M. tuberculosis sliding β-clamp does not interact directly with the NAD + -dependent DNA ligase

PLoS ONE

Volumn 7, Issue 4, 2012, Pages

  Kukshal, Vandna ^a   Khanam, Taran ^a   Chopra, Deepti ^a   Singh, Nidhi ^a   Sanyal, Sabyasachi ^a   Ramachandran, Ravishankar ^a  

^a CENTRAL DRUG RESEARCH INSTITUTE   (India)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; BACTERIAL PROTEIN; DIMER; DOUBLE STRANDED DNA; MONOMER; POLYDEOXYRIBONUCLEOTIDE SYNTHASE; SLIDING BETA CLAMP; UNCLASSIFIED DRUG; BETA SUBUNIT, DNA POLYMERASE III; DNA DIRECTED DNA POLYMERASE GAMMA; ESCHERICHIA COLI PROTEIN; POLYDEOXYRIBONUCLEOTIDE SYNTHASE (NAD);

ARTICLE; BINDING AFFINITY; CONTROLLED STUDY; CRYSTAL STRUCTURE; CRYSTALLIZATION; ESCHERICHIA COLI; IN VITRO STUDY; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PROTEIN DNA BINDING; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; CHEMICAL STRUCTURE; CHEMISTRY; ENZYMOLOGY; METABOLISM; PROTEIN MULTIMERIZATION; PROTEIN TERTIARY STRUCTURE; X RAY CRYSTALLOGRAPHY;

BACTERIAL PROTEINS; CRYSTALLOGRAPHY, X-RAY; DNA LIGASES; DNA POLYMERASE III; DNA, BACTERIAL; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; MODELS, MOLECULAR; MYCOBACTERIUM TUBERCULOSIS; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, TERTIARY;

EID: 84860132773     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0035702     Document Type: Article

References (34)

1. Kong XP, Onrust R, O'Donnell M, Kuriyan J, (1992) Three-dimensional structure of the beta subunit of E. coli DNA polymerase III holoenzyme: a sliding DNA clamp. Cell 69: 425-437.
2. Georgescu RE, Kim SS, Yurieva O, Kuriyan J, Kong XP, et al. (2008a) Structure of a sliding clamp on DNA. Cell 132: 43-54.
3. Hingorani MM, O'Donnell M, (1998) ATP binding to the Escherichia coli clamp loader powers opening of the ring-shaped clamp of DNA polymerase III holoenzyme. J Biol Chem 273: 24550-24563.
4. Matsumiya S, Ishino Y, Morikawa K, (2001) Crystal structure of an archaeal DNA sliding clamp: proliferating cell nuclear antigen from Pyrococcus furiosus, Prot Sci 10: 17-23.
5. Lopez de Saro FJ, O'Donnell M, (2001) Interaction of the β sliding clamp with MutS, ligase, and DNA polymerase I. Proc Natl Acad Sci USA 98: 8376-8380.
6. Levin DS, McKenna AE, Motycka TA, Matsumoto Y, Tomkinson AE, (2000) Interaction between PCNA and DNA ligase I is critical for joining of Okazaki fragments and long-patch base-excision repair. Curr Biol 10: 919-22.
7. Gomes XV, Burgers PM, (2000) Two modes of FEN1 binding to PCNA regulated by DNA. EMBO 19: 3811-3821.
8. Pascal JM, Tsodikov OV, Hura GL, Song W, Cotner EA, et al. (2006) Flexible Interface between DNA Ligase and PCNA Supports Conformational Switching and Efficient Ligation of DNA. Molecular cell 24: 279-291.
9. Argiriadi MA, Goedken ER, Bruck I, O'Donnell M, Kuriyan J, (2006) Crystal structure of a DNA polymerase sliding clamp from a Gram-positive bacterium. BMC Struct Biol 6: 2.
10. Georgescu RE, Yurieva O, Kim SS, Kuriyan J, Kong XP, et al. (2008b) Structure of a small-molecule inhibitor of a DNA polymerase sliding clamp. Proc Natl Acad Sci USA 105: 11116-11121.
11. Srivastava SK, Dube D, Kukshal V, Jha AK, Hajela K, et al. (2007) NAD+-dependent DNA ligase (Rv3014c) from Mycobacterium tuberculosis: Novel structure-function relationship and identification of a specific inhibitor. PROTEINS 69: 97-111.
12. Srivastava SK, Dube D, Tewari N, Dwivedi N, Tripathi RP, et al. (2005a) Mycobacterium tuberculosis NAD+-dependent DNA ligase is selectively inhibited by glycosylamines compared with human DNA ligase I. Nucl Acids Res 33: 7090-7101.
13. Srivastava SK, Tripathi RP, Ramachandran R, (2005b) NAD+-dependent DNA Ligase (Rv3014c) from Mycobacterium tuberculosis. Crystal structure of the adenylation domain and identification of novel inhibitors. J Biol Chem 280: 30273-30281.
14. Lopez de Saro FJ, Georgescu RE, Goodman MF, O'Donnell M, (2003) Competitive processivity-clamp usage by DNA polymerases during DNA replication and repair. EMBO 22: 6408-6418.
15. Tom S, Henricksen LA, Park MS, Bambara RA, (2001) DNA ligase I and proliferating cell nuclear antigen form a functional complex. J Biol Chem 276: 24817-24825.
16. Gui WJ, Lin SQ, Chen YY, Zhang XE, Bi LJ, et al. (2011) Crystal structure of DNA polymerase III beta sliding clamp from Mycobacterium tuberculosis. Biochem Biophys Res Comm 405: 272-277.
17. Krissinel E, Henrick K, (2007) Inference of macromolecular assemblies from crystalline state. J Mol Biol 372: 774-797.
18. Johnson A, O'Donnell M, (2005) Cellular DNA replicases: components and dynamics at the replication fork. Ann Rev Biochem 74: 283-315.
19. Kurz M, Dalrymple B, Wijffels G, Kongsuwan K, (2004) Interaction of the sliding clamp beta-subunit and Hda, a DnaA-related protein. J Bacteriol 186: 3508-3515.
20. Wijffels G, Dalrymple BP, Prosselkov P, Kongsuwan K, Epa VC, et al. (2004) Inhibition of protein interactions with the beta 2 sliding clamp of Escherichia coli DNA polymerase III by peptides from beta 2-binding proteins. Biochemistry 43: 5661-5671.
21. Jeruzalmi D, Yurieva O, Zhao Y, Young M, Stewart J, et al. (2001b) Mechanism of processivity clamp opening by the delta subunit wrench of the clamp loader complex of E. coli DNA polymerase III. Cell 106: 417-428.
22. Burnouf DY, Olieric V, Wagner J, Fujii S, Reinbolt J, et al. (2004) Structural and biochemical analysis of sliding clamp/ligand interactions suggest a competition between replicative and translesion DNA polymerases. J Mol Biol 335: 1187.
23. Weller GR, Kysela B, Roy R, Tonkin LM, Scanlan E, et al. (2002) Identification of a DNA nonhomologous end-joining complex in bacteria. Science 297: 1686-1689.
24. Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, et al. (1998) Nature 393: 537-544.
25. Aniukwu J, Glickman MS, Shuman S, (2008) The pathways and outcomes of mycobacterial NHEJ depend on the structure of the broken DNA ends. Genes & Dev 22: 512-527.
26. Gong C, Martins A, Bongiorno P, Glickman M, Shuman S, (2004) Biochemical and genetic analysis of the four DNA ligases of mycobacteria. J Biol Chem 279: 20594-20606.
27. Collaborative Computing Project No. 4 (1994) Acta Cryst D50: 760-763.
28. McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, et al. (2007) Phaser crystallographic software. J App Cryst 40: 658-674.
29. Murshudov GN, Vagin AA, Dodson EJ, (1997) Application of Maximum Likelihood Refinement. Acta Cryst 53: 240-255.
30. Emsley P, Cowtan K, (2004) Coot: model-building tools for molecular graphics. Acta Cryst 60: 2126-2132.
31. Laskowski RA, Moss DS, Thornton JM, (1993) Main-chain bond lengths and bond angles in protein structures. J Mol Biol 231: 1049-1067.
32. Potterton E, McNicholas S, Krissinel E, Cowtan K, Noble M, (2002) The CCP4 molecular-graphics project. Acta Cryst 58: 1955-1957.
33. DeLano WL, (2002) The PyMol Molecular Graphics System DeLano Scientific, San Carlos, CA, USA.
34. Lopez de Saro FJ, Georgescu RE, Goodman MF, O'Donnell M, (2003) Competitive processivity-clamp usage by DNA polymerases during DNA replication and repair. EMBO 22: 6408-6418.