to the endonuclease III/AlkA (3-methyladenine DNA glycosylase) superfamily.
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Affiliation(s)
- A Shekhtman
- Department of Physics, University at Albany, SUNY, NY 12222, USA
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29
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Dobbek H, Gremer L, Meyer O, Huber R. Crystal structure and mechanism of CO dehydrogenase, a molybdo iron-sulfur flavoprotein containing S-selanylcysteine. Proc Natl Acad Sci U S A 1999; 96:8884-9. [PMID: 10430865 PMCID: PMC17702 DOI: 10.1073/pnas.96.16.8884] [Citation(s) in RCA: 169] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
CO dehydrogenase from the aerobic bacterium Oligotropha carboxidovorans catalyzes the oxidation of CO with H(2)O, yielding CO(2), two electrons, and two H(+). Its crystal structure in the air-oxidized form has been determined to 2.2 A. The active site of the enzyme, which contains molybdenum with three oxygen ligands, molybdopterin-cytosine dinucleotide and S-selanylcysteine, delivers the electrons to an intramolecular electron transport chain composed of two types of [2Fe-2S] clusters and flavin-adenine dinucleotide. CO dehydrogenase is composed of an 88.7-kDa molybdoprotein (L), a 30. 2-kDa flavoprotein (M), and a 17.8-kDa iron-sulfur protein (S). It is organized as a dimer of LMS heterotrimers and resembles xanthine dehydrogenase/oxidase in many, but not all, aspects. A mechanism based on a structure with the bound suicide-substrate cyanide is suggested and displays the necessity of S-selanylcysteine for the catalyzed reaction.
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Affiliation(s)
- H Dobbek
- Max-Planck-Institut für Biochemie, Abteilung Strukturforschung, D-82152 Martinsried, Germany.
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30
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Bott R, Boelens R. The role of high-resolution structural studies in the development of commercial enzymes. Curr Opin Biotechnol 1999; 10:391-7. [PMID: 10449323 DOI: 10.1016/s0958-1669(99)80071-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Recent developments in both NMR and X-ray crystallography allow the analysis of commercial enzymes in unprecedented detail. The novel methods provide detailed insights into protein dynamics, establish the existence of special catalytic hydrogen bonds and define the ionization states at the enzyme active site. A more detailed understanding of how the changes in structure are related to altered function should facilitate the design of future commercial enzymes with improved performance for different environmental conditions.
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Affiliation(s)
- R Bott
- Genencor International Inc., 925 Page Mill Road, Palo Alto, CA 94304-1013, USA.
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McCallum SA, Hitchens TK, Rule GS. Solution structure of the carboxyl terminus of a human class Mu glutathione S-transferase: NMR assignment strategies in large proteins. J Mol Biol 1999; 285:2119-32. [PMID: 9925789 DOI: 10.1006/jmbi.1998.2428] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Strategies to obtain the NMR assignments for the HN, N, CO, Calpha and Cbeta resonance frequencies for the human class mu glutathione-S-transferase GSTM2-2 are reported. These assignments were obtained with deuterated protein using a combination of scalar and dipolar connectivities and various specific labeling schemes. The large size of this protein (55 kDa, homodimer) necessitated the development of a novel pulse sequence and specific labeling strategies. These aided in the identification of residue type and were essential components in determining sequence specific assignments. These assignments were utilized in this study to characterize the structure and dynamics of the carboxy-terminal residues in the unliganded protein. Previous crystallographic studies of this enzyme in complex with glutathione suggested that this region may be disordered, and that this disorder may be essential for catalysis. Furthermore, in the related class alpha protein extensive changes in conformation of the C terminus are observed upon ligand binding. On the basis of the results presented here, the time-averaged conformation of the carboxyl terminus of unliganded GSTM2-2 is similar to that seen in the crystal structure. NOE patterns and 1H-15N heteronuclear nuclear Overhauser enhancements suggest that this region of the enzyme does not undergo motion on a rapid time scale.
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Affiliation(s)
- S A McCallum
- Department of Biochemistry, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
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Gardner KH, Zhang X, Gehring K, Kay LE. Solution NMR Studies of a 42 KDa Escherichia Coli Maltose Binding Protein/β-Cyclodextrin Complex: Chemical Shift Assignments and Analysis. J Am Chem Soc 1998. [DOI: 10.1021/ja982019w] [Citation(s) in RCA: 116] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kevin H. Gardner
- Contribution from the: Protein Engineering Network Centres of Excellence and Departments of Medical Genetics and Microbiology, Biochemistry, and Chemistry, University of Toronto, Toronto ON M5S 1A8 Canada, and Department of Biochemistry and Montreal Joint Centre for Structural Biology, McGill University, Montreal QC H3G 1Y6 Canada
| | - Xiaochen Zhang
- Contribution from the: Protein Engineering Network Centres of Excellence and Departments of Medical Genetics and Microbiology, Biochemistry, and Chemistry, University of Toronto, Toronto ON M5S 1A8 Canada, and Department of Biochemistry and Montreal Joint Centre for Structural Biology, McGill University, Montreal QC H3G 1Y6 Canada
| | - Kalle Gehring
- Contribution from the: Protein Engineering Network Centres of Excellence and Departments of Medical Genetics and Microbiology, Biochemistry, and Chemistry, University of Toronto, Toronto ON M5S 1A8 Canada, and Department of Biochemistry and Montreal Joint Centre for Structural Biology, McGill University, Montreal QC H3G 1Y6 Canada
| | - Lewis E. Kay
- Contribution from the: Protein Engineering Network Centres of Excellence and Departments of Medical Genetics and Microbiology, Biochemistry, and Chemistry, University of Toronto, Toronto ON M5S 1A8 Canada, and Department of Biochemistry and Montreal Joint Centre for Structural Biology, McGill University, Montreal QC H3G 1Y6 Canada
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Gardner KH, Kay LE. The use of 2H, 13C, 15N multidimensional NMR to study the structure and dynamics of proteins. ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 1998; 27:357-406. [PMID: 9646872 DOI: 10.1146/annurev.biophys.27.1.357] [Citation(s) in RCA: 510] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
During the past thirty years, deuterium labeling has been used to improve the resolution and sensitivity of protein NMR spectra used in a wide variety of applications. Most recently, the combination of triple resonance experiments and 2H, 13C, 15N labeled samples has been critical to the solution structure determination of several proteins with molecular weights on the order of 30 kDa. Here we review the developments in isotopic labeling strategies, NMR pulse sequences, and structure-determination protocols that have facilitated this advance and hold promise for future NMR-based structural studies of even larger systems. As well, we detail recent progress in the use of solution 2H NMR methods to probe the dynamics of protein sidechains.
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Affiliation(s)
- K H Gardner
- Protein Engineering Network Centres of Excellence, University of Toronto, Ontario, Canada.
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Constantine KL, Friedrichs MS, Wittekind M, Jamil H, Chu CH, Parker RA, Goldfarb V, Mueller L, Farmer BT. Backbone and side chain dynamics of uncomplexed human adipocyte and muscle fatty acid-binding proteins. Biochemistry 1998; 37:7965-80. [PMID: 9609689 DOI: 10.1021/bi980203o] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Adipocyte lipid-binding protein (A-LBP) and muscle fatty acid-binding protein (M-FABP) are members of a family of small ( approximately 15 kDa) cytosolic proteins that are involved in the metabolism of fatty acids and other lipid-soluble molecules. Although highly homologous (65%) and structurally very similar, A-LBP and M-FABP display distinct ligand binding characteristics. Since ligand binding may be influenced by intrinsic protein dynamical properties, we have characterized the backbone and side chain dynamics of uncomplexed (apo) human A-LBP and M-FABP. Backbone dynamics were characterized by measurements of 15N T1 and T2 values and ¿1H¿-15N NOEs. These data were analyzed using model-free spectral density functions and reduced spectral density mapping. The dynamics of methyl-containing side chains were charaterized by measurements of 2H T1 and T1rho relaxation times of 13C1H22H groups. The 2H relaxation data were analyzed using the model-free approach. For A-LBP, 15N relaxation data were obtained for 111 residues and 2H relaxation data were obtained for 42 methyl groups. For M-FABP, 15N relaxation data were obtained for 111 residues and 2H relaxation data were obtained for 53 methyl groups. The intrinsic flexibilities of these two proteins are compared, with particular emphasis placed on binding pocket residues. There are a number of distinct dynamical differences among corresponding residues between the two proteins. In particular, many residues display greater backbone picosecond to nanosecond and/or microsecond to millisecond time scale mobility in A-LBP relative to M-FABP, including F57, K58, and most residues in alpha-helix 2 (residues 28-35). Variations in the dynamics of this region may play a role in ligand selectivity. The side chains lining the fatty acid binding pocket display a wide range of motional restriction in both proteins. Side chains showing distinct dynamical differences between the two proteins include those of residues 20, 29, and 51. This information provides a necessary benchmark for determining dynamical changes induced by ligand binding and may ultimately lead to an enhanced understanding of ligand affinity and selectivity among fatty acid-binding proteins.
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Affiliation(s)
- K L Constantine
- Department of Macromolecular NMR, Bristol-Myers Squibb Pharmaceutical Research Institute, Princeton, New Jersey 08543-4000, USA
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Abstract
Improvements in NMR instrumentation, higher magnetic field strengths, novel NMR experiments and new deuterium-labeling strategies have significantly increased the scope of structural problems that can now be addressed by solution NMR methods. To date, a number of structures of proteins of 30 kDa have been solved using multidimensional 15N,13C,2H NMR techniques, and this molecular weight limit will probably be surpassed in the near future.
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Affiliation(s)
- L E Kay
- Department of Medical Genetics, University of Toronto, Ontario, Canada.
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