1
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Chembazhi UV, Patil VV, Sah S, Reeve W, Tiwari RP, Woo E, Varshney U. Uracil DNA glycosylase (UDG) activities in Bradyrhizobium diazoefficiens: characterization of a new class of UDG with broad substrate specificity. Nucleic Acids Res 2017; 45:5863-5876. [PMID: 28369586 PMCID: PMC5449639 DOI: 10.1093/nar/gkx209] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 03/27/2017] [Indexed: 01/01/2023] Open
Abstract
Repair of uracils in DNA is initiated by uracil DNA glycosylases (UDGs). Family 1 UDGs (Ung) are the most efficient and ubiquitous proteins having an exquisite specificity for uracils in DNA. Ung are characterized by motifs A (GQDPY) and B (HPSPLS) sequences. We report a novel dimeric UDG, Blr0248 (BdiUng) from Bradyrhizobium diazoefficiens. Although BdiUng contains the motif A (GQDPA), it has low sequence identity to known UDGs. BdiUng prefers single stranded DNA and excises uracil, 5-hydroxymethyl-uracil or xanthine from it. BdiUng is impervious to inhibition by AP DNA, and Ugi protein that specifically inhibits family 1 UDGs. Crystal structure of BdiUng shows similarity with the family 4 UDGs in its overall fold but with family 1 UDGs in key active site residues. However, instead of a classical motif B, BdiUng has a uniquely extended protrusion explaining the lack of Ugi inhibition. Structural and mutational analyses of BdiUng have revealed the basis for the accommodation of diverse substrates into its substrate binding pocket. Phylogenetically, BdiUng belongs to a new UDG family. Bradyrhizobium diazoefficiens presents a unique scenario where the presence of at least four families of UDGs may compensate for the absence of an efficient family 1 homologue.
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Affiliation(s)
- Ullas Valiya Chembazhi
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Vinod Vikas Patil
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-Ro, Yuseon-Gu, Daejeon 34141, Republic of Korea.,Department of Bio-Analytical Science, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Shivjee Sah
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Wayne Reeve
- Centre for Rhizobium Studies, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150, Australia
| | - Ravi P Tiwari
- Centre for Rhizobium Studies, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150, Australia
| | - Euijeon Woo
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-Ro, Yuseon-Gu, Daejeon 34141, Republic of Korea.,Department of Bio-Analytical Science, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.,Centre for Rhizobium Studies, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150, Australia.,Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
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2
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Wang J, Pan M, Wei J, Liu X, Wang F. A C-HCR assembly of branched DNA nanostructures for amplified uracil-DNA glycosylase assays. Chem Commun (Camb) 2017; 53:12878-12881. [DOI: 10.1039/c7cc07057h] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The amplified and selective detection of uracil-DNA glycosylase was enabled by a two-layered cascaded hybridization chain reaction machinery.
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Affiliation(s)
- Jing Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan
- P. R. China
| | - Min Pan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan
- P. R. China
| | - Jie Wei
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan
- P. R. China
| | - Xiaoqing Liu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan
- P. R. China
| | - Fuan Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan
- P. R. China
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3
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Pedersen HL, Johnson KA, McVey CE, Leiros I, Moe E. Structure determination of uracil-DNA N-glycosylase from Deinococcus radiodurans in complex with DNA. ACTA ACUST UNITED AC 2015; 71:2137-49. [PMID: 26457437 DOI: 10.1107/s1399004715014157] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 07/27/2015] [Indexed: 11/10/2022]
Abstract
Uracil-DNA N-glycosylase (UNG) is a DNA-repair enzyme in the base-excision repair (BER) pathway which removes uracil from DNA. Here, the crystal structure of UNG from the extremophilic bacterium Deinococcus radiodurans (DrUNG) in complex with DNA is reported at a resolution of 1.35 Å. Prior to the crystallization experiments, the affinity between DrUNG and different DNA oligonucleotides was tested by electrophoretic mobility shift assays (EMSAs). As a result of this analysis, two 16 nt double-stranded DNAs were chosen for the co-crystallization experiments, one of which (16 nt AU) resulted in well diffracting crystals. The DNA in the co-crystal structure contained an abasic site (substrate product) flipped into the active site of the enzyme, with no uracil in the active-site pocket. Despite the high resolution, it was not possible to fit all of the terminal nucleotides of the DNA complex into electron density owing to disorder caused by a lack of stabilizing interactions. However, the DNA which was in contact with the enzyme, close to the active site, was well ordered and allowed detailed analysis of the enzyme-DNA interaction. The complex revealed that the interaction between DrUNG and DNA is similar to that in the previously determined crystal structure of human UNG (hUNG) in complex with DNA [Slupphaug et al. (1996). Nature (London), 384, 87-92]. Substitutions in a (here defined) variable part of the leucine loop result in a shorter loop (eight residues instead of nine) in DrUNG compared with hUNG; regardless of this, it seems to fulfil its role and generate a stabilizing force with the minor groove upon flipping out of the damaged base into the active site. The structure also provides a rationale for the previously observed high catalytic efficiency of DrUNG caused by high substrate affinity by demonstrating an increased number of long-range electrostatic interactions between the enzyme and the DNA. Interestingly, specific interactions between residues in the N-terminus of a symmetry-related molecule and the complementary DNA strand facing away from the active site were also observed which seem to stabilize the enzyme-DNA complex. However, the significance of this observation remains to be investigated. The results provide new insights into the current knowledge about DNA damage recognition and repair by uracil-DNA glycosylases.
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Affiliation(s)
- Hege Lynum Pedersen
- The Norwegian Structural Biology Center (NorStruct), Department of Chemistry, UiT - The Arctic University of Norway, 9037 Tromsø, Norway
| | - Kenneth A Johnson
- The Norwegian Structural Biology Center (NorStruct), Department of Chemistry, UiT - The Arctic University of Norway, 9037 Tromsø, Norway
| | - Colin E McVey
- Instituto de Tecnologia Química e Biológica (ITQB), Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | - Ingar Leiros
- The Norwegian Structural Biology Center (NorStruct), Department of Chemistry, UiT - The Arctic University of Norway, 9037 Tromsø, Norway
| | - Elin Moe
- The Norwegian Structural Biology Center (NorStruct), Department of Chemistry, UiT - The Arctic University of Norway, 9037 Tromsø, Norway
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4
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Sudha G, Singh P, Swapna LS, Srinivasan N. Weak conservation of structural features in the interfaces of homologous transient protein-protein complexes. Protein Sci 2015; 24:1856-73. [PMID: 26311309 DOI: 10.1002/pro.2792] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 08/13/2015] [Accepted: 08/17/2015] [Indexed: 12/21/2022]
Abstract
Residue types at the interface of protein-protein complexes (PPCs) are known to be reasonably well conserved. However, we show, using a dataset of known 3-D structures of homologous transient PPCs, that the 3-D location of interfacial residues and their interaction patterns are only moderately and poorly conserved, respectively. Another surprising observation is that a residue at the interface that is conserved is not necessarily in the interface in the homolog. Such differences in homologous complexes are manifested by substitution of the residues that are spatially proximal to the conserved residue and structural differences at the interfaces as well as differences in spatial orientations of the interacting proteins. Conservation of interface location and the interaction pattern at the core of the interfaces is higher than at the periphery of the interface patch. Extents of variability of various structural features reported here for homologous transient PPCs are higher than the variation in homologous permanent homomers. Our findings suggest that straightforward extrapolation of interfacial nature and inter-residue interaction patterns from template to target could lead to serious errors in the modeled complex structure. Understanding the evolution of interfaces provides insights to improve comparative modeling of PPC structures.
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Affiliation(s)
- Govindarajan Sudha
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Prashant Singh
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Lakshmipuram S Swapna
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, Karnataka, India
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5
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Sang PB, Srinath T, Patil AG, Woo EJ, Varshney U. A unique uracil-DNA binding protein of the uracil DNA glycosylase superfamily. Nucleic Acids Res 2015; 43:8452-63. [PMID: 26304551 PMCID: PMC4787834 DOI: 10.1093/nar/gkv854] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 08/11/2015] [Indexed: 11/19/2022] Open
Abstract
Uracil DNA glycosylases (UDGs) are an important group of DNA repair enzymes, which pioneer the base excision repair pathway by recognizing and excising uracil from DNA. Based on two short conserved sequences (motifs A and B), UDGs have been classified into six families. Here we report a novel UDG, UdgX, from Mycobacterium smegmatis and other organisms. UdgX specifically recognizes uracil in DNA, forms a tight complex stable to sodium dodecyl sulphate, 2-mercaptoethanol, urea and heat treatment, and shows no detectable uracil excision. UdgX shares highest homology to family 4 UDGs possessing Fe-S cluster. UdgX possesses a conserved sequence, KRRIH, which forms a flexible loop playing an important role in its activity. Mutations of H in the KRRIH sequence to S, G, A or Q lead to gain of uracil excision activity in MsmUdgX, establishing it as a novel member of the UDG superfamily. Our observations suggest that UdgX marks the uracil-DNA for its repair by a RecA dependent process. Finally, we observed that the tight binding activity of UdgX is useful in detecting uracils in the genomes.
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Affiliation(s)
- Pau Biak Sang
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Thiruneelakantan Srinath
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Aravind Goud Patil
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Eui-Jeon Woo
- Functional Genomic Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahakro, Yuseongu, Daejeon, South Korea
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, 560064, India
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6
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Arif SM, Geethanandan K, Mishra P, Surolia A, Varshney U, Vijayan M. Structural plasticity inMycobacterium tuberculosisuracil-DNA glycosylase (MtUng) and its functional implications. ACTA ACUST UNITED AC 2015; 71:1514-27. [DOI: 10.1107/s1399004715009311] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 05/15/2015] [Indexed: 12/29/2022]
Abstract
17 independent crystal structures of family I uracil-DNA glycosylase fromMycobacterium tuberculosis(MtUng) and its complexes with uracil and its derivatives, distributed among five distinct crystal forms, have been determined. Thermodynamic parameters of binding in the complexes have been measured using isothermal titration calorimetry. The two-domain protein exhibits open and closed conformations, suggesting that the closure of the domain on DNA binding involves conformational selection. Segmental mobility in the enzyme molecule is confined to a 32-residue stretch which plays a major role in DNA binding. Uracil and its derivatives can bind to the protein in two possible orientations. Only one of them is possible when there is a bulky substituent at the 5′ position. The crystal structures of the complexes provide a reasonable rationale for the observed thermodynamic parameters. In addition to providing fresh insights into the structure, plasticity and interactions of the protein molecule, the results of the present investigation provide a platform for structure-based inhibitor design.
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7
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Assefa NG, Niiranen L, Johnson KA, Leiros HKS, Smalås AO, Willassen NP, Moe E. Structural and biophysical analysis of interactions between cod and human uracil-DNA N-glycosylase (UNG) and UNG inhibitor (Ugi). ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2093-100. [PMID: 25084329 PMCID: PMC4118823 DOI: 10.1107/s1399004714011699] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 05/20/2014] [Indexed: 12/01/2022]
Abstract
Uracil-DNA N-glycosylase from Atlantic cod (cUNG) shows cold-adapted features such as high catalytic efficiency, a low temperature optimum for activity and reduced thermal stability compared with its mesophilic homologue human UNG (hUNG). In order to understand the role of the enzyme-substrate interaction related to the cold-adapted properties, the structure of cUNG in complex with a bacteriophage encoded natural UNG inhibitor (Ugi) has been determined. The interaction has also been analyzed by isothermal titration calorimetry (ITC). The crystal structure of cUNG-Ugi was determined to a resolution of 1.9 Å with eight complexes in the asymmetric unit related through noncrystallographic symmetry. A comparison of the cUNG-Ugi complex with previously determined structures of UNG-Ugi shows that they are very similar, and confirmed the nucleotide-mimicking properties of Ugi. Biophysically, the interaction between cUNG and Ugi is very strong and shows a binding constant (Kb) which is one order of magnitude larger than that for hUNG-Ugi. The binding of both cUNG and hUNG to Ugi was shown to be favoured by both enthalpic and entropic forces; however, the binding of cUNG to Ugi is mainly dominated by enthalpy, while the entropic term is dominant for hUNG. The observed differences in the binding properties may be explained by an overall greater positive electrostatic surface potential in the protein-Ugi interface of cUNG and the slightly more hydrophobic surface of hUNG.
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Affiliation(s)
- Netsanet Gizaw Assefa
- Department of Chemistry/Norstruct, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Laila Niiranen
- Department of Chemistry/Norstruct, UiT The Arctic University of Norway, 9037 Tromsø, Norway
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland
| | - Kenneth A. Johnson
- Department of Chemistry/Norstruct, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | | | - Arne Oskar Smalås
- Department of Chemistry/Norstruct, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Nils Peder Willassen
- Department of Chemistry/Norstruct, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Elin Moe
- Department of Chemistry/Norstruct, UiT The Arctic University of Norway, 9037 Tromsø, Norway
- Instituto de Tecnologia Quimica e Biologica (ITQB), Universidade Nova de Lisboa, Avenida da Republica (EAN), 2780-157 Oeiras, Portugal
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8
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Baños-Sanz JI, Mojardín L, Sanz-Aparicio J, Lázaro JM, Villar L, Serrano-Heras G, González B, Salas M. Crystal structure and functional insights into uracil-DNA glycosylase inhibition by phage Φ29 DNA mimic protein p56. Nucleic Acids Res 2013; 41:6761-73. [PMID: 23671337 PMCID: PMC3711442 DOI: 10.1093/nar/gkt395] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Uracil-DNA glycosylase (UDG) is a key repair enzyme responsible for removing uracil residues from DNA. Interestingly, UDG is the only enzyme known to be inhibited by two different DNA mimic proteins: p56 encoded by the Bacillus subtilis phage ϕ29 and the well-characterized protein Ugi encoded by the B. subtilis phage PBS1/PBS2. Atomic-resolution crystal structures of the B. subtilis UDG both free and in complex with p56, combined with site-directed mutagenesis analysis, allowed us to identify the key amino acid residues required for enzyme activity, DNA binding and complex formation. An important requirement for complex formation is the recognition carried out by p56 of the protruding Phe191 residue from B. subtilis UDG, whose side-chain is inserted into the DNA minor groove to replace the flipped-out uracil. A comparative analysis of both p56 and Ugi inhibitors enabled us to identify their common and distinctive features. Thereby, our results provide an insight into how two DNA mimic proteins with different structural and biochemical properties are able to specifically block the DNA-binding domain of the same enzyme.
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Affiliation(s)
- José Ignacio Baños-Sanz
- Departamento de Cristalografía y Biología Estructural, Instituto de Química-Física 'Rocasolano' (CSIC), Serrano 119, 28006 Madrid, Spain
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9
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Kawai A, Higuchi S, Tsunoda M, Nakamura KT, Miyamoto S. Purification, crystallization and preliminary X-ray analysis of uracil-DNA glycosylase from Sulfolobus tokodaii strain 7. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1102-5. [PMID: 22949205 PMCID: PMC3433208 DOI: 10.1107/s1744309112030278] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 07/03/2012] [Indexed: 11/10/2022]
Abstract
Uracil-DNA glycosylase (UDG) specifically removes uracil from DNA by catalyzing hydrolysis of the N-glycosidic bond, thereby initiating the base-excision repair pathway. Although a number of UDG structures have been determined, the structure of archaeal UDG remains unknown. In this study, a deletion mutant of UDG isolated from Sulfolobus tokodaii strain 7 (stoUDGΔ) and stoUDGΔ complexed with uracil were crystallized and analyzed by X-ray crystallography. The crystals were found to belong to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 52.2, b = 52.3, c = 74.7 Å and a = 52.1, b = 52.2, c = 74.1 Å for apo stoUDGΔ and stoUDGΔ complexed with uracil, respectively.
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Affiliation(s)
- Akito Kawai
- Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Kumamoto 860-0082, Japan
| | - Shigesada Higuchi
- Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Kumamoto 860-0082, Japan
| | - Masaru Tsunoda
- Faculty of Pharmacy, Iwaki Meisei University, 5-5-1 Chuodai-iino, Iwaki 970-8551, Japan
| | - Kazuo T. Nakamura
- School of Pharmacy, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo 142-8555, Japan
| | - Shuichi Miyamoto
- Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Kumamoto 860-0082, Japan
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10
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Asensio JL, Pérez-Lago L, Lázaro JM, González C, Serrano-Heras G, Salas M. Novel dimeric structure of phage φ29-encoded protein p56: insights into uracil-DNA glycosylase inhibition. Nucleic Acids Res 2011; 39:9779-88. [PMID: 21890898 PMCID: PMC3239192 DOI: 10.1093/nar/gkr667] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Protein p56 encoded by the Bacillus subtilis phage φ29 inhibits the host uracil-DNA glycosylase (UDG) activity. To get insights into the structural basis for this inhibition, the NMR solution structure of p56 has been determined. The inhibitor defines a novel dimeric fold, stabilized by a combination of polar and extensive hydrophobic interactions. Each polypeptide chain contains three stretches of anti-parallel β-sheets and a helical region linked by three short loops. In addition, microcalorimetry titration experiments showed that it forms a tight 2:1 complex with UDG, strongly suggesting that the dimer represents the functional form of the inhibitor. This was further confirmed by the functional analysis of p56 mutants unable to assemble into dimers. We have also shown that the highly anionic region of the inhibitor plays a significant role in the inhibition of UDG. Thus, based on these findings and taking into account previous results that revealed similarities between the association mode of p56 and the phage PBS-1/PBS-2-encoded inhibitor Ugi with UDG, we propose that protein p56 might inhibit the enzyme by mimicking its DNA substrate.
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Affiliation(s)
- Juan Luis Asensio
- Departamento de Química Orgánica Biológica, Instituto de Química Orgánica General, CSIC, 28006 Madrid, Spain.
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11
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Pérez-Lago L, Serrano-Heras G, Baños B, Lázaro JM, Alcorlo M, Villar L, Salas M. Characterization of Bacillus subtilis uracil-DNA glycosylase and its inhibition by phage φ29 protein p56. Mol Microbiol 2011; 80:1657-66. [PMID: 21542855 DOI: 10.1111/j.1365-2958.2011.07675.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Uracil-DNA glycosylase (UDG) is a conserved DNA repair enzyme involved in uracil excision from DNA. Here, we report the biochemical characterization of UDG encoded by Bacillus subtilis, a model low G+C Gram-positive organism. The purified enzyme removes uracil preferentially from single-stranded DNA over double-stranded DNA, exhibiting higher preference for U:G than U:A mismatches. Furthermore, we have identified key amino acids necessary for B. subtilis UDG activity. Our results showed that Asp-65 and His-187 are catalytic residues involved in glycosidic bond cleavage, whereas Phe-78 would participate in DNA recognition. Recently, it has been reported that B. subtilis phage φ29 encodes an inhibitor of the UDG enzyme, named protein p56, whose role has been proposed to ensure an efficient viral DNA replication, preventing the deleterious effect caused by UDG when it eliminates uracils present in the φ29 genome. In this work, we also show that a φ29-related phage, GA-1, encodes a p56-like protein with UDG inhibition activity. In addition, mutagenesis analysis revealed that residue Phe-191 of B. subtilis UDG is critical for the interaction with φ29 and GA-1 p56 proteins, suggesting that both proteins have similar mechanism of inhibition.
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Affiliation(s)
- Laura Pérez-Lago
- Instituto de Biología Molecular Eladio Viñuela, CSIC, Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain
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12
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Kaushal PS, Talawar RK, Varshney U, Vijayan M. Structure of uracil-DNA glycosylase from Mycobacterium tuberculosis: insights into interactions with ligands. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:887-92. [PMID: 20693660 PMCID: PMC2917283 DOI: 10.1107/s1744309110023043] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Accepted: 06/15/2010] [Indexed: 11/10/2022]
Abstract
Uracil N-glycosylase (Ung) is the most thoroughly studied of the group of uracil DNA-glycosylase (UDG) enzymes that catalyse the first step in the uracil excision-repair pathway. The overall structure of the enzyme from Mycobacterium tuberculosis is essentially the same as that of the enzyme from other sources. However, differences exist in the N- and C-terminal stretches and some catalytic loops. Comparison with appropriate structures indicate that the two-domain enzyme closes slightly when binding to DNA, while it opens slightly when binding to the proteinaceous inhibitor Ugi. The structural changes in the catalytic loops on complexation reflect the special features of their structure in the mycobacterial protein. A comparative analysis of available sequences of the enzyme from different sources indicates high conservation of amino-acid residues in the catalytic loops. The uracil-binding pocket in the structure is occupied by a citrate ion. The interactions of the citrate ion with the protein mimic those of uracil, in addition to providing insights into other possible interactions that inhibitors could be involved in.
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Affiliation(s)
- Prem Singh Kaushal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Ramappa K. Talawar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
| | - M. Vijayan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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13
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Zharkov DO, Mechetin GV, Nevinsky GA. Uracil-DNA glycosylase: Structural, thermodynamic and kinetic aspects of lesion search and recognition. Mutat Res 2010; 685:11-20. [PMID: 19909758 PMCID: PMC3000906 DOI: 10.1016/j.mrfmmm.2009.10.017] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2009] [Revised: 10/24/2009] [Accepted: 10/29/2009] [Indexed: 11/19/2022]
Abstract
Uracil appears in DNA as a result of cytosine deamination and by incorporation from the dUTP pool. As potentially mutagenic and deleterious for cell regulation, uracil must be removed from DNA. The major pathway of its repair is initiated by uracil-DNA glycosylases (UNG), ubiquitously found enzymes that hydrolyze the N-glycosidic bond of deoxyuridine in DNA. This review describes the current understanding of the mechanism of uracil search and recognition by UNG. The structure of UNG proteins from several species has been solved, revealing a specific uracil-binding pocket located in a DNA-binding groove. DNA in the complex with UNG is highly distorted to allow the extrahelical recognition of uracil. Thermodynamic studies suggest that UNG binds with appreciable affinity to any DNA, mainly due to the interactions with the charged backbone. The increase in the affinity for damaged DNA is insufficient to account for the exquisite specificity of UNG for uracil. This specificity is likely to result from multistep lesion recognition process, in which normal bases are rejected at one or several pre-excision stages of enzyme-substrate complex isomerization, and only uracil can proceed to enter the active site in a catalytically competent conformation. Search for the lesion by UNG involves random sliding along DNA alternating with dissociation-association events and partial eversion of undamaged bases for initial sampling.
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Affiliation(s)
- Dmitry O. Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia
- Department of Molecular Biology, Faculty of Natural Sciences, Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia
| | - Grigory V. Mechetin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia
| | - Georgy A. Nevinsky
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia
- Department of Molecular Biology, Faculty of Natural Sciences, Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia
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14
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Raeder ILU, Moe E, Willassen NP, Smalås AO, Leiros I. Structure of uracil-DNA N-glycosylase (UNG) from Vibrio cholerae: mapping temperature adaptation through structural and mutational analysis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:130-6. [PMID: 20124707 PMCID: PMC2815677 DOI: 10.1107/s1744309109052063] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Accepted: 12/03/2009] [Indexed: 11/10/2022]
Abstract
The crystal structure of Vibrio cholerae uracil-DNA N-glycosylase (vcUNG) has been determined to 1.5 A resolution. Based on this structure, a homology model of Aliivibrio salmonicida uracil-DNA N-glycosylase (asUNG) was built. A previous study demonstrated that asUNG possesses typical cold-adapted features compared with vcUNG, such as a higher catalytic efficiency owing to increased substrate affinity. Specific amino-acid substitutions in asUNG were suggested to be responsible for the increased substrate affinity and the elevated catalytic efficiency by increasing the positive surface charge in the DNA-binding region. The temperature adaptation of these enzymes has been investigated using structural and mutational analyses, in which mutations of vcUNG demonstrated an increased substrate affinity that more resembled that of asUNG. Visualization of surface potentials revealed a more positive potential for asUNG compared with vcUNG; a modelled double mutant of vcUNG had a potential around the substrate-binding region that was more like that of asUNG, thus rationalizing the results obtained from the kinetic studies.
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Affiliation(s)
- Inger Lin Uttakleiv Raeder
- Department of Chemistry, Faculty of Science, University of Tromsø, N-9037 Tromsø, Norway
- The Norwegian Structural Biology Centre, University of Tromsø, N-9037 Tromsø, Norway
| | - Elin Moe
- Department of Chemistry, Faculty of Science, University of Tromsø, N-9037 Tromsø, Norway
- The Norwegian Structural Biology Centre, University of Tromsø, N-9037 Tromsø, Norway
| | - Nils Peder Willassen
- The Norwegian Structural Biology Centre, University of Tromsø, N-9037 Tromsø, Norway
- Department of Molecular Biotechnology, Institute of Medical Biology, University of Tromsø, N-9037 Tromsø, Norway
| | - Arne O. Smalås
- Department of Chemistry, Faculty of Science, University of Tromsø, N-9037 Tromsø, Norway
- The Norwegian Structural Biology Centre, University of Tromsø, N-9037 Tromsø, Norway
| | - Ingar Leiros
- Department of Chemistry, Faculty of Science, University of Tromsø, N-9037 Tromsø, Norway
- The Norwegian Structural Biology Centre, University of Tromsø, N-9037 Tromsø, Norway
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15
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Bharti SK, Varshney U. Analysis of the impact of a uracil DNA glycosylase attenuated in AP-DNA binding in maintenance of the genomic integrity in Escherichia coli. Nucleic Acids Res 2010; 38:2291-301. [PMID: 20056657 PMCID: PMC2853124 DOI: 10.1093/nar/gkp1210] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Uracil DNA glycosylase (Ung) initiates the uracil excision repair pathway. We have earlier characterized the Y66W and Y66H mutants of Ung and shown that they are compromised by ∼7- and ∼170-fold, respectively in their uracil excision activities. In this study, fluorescence anisotropy measurements show that compared with the wild-type, the Y66W protein is moderately compromised and attenuated in binding to AP-DNA. Allelic exchange of ung in Escherichia coli with ung::kan, ungY66H:amp or ungY66W:amp alleles showed ∼5-, ∼3.0- and ∼2.0-fold, respectively increase in mutation frequencies. Analysis of mutations in the rifampicin resistance determining region of rpoB revealed that the Y66W allele resulted in an increase in A to G (or T to C) mutations. However, the increase in A to G mutations was mitigated upon expression of wild-type Ung from a plasmid borne gene. Biochemical and computational analyses showed that the Y66W mutant maintains strict specificity for uracil excision from DNA. Interestingly, a strain deficient in AP-endonucleases also showed an increase in A to G mutations. We discuss these findings in the context of a proposal that the residency of DNA glycosylase(s) onto the AP-sites they generate shields them until recruitment of AP-endonucleases for further repair.
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Affiliation(s)
- Sanjay Kumar Bharti
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012 and Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012 and Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
- *To whom correspondence should be addressed. Tel: +91 80 2293 2686; Fax: +91 80 2360 2697; ;
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16
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Castillo-Acosta VM, Estévez AM, Vidal AE, Ruiz-Perez LM, González-Pacanowska D. Depletion of dimeric all-alpha dUTPase induces DNA strand breaks and impairs cell cycle progression in Trypanosoma brucei. Int J Biochem Cell Biol 2008; 40:2901-13. [PMID: 18656547 DOI: 10.1016/j.biocel.2008.06.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Revised: 06/20/2008] [Accepted: 06/24/2008] [Indexed: 11/17/2022]
Abstract
The enzyme deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase) is responsible for the control of intracellular levels of dUTP thus controlling the incorporation of uracil into DNA during replication. Trypanosomes and certain eubacteria contain a dimeric dUTP-dUDPase belonging to the recently described superfamily of all-alpha NTP pyrophosphatases which bears no resemblance with typical eukaryotic trimeric dUTPases and presents unique properties regarding substrate specificity and product inhibition. While the biological trimeric enzymes have been studied in detail and the human enzyme has been proposed as a promising novel target for anticancer chemotherapeutic strategies, little is known regarding the biological function of dimeric proteins. Here, we show that in Trypanosoma brucei, the dimeric dUTPase is a nuclear enzyme and that down-regulation of activity by RNAi greatly reduces cell proliferation and increases the intracellular levels of dUTP. Defects in growth could be partially reverted by the addition of exogenous thymidine. dUTPase-depleted cells presented hypersensitivity to methotrexate, a drug that increases the intracellular pools of dUTP, and enhanced uracil-DNA glycosylase activity, the first step in base excision repair. The knockdown of activity produces numerous DNA strand breaks and defects in both S and G2/M progression. Multiple parasites with a single enlarged nucleus were visualized together with an enhanced population of anucleated cells. We conclude that dimeric dUTPases are strongly involved in the control of dUTP incorporation and that adequate levels of enzyme are indispensable for efficient cell cycle progression and DNA replication.
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Affiliation(s)
- Víctor M Castillo-Acosta
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas, Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento, s/n 18100-Armilla, Granada, Spain
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17
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Ræder ILU, Leiros I, Willassen NP, Smalås AO, Moe E. Uracil-DNA N-glycosylase (UNG) from the marine, psychrophilic bacterium Vibrio salmonicida shows cold adapted features. Enzyme Microb Technol 2008. [DOI: 10.1016/j.enzmictec.2008.02.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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18
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Olufsen M, Smalås AO, Brandsdal BO. Electrostatic interactions play an essential role in DNA repair and cold-adaptation of uracil DNA glycosylase. J Mol Model 2008; 14:201-13. [PMID: 18196298 DOI: 10.1007/s00894-007-0261-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2007] [Accepted: 12/03/2007] [Indexed: 01/01/2023]
Abstract
Life has adapted to most environments on earth, including low and high temperature niches. The increased catalytic efficiency and thermoliability observed for enzymes from organisms living in constantly cold regions when compared to their mesophilic and thermophilic cousins are poorly understood at the molecular level. Uracil DNA glycosylase (UNG) from cod (cUNG) catalyzes removal of uracil from DNA with an increased k(cat) and reduced K(m) relative to its warm-active human (hUNG) counterpart. Specific issues related to DNA repair and substrate binding/recognition (K(m)) are here investigated by continuum electrostatics calculations, MD simulations and free energy calculations. Continuum electrostatic calculations reveal that cUNG has surface potentials that are more complementary to the DNA potential at and around the catalytic site when compared to hUNG, indicating improved substrate binding. Comparative MD simulations combined with free energy calculations using the molecular mechanics-Poisson Boltzmann surface area (MM-PBSA) method show that large opposing energies are involved when forming the enzyme-substrate complexes. Furthermore, the binding free energies obtained reveal that the Michaelis-Menten complex is more stable for cUNG, primarily due to enhanced electrostatic properties, suggesting that energetic fine-tuning of electrostatics can be utilized for enzymatic temperature adaptation. Energy decomposition pinpoints the residual determinants responsible for this adaptation.
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Affiliation(s)
- Magne Olufsen
- The Norwegian Structural Biology Centre, Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
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19
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Olufsen M, Papaleo E, Smalås AO, Brandsdal BO. Ion pairs and their role in modulating stability of cold- and warm-active uracil DNA glycosylase. Proteins 2007; 71:1219-30. [DOI: 10.1002/prot.21815] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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20
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Crystal structure of vaccinia virus uracil-DNA glycosylase reveals dimeric assembly. BMC STRUCTURAL BIOLOGY 2007; 7:45. [PMID: 17605817 PMCID: PMC1936997 DOI: 10.1186/1472-6807-7-45] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2007] [Accepted: 07/02/2007] [Indexed: 11/13/2022]
Abstract
Background Uracil-DNA glycosylases (UDGs) catalyze excision of uracil from DNA. Vaccinia virus, which is the prototype of poxviruses, encodes a UDG (vvUDG) that is significantly different from the UDGs of other organisms in primary, secondary and tertiary structure and characteristic motifs. It adopted a novel catalysis-independent role in DNA replication that involves interaction with a viral protein, A20, to form the processivity factor. UDG:A20 association is essential for assembling of the processive DNA polymerase complex. The structure of the protein must have provisions for such interactions with A20. This paper provides the first glimpse into the structure of a poxvirus UDG. Results Results of dynamic light scattering experiments and native size exclusion chromatography showed that vvUDG is a dimer in solution. The dimeric assembly is also maintained in two crystal forms. The core of vvUDG is reasonably well conserved but the structure contains one additional β-sheet at each terminus. A glycerol molecule is found in the active site of the enzyme in both crystal forms. Interaction of this glycerol molecule with the protein possibly mimics the enzyme-substrate (uracil) interactions. Conclusion The crystal structures reveal several distinctive features of vvUDG. The new structural features may have evolved for adopting novel functions in the replication machinery of poxviruses. The mode of interaction between the subunits in the dimers suggests a possible model for binding to its partner and the nature of the processivity factor in the polymerase complex.
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21
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Olufsen M, Brandsdal BO, Smalås AO. Comparative unfolding studies of psychrophilic and mesophilic uracil DNA glycosylase: MD simulations show reduced thermal stability of the cold-adapted enzyme. J Mol Graph Model 2007; 26:124-34. [PMID: 17134924 DOI: 10.1016/j.jmgm.2006.10.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2006] [Revised: 10/17/2006] [Accepted: 10/18/2006] [Indexed: 11/22/2022]
Abstract
Uracil DNA glycosylase (UDG) is a DNA repair enzyme involved in the base excision repair (BER) pathway, removing misincorporated uracil from the DNA strand. The native and mutant forms of Atlantic cod and human UDG have previously been characterized in terms of kinetic and thermodynamic properties as well as the determination of several crystal structures. This data shows that the cold-adapted enzyme is more catalytically efficient but at the same time less resistant to heat compared to its warm-active counterpart. In this study, the structure-function relationship is further explored by means of comparative molecular dynamics (MD) simulations at three different temperatures (375, 400 and 425K) to gain a deeper insight into the structural features responsible for the reduced thermostability of the cold-active enzyme. The simulations show that there are distinct structural differences in the unfolding pathway between the two homologues, particularly evident in the N- and C-terminals. Distortion of the mesophilic enzyme is initiated simultaneously in the N- and C-terminal, while the C-terminal part plays a key role for the stability of the psychrophilic enzyme. The simulations also show that at certain temperatures the cold-adapted enzyme unfolds faster than the warm-active homologues in accordance with the lower thermal stability found experimentally.
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Affiliation(s)
- Magne Olufsen
- The Norwegian Structural Biology Centre, Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
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22
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Singh P, Talawar RK, Krishna PDV, Varshney U, Vijayan M. Overexpression, purification, crystallization and preliminary X-ray analysis of uracil N-glycosylase from Mycobacterium tuberculosis in complex with a proteinaceous inhibitor. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:1231-4. [PMID: 17142904 PMCID: PMC2225355 DOI: 10.1107/s1744309106045805] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2006] [Accepted: 10/31/2006] [Indexed: 11/11/2022]
Abstract
Uracil N-glycosylase is an enzyme which initiates the pathway of uracil-excision repair of DNA. The enzyme from Mycobacterium tuberculosis was co-expressed with a proteinaceous inhibitor from Bacillus subtilis phage and was crystallized in monoclinic space group C2, with unit-cell parameters a = 201.14, b = 64.27, c = 203.68 A, beta = 109.7 degrees. X-ray data from the crystal have been collected for structure analysis.
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Affiliation(s)
- Prem Singh
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Ramappa K. Talawar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
| | - P. D. V. Krishna
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
| | - M. Vijayan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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23
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Géoui T, Buisson M, Tarbouriech N, Burmeister WP. New insights on the role of the gamma-herpesvirus uracil-DNA glycosylase leucine loop revealed by the structure of the Epstein-Barr virus enzyme in complex with an inhibitor protein. J Mol Biol 2006; 366:117-31. [PMID: 17157317 DOI: 10.1016/j.jmb.2006.11.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2006] [Revised: 10/31/2006] [Accepted: 11/02/2006] [Indexed: 11/23/2022]
Abstract
Epstein-Barr virus (EBV) is a human gamma-herpesvirus. Within its 86 open reading frame containing genome, two enzymes avoiding uracil incorporation into DNA can be found: uracil triphosphate hydrolase and uracil-DNA glycosylase (UNG). The latter one excises uracil bases that are due to cytosine deamination or uracil misincorporation from double-stranded DNA substrates. The EBV enzyme belongs to family 1 UNGs. We solved the three-dimensional structure of EBV UNG in complex with the uracil-DNA glycosylase inhibitor protein (Ugi) from bacteriophage PBS-2 at a resolution of 2.3 A by X-ray crystallography. The structure of EBV UNG encoded by the BKRF3 reading frame shows the excellent global structural conservation within the solved examples of family 1 enzymes. Four out of the five catalytic motifs are completely conserved, whereas the fifth one, the leucine loop, carries a seven residue insertion. Despite this insertion, catalytic constants of EBV UNG are similar to those of other UNGs. Modelling of the EBV UNG-DNA complex shows that the longer leucine loop still contacts DNA and is likely to fulfil its role of DNA binding and deformation differently than the enzymes with previously solved structures. We could show that despite the evolutionary distance of EBV UNG from the natural host protein, bacteriophage Ugi binds with an inhibitory constant of 8 nM to UNG. This is due to an excellent specificity of Ugi for conserved elements of UNG, four of them corresponding to catalytic motifs and a fifth one corresponding to an important beta-turn structuring the catalytic site.
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Affiliation(s)
- Thibault Géoui
- Institut de Virologie Moléculaire et Structurale, FRE 2854 CNRS-UJF, BP 181, F-38042 Grenoble cedex 9, France
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24
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Berti PJ, McCann JAB. Toward a detailed understanding of base excision repair enzymes: transition state and mechanistic analyses of N-glycoside hydrolysis and N-glycoside transfer. Chem Rev 2006; 106:506-55. [PMID: 16464017 DOI: 10.1021/cr040461t] [Citation(s) in RCA: 211] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Paul J Berti
- Department of Chemistry, McMaster University, Hamilton, Ontario, Canada.
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25
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Timchenko AA, Kubareva EA, Volkov EM, Voronina OL, Lunin VG, Gonchar DA, Degtyarev SK, Timchenko MA, Kihara H, Kimura K. Structure of Escherichia coli uracil-DNA glycosylase and its complexes with nonhydrolyzable substrate analogues in solution studied by synchrotron small-angle X-ray scattering. Biophysics (Nagoya-shi) 2006. [DOI: 10.1134/s0006350906010015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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26
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Abstract
The discoveries of DNA mimicry by proteins inspired by Ugi experiments led by Dale Mosbaugh and his colleagues have sparked dramatic insights for our understanding of DNA and protein interactions. Currently only a small number protein mimics of DNA are known or suspected, including Ugi, HI1450, Ocr, TAF1, MfpA, and Dinl. These proteins are structurally diverse, but together they share common themes we define here. These mimics tend to resemble distorted rather than normal B-DNA, possibly to prevent cross-reactions with other DNA metabolizing proteins that should not be inhibited. Side-chain carboxylates of glutamates and aspartates functionally replace phosphates and thereby generate an overall charge pattern resembling the DNA phosphate backbone. Most protein mimics of DNA have strikingly hydrophobic cores that likely stabilize the protein fold despite substantial charge localization and a relatively small internal volume enforced by the restrictions from DNA size. These common characteristics for protein mimicry of DNA should prove useful for future identifications of DNA mimics, which seem likely to be found in bacteriophages, conjugative plasmids, eukaryotic viruses, and transcription machinery. We also suggest approaches to the design of novel DNA mimics to inhibit specific pathways and could be important for basic science applications and for use as therapeutic agents. Moreover, mimicry in general is of critical importance in that it provides an elegant mechanism by which interfaces can be reused to force sequential rather than simultaneous complex formations such as seen in systems involving polar protein assemblies and DNA repair machinery.
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Affiliation(s)
- Christopher D Putnam
- Ludwig Institute for Cancer Research, Department of Medicine, University of California, San Diego School of Medicine, La Jolla, 92093-0669, USA
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27
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Olufsen M, Smalås AO, Moe E, Brandsdal BO. Increased Flexibility as a Strategy for Cold Adaptation. J Biol Chem 2005; 280:18042-8. [PMID: 15749696 DOI: 10.1074/jbc.m500948200] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Uracil DNA glycosylase (UDG) is a DNA repair enzyme in the base excision repair pathway and removes uracil from the DNA strand. Atlantic cod UDG (cUDG), which is a cold-adapted enzyme, has been found to be up to 10 times more catalytically active in the temperature range 15-37 degrees C as compared with the warm-active human counterpart. The increased catalytic activity of cold-adapted enzymes as compared with their mesophilic homologues are partly believed to be caused by an increase in the structural flexibility. However, no direct experimental evidence supports the proposal of increased flexibility of cold-adapted enzymes. We have used molecular dynamics simulations to gain insight into the structural flexibility of UDG. The results from these simulations show that an important loop involved in DNA recognition (the Leu(272) loop) is the most flexible part of the cUDG structure and that the human counterpart has much lower flexibility in the Leu(272) loop. The flexibility in this loop correlates well with the experimental k(cat)/K(m) values. Thus, the data presented here add strong support to the idea that flexibility plays a central role in adaptation to cold environments.
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Affiliation(s)
- Magne Olufsen
- Norwegian Structural Biology Centre, University of Tromsø, N-9037 Tromsø, Norway
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28
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Moe E, Leiros I, Riise EK, Olufsen M, Lanes O, Smalås A, Willassen NP. Optimisation of the surface electrostatics as a strategy for cold adaptation of uracil-DNA N-glycosylase (UNG) from Atlantic cod (Gadus morhua). J Mol Biol 2004; 343:1221-30. [PMID: 15491608 DOI: 10.1016/j.jmb.2004.09.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2004] [Revised: 09/01/2004] [Accepted: 09/03/2004] [Indexed: 11/29/2022]
Abstract
Cold-adapted enzymes are characterised by an increased catalytic efficiency and reduced temperature stability compared to their mesophilic counterparts. Lately, it has been suggested that an optimisation of the electrostatic surface potential is a strategy for cold adaptation for some enzymes. A visualisation of the electrostatic surface potential of cold-adapted uracil-DNA N-glycosylase (cUNG) from Atlantic cod indicates a more positively charged surface near the active site compared to human UNG (hUNG). In order to investigate the importance of the altered surface potential for the cold-adapted features of cod UNG, six mutants have been characterised and compared to cUNG and hUNG. The cUNG quadruple mutant (V171E, K185V, H250Q and H275Y) and four corresponding single mutants all comprise substitutions of residues present in the human enzyme. A human UNG mutant, E171V, comprises the equivalent residue found in cod UNG. In addition, crystal structures of the single mutants V171E and E171V have been determined. Results from the study show that a more negative electrostatic surface potential reduces the activity and increases the stability of cod UNG, and suggest an optimisation of the surface potential as a strategy for cold-adaptation of this enzyme. Val171 in cod UNG is especially important in this respect.
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Affiliation(s)
- Elin Moe
- Department of Molecular Biotechnology, Institute of Medical Biology, Faculty of Medicine, University of Tromsø, N-9037 Tromsø, Norway
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29
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Kumar P, Krishna K, Srinivasan R, Ajitkumar P, Varshney U. Mycobacterium tuberculosis and Escherichia coli nucleoside diphosphate kinases lack multifunctional activities to process uracil containing DNA. DNA Repair (Amst) 2004; 3:1483-92. [PMID: 15380104 DOI: 10.1016/j.dnarep.2004.06.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2004] [Indexed: 11/23/2022]
Abstract
E. coli nucleoside diphosphate kinase (EcoNDK) is an important cellular enzyme required to maintain balanced nucleotide pools in the cells. Recently, it was reported that EcoNDK is also a multifunctional base excision repair enzyme, possessing uracil-DNA glycosylase (UDG) and AP-DNA processing activities. We investigated for the presence of such activities in M. tuberculosis NDK (MtuNDK), which shares 45.2% identity, and 52.6% similarity with EcoNDK. In contrast to the robust uracil excision activity reported for EcoNDK, MtuNDK preparation exhibited very poor excision of uracil from DNA. However, this activity was undetectable when MtuNDK was purified from an ung(-) strain of E. coli, or when the assays were performed in the presence of extremely low amounts of a highly specific proteinaceous inhibitor, Ugi which forms an extremely tight complex with the host Ung (UDG), showing that MtuNDK preparation was contaminated with UDG. Reinvestigation of uracil processing activity of EcoNDK, showed that even this protein lacked UDG activity. All preparations of NDK were shown to be active by their autophosphorylation activity. Ugi neither displayed a physical interaction with EcoNDK nor did it affect autophosphorylation of NDKs. Further, neither of the NDK preparations processed the AP-DNA generated by UDG treatment of the uracil containing DNA duplexes. However, partially purified preparations of NDK did process such DNA substrates.
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Affiliation(s)
- Pradeep Kumar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
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30
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Peña-Diaz J, Akbari M, Sundheim O, Farez-Vidal ME, Andersen S, Sneve R, Gonzalez-Pacanowska D, Krokan HE, Slupphaug G. Trypanosoma cruzi contains a single detectable uracil-DNA glycosylase and repairs uracil exclusively via short patch base excision repair. J Mol Biol 2004; 342:787-99. [PMID: 15342237 DOI: 10.1016/j.jmb.2004.07.043] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2004] [Revised: 07/08/2004] [Accepted: 07/12/2004] [Indexed: 11/23/2022]
Abstract
Enzymes involved in genomic maintenance of human parasites are attractive targets for parasite-specific drugs. The parasitic protozoan Trypanosoma cruzi contains at least two enzymes involved in the protection against potentially mutagenic uracil, a deoxyuridine triphosphate nucleotidohydrolase (dUTPase) and a uracil-DNA glycosylase belonging to the highly conserved UNG-family. Uracil-DNA glycosylase activities excise uracil from DNA and initiate a multistep base-excision repair (BER) pathway to restore the correct nucleotide sequence. Here we report the biochemical characterisation of T.cruzi UNG (TcUNG) and its contribution to the total uracil repair activity in T.cruzi. TcUNG is shown to be the major uracil-DNA glycosylase in T.cruzi. The purified recombinant TcUNG exhibits substrate preference for removal of uracil in the order ssU>U:G>U:A, and has no associated thymine-DNA glycosylase activity. T.cruzi apparently repairs U:G DNA substrate exclusively via short-patch BER, but the DNA polymerase involved surprisingly displays a vertebrate POLdelta-like pattern of inhibition. Back-up UDG activities such as SMUG, TDG and MBD4 were not found, underlying the importance of the TcUNG enzyme in protection against uracil in DNA and as a potential target for drug therapy.
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Affiliation(s)
- Javier Peña-Diaz
- Instituto de Parasitologia y Biomedicina "Lopez Neyra", Consejo Superior de Investigaciones Cientificas, C/Ventanilla 11, 18001 Granada, Spain
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31
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Acharya N, Talawar RK, Purnapatre K, Varshney U. Use of sequence microdivergence in mycobacterial ortholog to analyze contributions of the water-activating loop histidine of Escherichia coli uracil-DNA glycosylase in reactant binding and catalysis. Biochem Biophys Res Commun 2004; 320:893-9. [PMID: 15240132 DOI: 10.1016/j.bbrc.2004.06.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2004] [Indexed: 10/26/2022]
Abstract
Uracil-DNA glycosylase (Ung), a DNA repair enzyme, pioneers uracil excision repair pathway. Structural determinations and mutational analyses of the Ung class of proteins have greatly facilitated our understanding of the mechanism of uracil excision from DNA. More recently, a hybrid quantum-mechanical/molecular mechanical analysis revealed that while the histidine (H67 in EcoUng) of the GQDPYH motif (omega loop) in the active site pocket is important in positioning the reactants, it makes an unfavorable energetic contribution (penalty) in achieving the transition state intermediate. Mutational analysis of this histidine is unavailable from any of the Ung class of proteins. A complication in demonstrating negative role of a residue, especially when located within the active site pocket, is that the mutants with enhanced activity are rarely obtained. Interestingly, unlike the most Ung proteins, the H67 equivalent in the omega loop in mycobacterial Ung is represented by P67. Exploiting this natural diversity to maintain structural integrity of the active site, we transplanted an H67P mutation in EcoUng. Uracil inhibition assays and binding of a proteinaceous inhibitor, Ugi (a transition state substrate mimic), with the mutant (H67P) revealed that its active site pocket was not perturbed. The catalytic efficiency (Vmax/Km) of the mutant was similar to that of the wild type Ung. However, the mutant showed increased Km and Vmax. Together with the data from a double mutation H67P/G68T, these observations provide the first biochemical evidence for the proposed diverse roles of H67 in catalysis by Ung.
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Affiliation(s)
- Narottam Acharya
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
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32
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Acharya N, Talawar RK, Saikrishnan K, Vijayan M, Varshney U. Substitutions at tyrosine 66 of Escherichia coli uracil DNA glycosylase lead to characterization of an efficient enzyme that is recalcitrant to product inhibition. Nucleic Acids Res 2004; 31:7216-26. [PMID: 14654697 PMCID: PMC291862 DOI: 10.1093/nar/gkg918] [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: 11/12/2022] Open
Abstract
Uracil DNA glycosylase (UDG), a ubiquitous and highly specific enzyme, commences the uracil excision repair pathway. Structural studies have shown that the tyrosine in a highly conserved GQDPY water-activating loop of UDGs blocks the entry of thymine or purines into the active site pocket. To further understand the role of this tyrosine (Y66 in Escherichia coli UDG), we have overproduced and characterized Y66F, Y66H, Y66L and Y66W mutants. The complexes of the wild-type, Y66F, Y66H and Y66L UDGs with uracil DNA glycosylase inhibitor (Ugi) (a proteinaceous substrate mimic) were stable to 8 M urea. However, some dissociation of the complex involving the Y66W UDG occurred at this concentration of urea. The catalytic efficiencies (V(max) / K(m)) of the Y66L and Y66F mutants were similar to those of the wild-type UDG. However, the Y66W and Y66H mutants were approximately 7- and approximately 173-fold compromised, respectively, in their activities. Interestingly, the Y66W mutation has resulted in an enzyme which is resistant to product inhibition. Preferential utilization of a substrate enabling a long range contact between the -5 phosphate (upstream to the scissile uracil) and the enzyme, and the results of modeling studies showing that the uracil-binding cavity of Y66W is wider than those of the wild type and other mutant UDGs, suggest a weaker interaction between uracil and the Y66W mutant. Furthermore, the fluorescence spectroscopy of UDGs and their complexes with Ugi, in the presence of uracil or its analog, 5-bromouracil, suggests compromised binding of uracil in the active site pocket of the Y66W mutant. Lack of inhibition of the Y66W UDG by apyrimidinic DNA (AP-DNA) is discussed to highlight a potential additional role of Y66 in shielding the toxic effects of AP-DNA, by lowering the rate of its release for subsequent recognition by an AP endonuclease.
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Affiliation(s)
- Narottam Acharya
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560 012, India
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33
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Venkatesh J, Kumar P, Krishna PSM, Manjunath R, Varshney U. Importance of uracil DNA glycosylase in Pseudomonas aeruginosa and Mycobacterium smegmatis, G+C-rich bacteria, in mutation prevention, tolerance to acidified nitrite, and endurance in mouse macrophages. J Biol Chem 2003; 278:24350-8. [PMID: 12679366 DOI: 10.1074/jbc.m302121200] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Uracil DNA glycosylase (Ung (or UDG)) initiates the excision repair of an unusual base, uracil, in DNA. Ung is a highly conserved protein found in all organisms. Paradoxically, loss of this evolutionarily conserved enzyme has not been seen to result in severe growth phenotypes in the cellular life forms. In this study, we chose G+C-rich genome containing bacteria (Pseudomonas aeruginosa and Mycobacterium smegmatis) as model organisms to investigate the biological significance of ung. Ung deficiency was created either by expression of a highly specific inhibitor protein, Ugi, and/or by targeted disruption of the ung gene. We show that abrogation of Ung activity in P. aeruginosa and M. smegmatis confers upon them an increased mutator phenotype and sensitivity to reactive nitrogen intermediates generated by acidified nitrite. Also, in a mouse macrophage infection model, P. aeruginosa (Ung-) shows a significant decrease in its survival. Infections of the macrophages with M. smegmatis show an initial increase in the bacterial counts that remain for up to 48 h before a decline. Interestingly, abrogation of Ung activity in M. smegmatis results in nearly a total abolition of their multiplication and a much-decreased residency in macrophages stimulated with interferon gamma. These observations suggest Ung as a useful target to control growth of G+C-rich bacteria.
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Affiliation(s)
- Jeganathan Venkatesh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560 012 India
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34
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Acharya N, Kumar P, Varshney U. Complexes of the uracil-DNA glycosylase inhibitor protein, Ugi, with Mycobacterium smegmatis and Mycobacterium tuberculosis uracil-DNA glycosylases. MICROBIOLOGY (READING, ENGLAND) 2003; 149:1647-1658. [PMID: 12855717 DOI: 10.1099/mic.0.26228-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Uracil, a promutagenic base, appears in DNA either by deamination of cytosine or by incorporation of dUMP by DNA polymerases. This unconventional base in DNA is removed by uracil-DNA glycosylase (UDG). Interestingly, a bacteriophage-encoded short polypeptide, UDG inhibitor (Ugi), specifically inhibits UDGs by forming a tight complex. Three-dimensional structures of the complexes of Ugi with UDGs from Escherichia coli, human and herpes simplex virus have shown that two of the structural elements in Ugi, the hydrophobic pocket and the beta1-edge, establish key interactions with UDGs. In this report the characterization of complexes of Ugi with UDGs from Mycobacterium tuberculosis, a pathogenic bacterium, and Mycobacterium smegmatis, a widely used model organism for the former, is described. Unlike the E. coli (Eco) UDG-Ugi complex, which is stable to treatment with 8 M urea, the mycobacterial UDG-Ugi complexes dissociate in 5-6 M urea. Furthermore, the Ugi from the complexes of mycobacterial UDGs can be exchanged by the DNA substrate. Interestingly, while EcoUDG sequestered Ugi into the EcoUDG-Ugi complex when incubated with mycobacterial UDG-Ugi complexes, even a large excess of mycobacterial UDGs failed to sequester Ugi from the EcoUDG-Ugi complex. However, the M. tuberculosis (Mtu) UDG-Ugi complex was seen when MtuUDG was incubated with M. smegmatis (Msm) UDG-Ugi or EcoUDG(L191G)-Ugi complexes. The reversible nature of the complexes of Ugi with mycobacterial UDGs (which naturally lack some of the structural elements important for interaction with the beta1-edge of Ugi) and with mutants of EcoUDG (which are deficient in interaction with the hydrophobic pocket of Ugi) highlights the significance of both classes of interaction in formation of UDG-Ugi complexes. Furthermore, it is shown that even though mycobacterial UDG-Ugi complexes dissociate in 5-6 M urea, Ugi is still a potent inhibitor of UDG activity in mycobacteria.
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Affiliation(s)
- Narottam Acharya
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560 012, India
| | - Pradeep Kumar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560 012, India
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560 012, India
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Acharya N, Roy S, Varshney U. Mutational analysis of the uracil DNA glycosylase inhibitor protein and its interaction with Escherichia coli uracil DNA glycosylase. J Mol Biol 2002; 321:579-90. [PMID: 12206774 DOI: 10.1016/s0022-2836(02)00654-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Uracil DNA glycosylase inhibitor (Ugi), a protein of 9.4 kDa consists of a five-stranded antiparallel beta sheet flanked on either side by single alpha helices, forms an exclusive complex with uracil DNA glycosylases (UDGs) that is stable in 8M urea. We report on the mutational analysis of various structural elements in Ugi, two of which (hydrophobic pocket and the beta1 edge) establish key interactions with Escherichia coli UDG. The point mutations in helix alpha1 (amino acid residues 3-14) do not affect the stability of the UDG-Ugi complexes in urea. And, while the complex of the deltaN13 mutant with UDG is stable in only approximately 4M urea, its overall structure and thermostability are maintained. The identity of P37, stacked between P26 and W68, was not important for the maintenance of the hydrophobic pocket or for the stability of the complex. However, the M24K mutation at the rim of the hydrophobic pocket lowered the stability of the complex in 6M urea. On the other hand, non-conservative mutations E49G, D61G (cancels the only ionic interaction with UDG) and N76K, in three of the loops connecting the beta strands, conferred no such phenotype. The L23R and S21P mutations (beta1 edge) at the UDG-Ugi interface, and the N35D mutation far from the interface resulted in poor stability of the complex. However, the stability of the complexes was restored in the L23A, S21T and N35A mutations. These analyses and the studies on the exchange of Ugi mutants in preformed complexes with the substrate or the native Ugi have provided insights into the two-step mechanism of UDG-Ugi complex formation. Finally, we discuss the application of the Ugi isolates in overproduction of UDG mutants, toxic to cells.
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Affiliation(s)
- Narottam Acharya
- Department of Microbiology and Cell Biology, Indian Institute of Science, 560 012, Bangalore, India
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36
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Handa P, Acharya N, Varshney U. Effects of mutations at tyrosine 66 and asparagine 123 in the active site pocket of Escherichia coli uracil DNA glycosylase on uracil excision from synthetic DNA oligomers: evidence for the occurrence of long-range interactions between the enzyme and substrate. Nucleic Acids Res 2002; 30:3086-95. [PMID: 12136091 PMCID: PMC135746 DOI: 10.1093/nar/gkf425] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Uracil DNA glycosylase (UDG), a highly conserved DNA repair enzyme, excises uracil from DNA. Crystal structures of several UDGs have identified residues important for their exquisite specificity in detection and removal of uracil. Of these, Y66 and N123 in Escherichia coli UDG have been proposed to restrict the entry of non-uracil residues into the active site pocket. In this study, we show that the uracil excision activity of the Y66F mutant was similar to that of the wild-type protein, whereas the activities of the other mutants (Y66C, Y66S, N123D, N123E and N123Q) were compromised approximately 1000-fold. The latter class of mutants showed an increased dependence on the substrate chain length and suggested the existence of long-range interactions of the substrate with UDG. Investigation of the phosphate interactions by the ethylation interference assay reaffirmed the key importance of the -1, +1 and +2 phosphates (with respect to the scissile uracil) to the enzyme activity. Interestingly, this assay also revealed an additional interference at the -5 position phosphate, whose presence in the substrate had a positive effect on substrate utilisation by the mutants that do not possess a full complement of interactions in the active site pocket. Such long-range interactions may be crucial even for the wild-type enzyme under in vivo conditions. Further, our results suggest that the role of Y66 and N123 in UDG is not restricted merely to preventing the entry of non-uracil residues. We discuss their additional roles in conferring stability to the transition state enzyme-substrate complex and/or enhancing the leaving group quality of the uracilate anion during catalysis.
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Affiliation(s)
- Priya Handa
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
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37
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Wong I, Lundquist AJ, Bernards AS, Mosbaugh DW. Presteady-state analysis of a single catalytic turnover by Escherichia coli uracil-DNA glycosylase reveals a "pinch-pull-push" mechanism. J Biol Chem 2002; 277:19424-32. [PMID: 11907039 DOI: 10.1074/jbc.m201198200] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Uracil-DNA glycosylase catalyzes the excision of uracils from DNA via a mechanism where the uracil is extrahelically flipped out of the DNA helix into the enzyme active site. A conserved leucine is inserted into the DNA duplex space vacated by the uracil leading to the paradigmatic "push-pull" mechanism of nucleotide flipping. However, the order of these two steps during catalysis has not been conclusively established. We report a complete kinetic analysis of a single catalytic turnover using a hydrolyzable duplex oligodeoxyribonucleotide substrate containing a uracil:2-aminopurine base pair. Rapid chemical-quenched-flow methods defined the kinetics of excision at the active site during catalysis. Stopped-flow fluorometry monitoring the 2-aminopurine fluorescence defined the kinetics of uracil flipping. Parallel experiments detecting the protein fluorescence showed a slower Leu(191) insertion step occurring after nucleotide flipping but before excision. The inserted Leu(191) acts as a doorstop to prevent the return of the flipped-out uracil residue, thereby facilitating the capture of the uracil in the active site and does not play a direct role in "pushing" the uracil out of the DNA helix. The results define for the first time the proper sequence of events during a catalytic cycle and establish a "pull-push", as opposed to a "push-pull", mechanism for nucleotide flipping.
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Affiliation(s)
- Isaac Wong
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, USA.
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38
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Acharya N, Varshney U. Biochemical properties of single-stranded DNA-binding protein from Mycobacterium smegmatis, a fast-growing mycobacterium and its physical and functional interaction with uracil DNA glycosylases. J Mol Biol 2002; 318:1251-64. [PMID: 12083515 DOI: 10.1016/s0022-2836(02)00053-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The single-stranded DNA-binding proteins (SSBs) are vital to virtually all DNA functions. Here, we report on the biochemical properties of SSB from a fast-growing mycobacteria, Mycobacterium smegmatis, and the interaction of the homotetrameric SSBs with uracil DNA glycosylases (UDGs) from M. smegmatis (Msm), Mycobacterium tuberculosis (Mtu) and Escherichia coli (Eco). UDG is a crucial DNA repair enzyme, which removes the promutagenic uracil residues. MsmSSB stimulates activity of the homologous Msm UDG and of the heterologous Mtu-, and Eco-UDGs. On the contrary, while the MtuSSB stimulates the Mtu UDG, it inhibits the other two UDGs. Although the MsmSSB shares 84% identity with MtuSSB, the two are strikingly different, in that MsmSSB contains a glycine-rich segment (11 out of 13 residues) in the spacer connecting the N-terminal DNA-binding domain with the C-terminal acidic tail. While the DNA-binding properties of MsmSSB, such as its affinity to oligomeric DNA, requirement of minimum size DNA and the modes of interaction are indistinguishable from those of Eco-, and Mtu-SSBs, it is unclear if the glycine-rich segment confers structural advantage to MsmSSB, responsible for its stimulatory effect on all UDGs tested. More importantly, by using a small polypeptide inhibitor of UDGs, and the deletion mutants of SSBs, we suggest that the C-terminal acidic tail of the SSBs interacts within the DNA-binding groove of the UDGs, and propose a role for SSBs in the recruitment of UDGs to the damaged DNA.
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Affiliation(s)
- Narottam Acharya
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore
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Hosfield DJ, Daniels DS, Mol CD, Putnam CD, Parikh SS, Tainer JA. DNA damage recognition and repair pathway coordination revealed by the structural biochemistry of DNA repair enzymes. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2002; 68:315-47. [PMID: 11554309 DOI: 10.1016/s0079-6603(01)68110-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Cells have evolved distinct mechanisms for both preventing and removing mutagenic and lethal DNA damage. Structural and biochemical characterization of key enzymes that function in DNA repair pathways are illuminating the biological and chemical mechanisms that govern initial lesion detection, recognition, and excision repair of damaged DNA. These results are beginning to reveal a higher level of DNA repair coordination that ensures the faithful repair of damaged DNA. Enzyme-induced DNA distortions allow for the specific recognition of distinct extrahelical lesions, as well as tight binding to cleaved products, which has implications for the ordered transfer of unstable DNA repair intermediates between enzymes during base excision repair.
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Affiliation(s)
- D J Hosfield
- Department of Molecular Biology, Skaggs Institute for Chemical Biology, Scripps Research Institute, La Jolla, California 92037, USA
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40
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Mokkapati SK, Fernández de Henestrosa AR, Bhagwat AS. Escherichia coli DNA glycosylase Mug: a growth-regulated enzyme required for mutation avoidance in stationary-phase cells. Mol Microbiol 2001; 41:1101-11. [PMID: 11555290 DOI: 10.1046/j.1365-2958.2001.02559.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The Escherichia coli DNA glycosylase Mug excises 3,N(4)-ethenocytosines (epsilon C) and uracils from DNA, but its biological function is obscure. This is because epsilon C is not found in E. coli DNA, and uracil-DNA glycosylase (Ung), a distinct enzyme, is much more efficient at removing uracils from DNA than Mug. We find that Mug is overexpressed as cells enter stationary phase, and it is maintained at a fairly high level in resting cells. This is true of cells grown in rich or minimal media, and the principal regulation of mug is at the level of mRNA. Although the expression of mug is strongly dependent on the stationary-phase sigma factor, sigma(S), when cells are grown in minimal media, it shows only a modest dependence on sigma(S) when cells are grown in rich media. When mug cells are maintained in stationary phase for several days, they acquire many more mutations than their mug(+) counterparts. This is true in ung as well as ung(+) cells, and a majority of new mutations may not be C to T. Our results show that the biological role of Mug parallels its expression in cells. It is expressed poorly in exponentially growing cells and has no apparent role in mutation avoidance in these cells. In contrast, Mug is fairly abundant in stationary-phase cells and has an important anti-mutator role at this stage of cell growth. Thus, Mug joins a very small coterie of DNA repair enzymes whose principal function is to avoid mutations in stationary-phase cells.
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Affiliation(s)
- S K Mokkapati
- Department of Chemistry, 463 Chemistry Building, Wayne State University, Detroit, MI 48202, USA
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41
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Handa P, Roy S, Varshney U. The role of leucine 191 of Escherichia coli uracil DNA glycosylase in the formation of a highly stable complex with the substrate mimic, ugi, and in uracil excision from the synthetic substrates. J Biol Chem 2001; 276:17324-31. [PMID: 11278852 DOI: 10.1074/jbc.m011166200] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Uracil DNA glycosylase (UDG), a highly conserved DNA repair enzyme, initiates the uracil excision repair pathway. Ugi, a bacteriophage-encoded peptide, potently inhibits UDGs by serving as a remarkable substrate mimic. Structure determination of UDGs has identified regions important for the exquisite specificity in the detection and removal of uracils from DNA and in their interaction with Ugi. In this study, we carried out mutational analysis of the Escherichia coli UDG at Leu191 within the 187HPSPLS192 motif (DNA intercalation loop). We show that with the decrease in side chain length at position 191, the stability of the UDG-Ugi complexes regresses. Further, while the L191V and L191F mutants were as efficient as the wild type protein, the L191A and L191G mutants retained only 10 and 1% of the enzymatic activity, respectively. Importantly, however, substitution of Leu191 with smaller side chains had no effect on the relative efficiencies of uracil excision from the single-stranded and a corresponding double-stranded substrate. Our results suggest that leucine within the HPSPLS motif is crucial for the uracil excision activity of UDG, and it contributes to the formation of a physiologically irreversible complex with Ugi. We also envisage a role for Leu191 in stabilizing the productive enzyme-substrate complex.
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Affiliation(s)
- P Handa
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560 012, India
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42
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Datta S, Prabu MM, Vaze MB, Ganesh N, Chandra NR, Muniyappa K, Vijayan M. Crystal structures of Mycobacterium tuberculosis RecA and its complex with ADP-AlF(4): implications for decreased ATPase activity and molecular aggregation. Nucleic Acids Res 2000; 28:4964-73. [PMID: 11121488 PMCID: PMC115232 DOI: 10.1093/nar/28.24.4964] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Sequencing of the complete genome of Mycobacterium tuberculosis, combined with the rapidly increasing need to improve tuberculosis management through better drugs and vaccines, has initiated extensive research on several key proteins from the pathogen. RecA, a ubiquitous multifunctional protein, is a key component of the processes of homologous genetic recombination and DNA repair. Structural knowledge of MtRecA is imperative for a full understanding of both these activities and any ensuing application. The crystal structure of MtRecA, presented here, has six molecules in the unit cell forming a 6(1) helical filament with a deep groove capable of binding DNA. The observed weakening in the higher order aggregation of filaments into bundles may have implications for recombination in mycobacteria. The structure of the complex reveals the atomic interactions of ADP-AlF(4), an ATP analogue, with the P-loop-containing binding pocket. The structures explain reduced levels of interactions of MtRecA with ATP, despite sharing the same fold, topology and high sequence similarity with EcRecA. The formation of a helical filament with a deep groove appears to be an inherent property of MtRecA. The histidine in loop L1 appears to be positioned appropriately for DNA interaction.
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Affiliation(s)
- S Datta
- Molecular Biophysics Unit, Department of Biochemistry and Bioinformatics Centre, Indian Institute of Science, Bangalore 560 012, India
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43
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Lanes O, Guddal PH, Gjellesvik DR, Willassen NP. Purification and characterization of a cold-adapted uracil-DNA glycosylase from Atlantic cod (Gadus morhua). Comp Biochem Physiol B Biochem Mol Biol 2000; 127:399-410. [PMID: 11126771 DOI: 10.1016/s0305-0491(00)00271-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Uracil-DNA glycosylase (UDG; UNG) has been purified 17000-fold from Atlantic cod liver (Gadus morhua). The enzyme has an apparent molecular mass of 25 kDa, as determined by gel filtration, and an isoelectric point above 9.0. Atlantic cUNG is inhibited by the specific UNG inhibitor (Ugi) from the Bacillus subtilis bacteriophage (PBS2), and has a 2-fold higher activity for single-stranded DNA than for double-stranded DNA. cUNG has an optimum activity between pH 7.0-9.0 and 25-50 mM NaCl, and a temperature optimum of 41 degrees C. Cod UNG was compared with the recombinant human UNG (rhUNG), and was found to have slightly higher relative activity at low temperatures compared with their respective optimum temperatures. Cod UNG is also more pH- and temperature labile than rhUNG. At pH 10.0, the recombinant human UNG had 66% residual activity compared with only 0.4% for the Atlantic cUNG. At 50 degrees C, cUNG had a half-life of 0.5 min compared with 8 min for the rhUNG. These activity and stability experiments reveal cold-adapted features in cUNG.
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Affiliation(s)
- O Lanes
- Department of Biotechnology, Institute of Medical Biology, Faculty of Medicine, University of Tromsø, Norway
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44
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Abstract
Uracil-DNA glycosylase (UDG) functions as a sentry guarding against uracil in DNA. UDG initiates DNA base excision repair (BER) by hydrolyzing the uracil base from the deoxyribose. As one of the best studied DNA glycosylases, a coherent and complete functional mechanism is emerging that combines structural and biochemical results. This functional mechanism addresses the detection of uracil bases within a vast excess of normal DNA, the features of the enzyme that drive catalysis, and coordination of UDG with later steps of BER while preventing the release of toxic intermediates. Many of the solutions that UDG has evolved to overcome the challenges of policing the genome are shared by other DNA glycosylases and DNA repair enzymes, and thus appear to be general.
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Affiliation(s)
- S S Parikh
- Department of Molecular Biology, Skaggs Institute for Chemical Biology, The Scripps Research Institute, MB4, 10550 North Torrey Pines Road, La Jolla, CA 92037-1027, USA
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45
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Sandigursky M, Franklin WA. Uracil-DNA glycosylase in the extreme thermophile Archaeoglobus fulgidus. J Biol Chem 2000; 275:19146-9. [PMID: 10777501 DOI: 10.1074/jbc.m001995200] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Uracil-DNA glycosylase (UDG) is an essential enzyme for maintaining genomic integrity. Here we describe a UDG from the extreme thermophile Archaeoglobus fulgidus. The enzyme is a member of a new class of enzymes found in prokaryotes that is distinct from the UDG enzyme found in Escherichia coli, eukaryotes, and DNA-containing viruses. The A. fulgidus UDG is extremely thermostable, maintaining full activity after heating for 1.5 h at 95 degrees C. The protein is capable of removing uracil from double-stranded DNA containing either a U/A or U/G base pair as well as from single-stranded DNA. This enzyme is product-inhibited by both uracil and apurinic/apyrimidinic sites. The A. fulgidus UDG has a high degree of similarity at the primary amino acid sequence level to the enzyme found in Thermotoga maritima, a thermophilic eubacteria, and suggests a conserved mechanism of UDG-initiated base excision repair in archaea and thermophilic eubacteria.
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Affiliation(s)
- M Sandigursky
- Departments of Radiology and Radiation Oncology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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Purnapatre K, Handa P, Venkatesh J, Varshney U. Differential effects of single-stranded DNA binding proteins (SSBs) on uracil DNA glycosylases (UDGs) from Escherichia coli and mycobacteria. Nucleic Acids Res 1999; 27:3487-92. [PMID: 10446237 PMCID: PMC148591 DOI: 10.1093/nar/27.17.3487] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Deamination of cytosines results in accumulation of uracil residues in DNA, which unless repaired lead to GC-->AT transition mutations. Uracil DNA glyco-sylase excises uracil residues from DNA and initiates the base excision repair pathway to safeguard the genomic integrity. In this study, we have investigated the effect of single-stranded DNA binding proteins (SSBs) from Escherichia coli (Eco SSB) and Mycobacterium tuberculosis (Mtu SSB) on uracil excision from synthetic substrates by uracil DNA glycosylases (UDGs) from E. coli, Mycobacterium smegmatis and M.tuberculosis (referred to as Eco -, Msm - and Mtu UDGs respectively). Presence of SSBs with all the three UDGs resulted in decreased efficiency of uracil excision from a single-stranded 'unstructured' oligonucleo-tide, SS-U9. On the other hand, addition of Eco SSB to Eco UDG, or Mtu SSB to Mtu UDG reactions resulted in increased efficiency of uracil excision from a hairpin oligonucleotide containing dU at the second position in a tetraloop (Loop-U2). Interestingly, the efficiency of uracil excision by Msm UDG from the same substrate was decreased in the presence of either Eco- or Mtu SSBs. Furthermore, Mtu SSB also decreased uracil excision from Loop-U2 by Eco UDG. Our studies using surface plasmon resonance technique demonstrated interactions between the homologous combinations of SSBs and UDGs. Heterologous combinations either did not show detectable interaction (Eco SSB with Mtu UDG) or showed a relatively weaker interaction (Mtu SSB with Eco UDG). Taken together, our studies suggest differential interactions between the two groups (SSBs and UDGs) of the highly conserved proteins. Such studies may provide important clues to design selective inhibitors against this important class of DNA repair enzymes.
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Affiliation(s)
- K Purnapatre
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
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Reddy GB, Purnapatre K, Lawrence R, Roy S, Varshney U, Surolia A. Linear free-energy model description of the conformational stability of uracil-DNA glycosylase inhibitor A thermodynamic characterization of interaction with denaturant and cold denaturation. EUROPEAN JOURNAL OF BIOCHEMISTRY 1999; 261:610-7. [PMID: 10215876 DOI: 10.1046/j.1432-1327.1999.00271.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The equilibrium unfolding of uracil DNA glycosylase inhibitor (Ugi), a small acidic protein of molecular mass 9474 Da, has been studied by a combination of thermal-induced and guanidine hydrochloride (GdnCl)-induced denaturation. The analysis of the denaturation data provides a measure of the changes in conformational free energy, enthalpy, entropy and heat capacity DeltaCp that accompany the equilibrium unfolding of Ugi over a wide range of temperature and GdnCl concentration. The unfolding of Ugi is a simple two-state, reversible process. The protein undergoes both low-temperature and high-temperature unfolding even in the absence of GdnCl but more so in the presence of denaturant. The data are consistent with the linear free-energy model and with a temperature independent DeltaCp over the large temperature range of unfolding. The small DeltaCp (6.52 kJ.mol-1.K-1) for the unfolding of Ugi, is perhaps a reflection of a relatively small, buried hydrophobic core in the folded form of this small monomeric protein. Despite a relatively low value of DeltaG(H2O), 7.40 kJ.mol-1 at pH 8.3, Ugi displays considerable stability with the temperature of maximum stability being 301.6 K.
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Affiliation(s)
- G B Reddy
- Molecular Biophysics Unit, Indian Insitute of Science, Bangalor, India
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