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He F, Bravo M, Fan L. Helicases required for nucleotide excision repair: structure, function and mechanism. Enzymes 2023; 54:273-304. [PMID: 37945175 DOI: 10.1016/bs.enz.2023.05.002] [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] [Indexed: 11/12/2023]
Abstract
Nucleotide excision repair (NER) is a major DNA repair pathway conserved from bacteria to humans. Various DNA helicases, a group of enzymes capable of separating DNA duplex into two strands through ATP binding and hydrolysis, are required by NER to unwind the DNA duplex around the lesion to create a repair bubble and for damage verification and removal. In prokaryotes, UvrB helicase is required for repair bubble formation and damage verification, while UvrD helicase is responsible for the removal of the excised damage containing single-strand (ss) DNA fragment. In addition, UvrD facilitates transcription-coupled repair (TCR) by backtracking RNA polymerase stalled at the lesion. In eukaryotes, two helicases XPB and XPD from the transcription factor TFIIH complex fulfill the helicase requirements of NER. Interestingly, homologs of all these four helicases UvrB, UvrD, XPB, and XPD have been identified in archaea. This review summarizes our current understanding about the structure, function, and mechanism of these four helicases.
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Affiliation(s)
- Feng He
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, United States
| | - Marco Bravo
- Department of Biochemistry, University of California, Riverside, CA, United States
| | - Li Fan
- Department of Biochemistry, University of California, Riverside, CA, United States.
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2
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Sanchez-Pulido L, Ponting CP. Extending the Horizon of Homology Detection with Coevolution-based Structure Prediction. J Mol Biol 2021; 433:167106. [PMID: 34139218 PMCID: PMC8527833 DOI: 10.1016/j.jmb.2021.167106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/09/2021] [Accepted: 06/09/2021] [Indexed: 12/12/2022]
Abstract
Traditional sequence analysis algorithms fail to identify distant homologies when they lie beyond a detection horizon. In this review, we discuss how co-evolution-based contact and distance prediction methods are pushing back this homology detection horizon, thereby yielding new functional insights and experimentally testable hypotheses. Based on correlated substitutions, these methods divine three-dimensional constraints among amino acids in protein sequences that were previously devoid of all annotated domains and repeats. The new algorithms discern hidden structure in an otherwise featureless sequence landscape. Their revelatory impact promises to be as profound as the use, by archaeologists, of ground-penetrating radar to discern long-hidden, subterranean structures. As examples of this, we describe how triplicated structures reflecting longin domains in MON1A-like proteins, or UVR-like repeats in DISC1, emerge from their predicted contact and distance maps. These methods also help to resolve structures that do not conform to a "beads-on-a-string" model of protein domains. In one such example, we describe CFAP298 whose ubiquitin-like domain was previously challenging to perceive owing to a large sequence insertion within it. More generally, the new algorithms permit an easier appreciation of domain families and folds whose evolution involved structural insertion or rearrangement. As we exemplify with α1-antitrypsin, coevolution-based predicted contacts may also yield insights into protein dynamics and conformational change. This new combination of structure prediction (using innovative co-evolution based methods) and homology inference (using more traditional sequence analysis approaches) shows great promise for bringing into view a sea of evolutionary relationships that had hitherto lain far beyond the horizon of homology detection.
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Affiliation(s)
- Luis Sanchez-Pulido
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK.
| | - Chris P Ponting
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK.
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3
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Kraithong T, Hartley S, Jeruzalmi D, Pakotiprapha D. A Peek Inside the Machines of Bacterial Nucleotide Excision Repair. Int J Mol Sci 2021; 22:ijms22020952. [PMID: 33477956 PMCID: PMC7835731 DOI: 10.3390/ijms22020952] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 12/13/2022] Open
Abstract
Double stranded DNA (dsDNA), the repository of genetic information in bacteria, archaea and eukaryotes, exhibits a surprising instability in the intracellular environment; this fragility is exacerbated by exogenous agents, such as ultraviolet radiation. To protect themselves against the severe consequences of DNA damage, cells have evolved at least six distinct DNA repair pathways. Here, we review recent key findings of studies aimed at understanding one of these pathways: bacterial nucleotide excision repair (NER). This pathway operates in two modes: a global genome repair (GGR) pathway and a pathway that closely interfaces with transcription by RNA polymerase called transcription-coupled repair (TCR). Below, we discuss the architecture of key proteins in bacterial NER and recent biochemical, structural and single-molecule studies that shed light on the lesion recognition steps of both the GGR and the TCR sub-pathways. Although a great deal has been learned about both of these sub-pathways, several important questions, including damage discrimination, roles of ATP and the orchestration of protein binding and conformation switching, remain to be addressed.
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Affiliation(s)
- Thanyalak Kraithong
- Doctor of Philosophy Program in Biochemistry (International Program), Faculty of Science, Mahidol University, Bangkok 10400, Thailand;
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Silas Hartley
- Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031, USA;
- Doctor of Philosophy Programs in Biochemistry, Biology and Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
| | - David Jeruzalmi
- Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031, USA;
- Doctor of Philosophy Programs in Biochemistry, Biology and Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
- Correspondence: (D.J.); (D.P.)
| | - Danaya Pakotiprapha
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Correspondence: (D.J.); (D.P.)
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4
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Thakur M, Muniyappa K. Deciphering the essentiality and function of SxSx motif in Mycobacterium tuberculosis UvrB. Biochimie 2020; 170:94-105. [PMID: 31923481 DOI: 10.1016/j.biochi.2020.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 01/06/2020] [Indexed: 10/25/2022]
Abstract
The UvrB subunit is a central component of the UvrABC incision complex and plays a pivotal role in damage recognition, strand excision and repair synthesis. A conserved structural motif (the SxSx motif) present in UvrB is analogous to a similar motif (TxGx) in the helicases of superfamily 2, whose function is not fully understood. To elucidate the significance of the SxSx (Ser143-Val144-Ser145-Cys146) motif in Mycobacterium tuberculosis UvrB (MtUvrB), different variants of MtUvrB subunit were constructed and characterized. The SxSx motif indeed was found to be essential for MtUvrB function: while Ser143 and Cys146 residues within this motif were crucial for MtUvrB function, Ser145 plays an important but less essential role. The SxSx motif-deleted mutant was drastically attenuated and three single (S143A, S145A and C146A) mutants and a double (S143A/S145A) mutant exhibited various degrees of severity in their DNA-binding, DNA helicase and ATPase activities. Taken together, these results highlight a hitherto unrecognized role for SxSx motif in the catalytic activities of UvrB.
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Affiliation(s)
- Manoj Thakur
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - K Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India.
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5
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Lahiri S, Rizzi M, Rossi F, Miggiano R. Mycobacterium tuberculosis
UvrB forms dimers in solution and interacts with UvrA in the absence of ligands. Proteins 2017; 86:98-109. [DOI: 10.1002/prot.25412] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 10/19/2017] [Accepted: 10/27/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Samarpita Lahiri
- DSF-Dipartimento di Scienze del Farmaco; University of Piemonte Orientale; Novara Italy
| | - Menico Rizzi
- DSF-Dipartimento di Scienze del Farmaco; University of Piemonte Orientale; Novara Italy
| | - Franca Rossi
- DSF-Dipartimento di Scienze del Farmaco; University of Piemonte Orientale; Novara Italy
| | - Riccardo Miggiano
- DSF-Dipartimento di Scienze del Farmaco; University of Piemonte Orientale; Novara Italy
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6
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Van Houten B, Kad N. Investigation of bacterial nucleotide excision repair using single-molecule techniques. DNA Repair (Amst) 2014; 20:41-48. [PMID: 24472181 PMCID: PMC5053424 DOI: 10.1016/j.dnarep.2013.10.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 10/31/2013] [Indexed: 12/23/2022]
Abstract
Despite three decades of biochemical and structural analysis of the prokaryotic nucleotide excision repair (NER) system, many intriguing questions remain with regard to how the UvrA, UvrB, and UvrC proteins detect, verify and remove a wide range of DNA lesions. Single-molecule techniques have begun to allow more detailed understanding of the kinetics and action mechanism of this complex process. This article reviews how atomic force microscopy and fluorescence microscopy have captured new glimpses of how these proteins work together to mediate NER.
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Affiliation(s)
- Bennett Van Houten
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Neil Kad
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
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7
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Abstract
Nucleotide excision repair (NER) has allowed bacteria to flourish in many different niches around the globe that inflict harsh environmental damage to their genetic material. NER is remarkable because of its diverse substrate repertoire, which differs greatly in chemical composition and structure. Recent advances in structural biology and single-molecule studies have given great insight into the structure and function of NER components. This ensemble of proteins orchestrates faithful removal of toxic DNA lesions through a multistep process. The damaged nucleotide is recognized by dynamic probing of the DNA structure that is then verified and marked for dual incisions followed by excision of the damage and surrounding nucleotides. The opposite DNA strand serves as a template for repair, which is completed after resynthesis and ligation.
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Affiliation(s)
- Caroline Kisker
- Rudolf-Virchow-Center for Experimental Biomedicine, University of Wuerzburg, 97080 Wuerzburg, Germany.
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8
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Sanchez-Pulido L, Ponting CP. Structure and evolutionary history of DISC1. Hum Mol Genet 2011; 20:R175-81. [DOI: 10.1093/hmg/ddr374] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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9
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Aramini JM, Sharma S, Huang YJ, Swapna GVT, Ho CK, Shetty K, Cunningham K, Ma LC, Zhao L, Owens LA, Jiang M, Xiao R, Liu J, Baran MC, Acton TB, Rost B, Montelione GT. Solution NMR structure of the SOS response protein YnzC from Bacillus subtilis. Proteins 2008; 72:526-30. [PMID: 18431750 DOI: 10.1002/prot.22064] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- James M Aramini
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA.
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10
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Pakotiprapha D, Inuzuka Y, Bowman BR, Moolenaar GF, Goosen N, Jeruzalmi D, Verdine GL. Crystal structure of Bacillus stearothermophilus UvrA provides insight into ATP-modulated dimerization, UvrB interaction, and DNA binding. Mol Cell 2007; 29:122-33. [PMID: 18158267 DOI: 10.1016/j.molcel.2007.10.026] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2007] [Revised: 09/05/2007] [Accepted: 10/10/2007] [Indexed: 10/22/2022]
Abstract
The nucleotide excision repair pathway corrects many structurally unrelated DNA lesions. Damage recognition in bacteria is performed by UvrA, a member of the ABC ATPase superfamily whose functional form is a dimer with four nucleotide-binding domains (NBDs), two per protomer. In the 3.2 A structure of UvrA from Bacillus stearothermophilus, we observe that the nucleotide-binding sites are formed in an intramolecular fashion and are not at the dimer interface as is typically found in other ABC ATPases. UvrA also harbors two unique domains; we show that one of these is required for interaction with UvrB, its partner in lesion recognition. In addition, UvrA contains three zinc modules, the number and ligand sphere of which differ from previously published models. Structural analysis, biochemical experiments, surface electrostatics, and sequence conservation form the basis for models of ATP-modulated dimerization, UvrA-UvrB interaction, and DNA binding during the search for lesions.
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Affiliation(s)
- Danaya Pakotiprapha
- Department of Molecular and Cellular Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA
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11
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DellaVecchia MJ, Merritt WK, Peng Y, Kirby TW, DeRose EF, Mueller GA, Van Houten B, London RE. NMR analysis of [methyl-13C]methionine UvrB from Bacillus caldotenax reveals UvrB-domain 4 heterodimer formation in solution. J Mol Biol 2007; 373:282-95. [PMID: 17822711 PMCID: PMC2626275 DOI: 10.1016/j.jmb.2007.07.045] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2007] [Revised: 07/18/2007] [Accepted: 07/19/2007] [Indexed: 11/19/2022]
Abstract
UvrB is a central DNA damage recognition protein involved in bacterial nucleotide excision repair. Structural information has been limited by the apparent disorder of the C-terminal domain 4 in crystal structures of intact UvrB; in solution, the isolated domain 4 is found to form a helix-loop-helix dimer. In order to gain insight into the behavior of UvrB in solution, we have performed NMR studies on [methyl-13C]methionine-labeled UvrB from Bacillus caldotenax (molecular mass=75 kDa). The 13 methyl resonances were assigned on the basis of site-directed mutagenesis and domain deletion. Solvent accessibility was assessed based on the relaxation and chemical shift responses of the probe methyl resonances to the stable nitroxide, 4-hydroxy-2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPOL). M632, located at the potential dimer interface of domain 4, provides an ideal probe for UvrB dimerization behavior. The M632 resonance of UvrB is very broad, consistent with some degree of monomer-dimer exchange and/or conformational instability of the exposed dimer interface. Upon addition of unlabeled domain 4 peptide, the M632 resonance of UvrB sharpens and shifts to a position consistent with a UvrB-domain 4 heterodimer. A dissociation constant (KD) value of 3.3 microM for the binding constant of UvrB with the domain 4 peptide was derived from surface plasmon resonance studies. Due to the flexibility of the domain 3-4 linker, inferred from limited proteolysis data and from the relaxation behavior of linker residue M607, the position of domain 4 is constrained not by the stiffness of the linking segment but by direct interactions with domains 1-3 in UvrB. In summary, UvrB homodimerization is disfavored, while domain 4 homodimerization and UvrB-domain 4 heterodimerization are allowed.
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Affiliation(s)
- Matthew J DellaVecchia
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
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12
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Wang H, DellaVecchia MJ, Skorvaga M, Croteau DL, Erie DA, Van Houten B. UvrB domain 4, an autoinhibitory gate for regulation of DNA binding and ATPase activity. J Biol Chem 2006; 281:15227-37. [PMID: 16595666 DOI: 10.1074/jbc.m601476200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
UvrB, a central DNA damage recognition protein in bacterial nucleotide excision repair, has weak affinity for DNA, and its ATPase activity is activated by UvrA and damaged DNA. Regulation of DNA binding and ATP hydrolysis by UvrB is poorly understood. Using atomic force microscopy and biochemical assays, we found that truncation of domain 4 of Bacillus caldotenax UvrB (UvrBDelta4) leads to multiple changes in protein function. Protein dimerization decreases with an approximately 8-fold increase of the equilibrium dissociation constant and an increase in DNA binding. Loss of domain 4 causes the DNA binding mode of UvrB to change from dimer to monomer, and affinity increases with the apparent dissociation constants on nondamaged and damaged single-stranded DNA decreasing 22- and 14-fold, respectively. ATPase activity by UvrBDelta4 increases 14- and 9-fold with and without single-stranded DNA, respectively, and UvrBDelta4 supports UvrA-independent damage-specific incision by Cho on a bubble DNA substrate. We propose that other than its previously discovered role in regulating protein-protein interactions, domain 4 is an autoinhibitory domain regulating the DNA binding and ATPase activities of UvrB.
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Affiliation(s)
- Hong Wang
- Laboratory of Molecular Genetics, NIEHS, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina 27709, USA
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13
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Hible G, Renault L, Schaeffer F, Christova P, Zoe Radulescu A, Evrin C, Gilles AM, Cherfils J. Calorimetric and crystallographic analysis of the oligomeric structure of Escherichia coli GMP kinase. J Mol Biol 2005; 352:1044-59. [PMID: 16140325 DOI: 10.1016/j.jmb.2005.07.042] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2005] [Revised: 07/11/2005] [Accepted: 07/14/2005] [Indexed: 10/25/2022]
Abstract
Guanosine monophosphate kinases (GMPKs), which catalyze the phosphorylation of GMP and dGMP to their diphosphate form, have been characterized as monomeric enzymes in eukaryotes and prokaryotes. Here, we report that GMPK from Escherichia coli (ecGMPK) assembles in solution and in the crystal as several different oligomers. Thermodynamic analysis of ecGMPK using differential scanning calorimetry shows that the enzyme is in equilibrium between a dimer and higher order oligomers, whose relative amounts depend on protein concentration, ionic strength, and the presence of ATP. Crystallographic structures of ecGMPK in the apo, GMP and GDP-bound forms were solved at 3.2A, 2.9A and 2.4A resolution, respectively. ecGMPK forms a hexamer with D3 symmetry in all crystal forms, in which the two nucleotide-binding domains are able to undergo closure comparable to that of monomeric GMPKs. The 2-fold and 3-fold interfaces involve a 20-residue C-terminal extension and a sequence signature, respectively, that are missing from monomeric eukaryotic GMPKs, explaining why ecGMPK forms oligomers. These signatures are found in GMPKs from proteobacteria, some of which are human pathogens. GMPKs from these bacteria are thus likely to form the same quaternary structures. The shift of the thermodynamic equilibrium towards the dimer at low ecGMPK concentration together with the observation that inter-subunit interactions partially occlude the ATP-binding site in the hexameric structure suggest that the dimer may be the active species at physiological enzyme concentration.
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Affiliation(s)
- Guillaume Hible
- Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, Gif sur Yvette 91198, France
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14
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Van Houten B, Croteau DL, DellaVecchia MJ, Wang H, Kisker C. 'Close-fitting sleeves': DNA damage recognition by the UvrABC nuclease system. Mutat Res 2005; 577:92-117. [PMID: 15927210 DOI: 10.1016/j.mrfmmm.2005.03.013] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2005] [Revised: 03/11/2005] [Accepted: 03/11/2005] [Indexed: 05/02/2023]
Abstract
DNA damage recognition represents a long-standing problem in the field of protein-DNA interactions. This article reviews our current knowledge of how damage recognition is achieved in bacterial nucleotide excision repair through the concerted action of the UvrA, UvrB, and UvrC proteins.
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Affiliation(s)
- Bennett Van Houten
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, 111 Alexander Drive, MD D3-01, Research Triangle Park, NC 27709, USA
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15
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Truglio JJ, Croteau DL, Skorvaga M, DellaVecchia MJ, Theis K, Mandavilli BS, Van Houten B, Kisker C. Interactions between UvrA and UvrB: the role of UvrB's domain 2 in nucleotide excision repair. EMBO J 2004; 23:2498-509. [PMID: 15192705 PMCID: PMC449773 DOI: 10.1038/sj.emboj.7600263] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2004] [Accepted: 05/11/2004] [Indexed: 11/09/2022] Open
Abstract
Nucleotide excision repair (NER) is a highly conserved DNA repair mechanism present in all kingdoms of life. UvrB is a central component of the bacterial NER system, participating in damage recognition, strand excision and repair synthesis. None of the three presently available crystal structures of UvrB has defined the structure of domain 2, which is critical for the interaction with UvrA. We have solved the crystal structure of the UvrB Y96A variant, which reveals a new fold for domain 2 and identifies highly conserved residues located on its surface. These residues are restricted to the face of UvrB important for DNA binding and may be critical for the interaction of UvrB with UvrA. We have mutated these residues to study their role in the incision reaction, formation of the pre-incision complex, destabilization of short duplex regions in DNA, binding to UvrA and ATP hydrolysis. Based on the structural and biochemical data, we conclude that domain 2 is required for a productive UvrA-UvrB interaction, which is a pre-requisite for all subsequent steps in nucleotide excision repair.
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Affiliation(s)
- James J Truglio
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY, USA
| | - Deborah L Croteau
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Milan Skorvaga
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
- Department of Molecular Genetics, Cancer Research Institute, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Matthew J DellaVecchia
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Karsten Theis
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY, USA
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Bhaskar S Mandavilli
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Bennett Van Houten
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA. Tel.: +1 919 541 2799; E-mail:
| | - Caroline Kisker
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY, USA
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY 11794-5115, USA. Tel.: +1 631 632 1465; Fax: +1 631 632 1555; E-mail:
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16
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Zoetewey DL, Tripet BP, Kutateladze TG, Overduin MJ, Wood JM, Hodges RS. Solution Structure of the C-terminal Antiparallel Coiled-coil Domain from Escherichia coli Osmosensor ProP. J Mol Biol 2003; 334:1063-76. [PMID: 14643666 DOI: 10.1016/j.jmb.2003.10.020] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Bacteria respond to increasing medium osmolality by accumulating organic solutes that are compatible with cellular functions. Transporter ProP of Escherichia coli, a proton symporter and a member of the major facilitator superfamily, senses osmotic shifts and responds by importing osmolytes such as glycine betaine. ProP contains a cytoplasmic, C-terminal extension that is essential for its activity. A peptide corresponding to the C-terminal extension of ProP forms a homodimeric alpha-helical coiled-coil even though some of its heptad a positions are not occupied by hydrophobic amino acid residues. Unexpectedly, amino acid replacement R488I, occurring at a heptad a position, destabilized the coiled-coil formed by the ProP peptide and attenuated the response of the intact transporter to osmotic upshifts in vivo. Thus, ProP was proposed to dimerize via an antiparallel coiled-coil. We used nuclear magnetic resonance (NMR) spectroscopy to determine the structure of the synthetic peptide corresponding to residues 468-497 of ProP. This region did form an antiparallel coil-coil in which critical residue R488 specifies the antiparallel coiled-coil orientation by forming stabilizing salt-bridges. Charged residues (both acidic and basic) are clustered on the c/g surface of the coiled-coil whereas polar residues are distributed on the b/e surface. This causes the structure to be bent, in contrast to other known antiparallel coiled-coils (those from the hepatitis delta antigen (PDB ID code 1A92) and the bovine F(1) ATPase inhibitor protein (PDB ID code 1HF9)). The coiled-coil and its possible importance for osmosensing are discussed.
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Affiliation(s)
- David L Zoetewey
- Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Denver, CO 80262, USA
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