Evaluation and classification of RING-finger domains encoded by the Arabidopsis genome

Genome Biology

Volumn 3, Issue 4, 2002, Pages

  Kosarev, Peter ^a   Mayer, Klaus Fx ^a   Hardtke, Christian S ^b  

^a INSTITUTE OF EPIDEMIOLOGY   (Germany)

^b MCGILL UNIVERSITY   (Canada)

Author keywords

Additional Data File; Additional Domain; Arabidopsis Protein; Metal Ligand; Ring Domain

Indexed keywords

ARABIDOPSIS PROTEIN; PROTEOME;

ARABIDOPSIS; ARTICLE; BIOLOGY; CHEMISTRY; CLASSIFICATION; GENETICS; GENOME; MOLECULAR GENETICS; PROTEIN MOTIF; PROTEIN TERTIARY STRUCTURE; SEQUENCE ANALYSIS;

AMINO ACID MOTIFS; ARABIDOPSIS; ARABIDOPSIS PROTEINS; COMPUTATIONAL BIOLOGY; GENOME, PLANT; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, TERTIARY; PROTEOME; SEQUENCE ANALYSIS, PROTEIN;

EID: 17544404364     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2002-3-4-research0016     Document Type: Article

References (39)

1. The Arabidopsis Genome Initiative: Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000, 408: 796-815. 10.1038/35048692. DOI: 10.1038/35048692
2. Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MD, et al: InterPro - an integrated documentation resource for protein families, domains and functional sites. Bioinformatics. 2000, 16: 1145-1150. 10.1093/bioinformatics/16.12.1145. DOI: 10.1093/bioinformatics/16.12.1145
3. Rubin GM, Yandell MD, Wortman JR, Gabor Miklos GL, Nelson CR, Hariharan IK, Fortini ME, Li PW, Apweiler R, Fleischmann W, et al: Comparative genomics of the eukaryotes. Science. 2000, 287: 2204-2215. 10.1126/science.287.5461.2204. DOI: 10.1126/science.287.5461.2204
4. Freemont PS, Hanson IM, Trowsdale J: A novel cysteine-rich sequence motif. Cell. 1991, 64: 483-484. DOI: 10.1016/0092-8674(91)90229-R
5. Lovering R, Hanson IM, Borden KL, Martin S, O'Reilly NJ, Evan GI, Rahman D, Pappin DJ, Trowsdale J, Freemont PS: Identification and preliminary characterization of a protein motif related to the zinc finger. Proc Natl Acad Sci USA. 1993, 90: 2112-2116. DOI: 10.1073/pnas.90.6.2112
6. Aasland R, Gibson TJ, Stewart AF: The PHD finger: implications for chromatin-mediated transcriptional regulation. Trends Biochem Sci. 1995, 20: 56-59. 10.1016/S0968-0004(00)88957-4. DOI: 10.1016/S0968-0004(00)88957-4
7. Dawid IB, Breen JJ, Toyama R: LIM domains: multiple roles as adapters and functional modifiers in protein interactions. Trends Genet. 1998, 14: 156-162. 10.1016/S0168-9525(98)01424-3. DOI: 10.1016/S0168-9525(98)01424-3
8. Borden KL, Boddy MN, Lally J, O'Reilly NJ, Martin S, Howe K, Solomon E, Freemont PS: The solution structure of the RING finger domain from the acute promyelocytic leukaemia proto-oncoprotein PML. EMBO J. 1995, 14: 1532-1541.
9. Barlow PN, Luisi B, Milner A, Elliott M, Everett R: Structure of the C3HC4 domain by 1H-nuclear magnetic resonance spectroscopy. A new structural class of zinc-finger. J Mol Biol. 1994, 237: 201-211. 10.1006/jmbi.1994.1222. DOI: 10.1006/jmbi.1994.1222
10. Bellon SF, Rodgers KK, Schatz DG, Coleman JE, Steitz TA: Crystal structure of the RAG1 dimerization domain reveals multiple zinc-binding motifs including a novel zinc binuclear cluster. Nat Struct Biol. 1997, 4: 586-591. DOI: 10.1038/nsb0797-586
11. Perez-Alvarado GC, Miles C, Michelsen JW, Louis HA, Winge DR, Beckerle MC, Summers MF: Structure of the carboxy-terminal LIM domain from the cysteine rich protein CRP. Nat Struct Biol. 1994, 1: 388-398. DOI: 10.1038/nsb0694-388
12. Perez-Alvarado GC, Kosa JL, Louis HA, Beckerle MC, Winge DR, Summers MF: Structure of the cysteine-rich intestinal protein, CRIP. J Mol Biol. 1996, 257: 153-174. 10.1006/jmbi.1996.0153. DOI: 10.1006/jmbi.1996.0153
13. Konrat R, Weiskirchen R, Krautler B, Bister K: Solution structure of the carboxyl-terminal LIM domain from quail cysteine-rich protein CRP2. J Biol Chem. 1997, 272: 12001-12007. 10.1074/jbc.272.18.12001. DOI: 10.1074/jbc.272.18.12001
14. Capili AD, Schultz DC, Rauscher FJ, Borden KL: Solution structure of the PHD domain from the KAP-1 corepressor: structural determinants for PHD, RING and LIM zinc-binding domains. EMBO J. 2001, 20: 165-177. 10.1093/emboj/20.1.165. DOI: 10.1093/emboj/20.1.165
15. Peng H, Begg GE, Schultz DC, Friedman JR, Jensen DE, Speicher DW, Rauscher FJ: Reconstitution of the KRAB-KAP-1 repressor complex: a model system for defining the molecular anatomy of RING-B box-coiled-coil domain-mediated protein-protein interactions. J Mol Biol. 2000, 295: 1139-1162. 10.1006/jmbi.1999.3402. DOI: 10.1006/jmbi.1999.3402
16. Kentsis A, Dwyer EC, Perez JM, Sharma M, Chen A, Pan ZQ, Borden KL: The RING domains of the promyelocytic leukemia protein PML and the arenaviral protein Z repress translation by directly inhibiting translation initiation factor eIF4E. J Mol Biol. 2001, 312: 609-623. 10.1006/jmbi.2001.5003. DOI: 10.1006/jmbi.2001.5003
17. Borden KL: RING domains: master builders of molecular scaffolds?. J Mol Biol. 2000, 295: 1103-1112. 10.1006/jmbi.1999.3429. DOI: 10.1006/jmbi.1999.3429
18. Lorick KL, Jensen JP, Fang S, Ong AM, Hatakeyama S, Weissman AM: RING fingers mediate ubiquitin-conjugating enzyme (E2)-dependent ubiquitination. Proc Natl Acad Sci USA. 1999, 96: 11364-11369. 10.1073/pnas.96.20.11364. DOI: 10.1073/pnas.96.20.11364
19. Jackson PK, Eldridge AG, Freed E, Furstenthal L, Hsu JY, Kaiser BK, Reimann JD: The lore of the RINGs: substrate recognition and catalysis by ubiquitin ligases. Trends Cell Biol. 2000, 10: 429-439. 10.1016/S0962-8924(00)01834-1. DOI: 10.1016/S0962-8924(00)01834-1
20. Analysis of RING Finger domain proteins encoded by the Arabidopsis thaliana genome. [http://mips.gsf.de/proj/thal/ring/index.html]
21. Evaluation and classification of RING finger domains encoded by the Arabidopsis thaliana genome. [http://www.mcgill.ca/Biology/faculty/hardtke/ARARINGS/AraRINGindex.html]
22. Gervais V, Busso D, Wasielewski E, Poterszman A, Egly JM, Thierry JC, Kieffer B: Solution structure of the N-terminal domain of the human TFIIH MAT1 subunit: new insights into the RING finger family. J Biol Chem. 2001, 276: 7457-7464. 10.1074/jbc.M007963200. DOI: 10.1074/jbc.M007963200
23. Saurin AJ, Borden KL, Boddy MN, Freemont PS: Does this have a familiar RING?. Trends Biochem Sci. 1996, 21: 208-214. 10.1016/0968-0004(96)10036-0. DOI: 10.1016/S0968-0004(96)80017-X
24. Azevedo C, Santos-Rosa MJ, Shirasu K: The U-box protein family in plants. Trends Plant Sci. 2001, 6: 354-358. 10.1016/S1360-1385(01)01960-4. DOI: 10.1016/S1360-1385(01)01960-4
25. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol. 1990, 215: 403-410. 10.1006/jmbi.1990.9999. DOI: 10.1016/S0022-2836(05)80360-2
26. Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22: 4673-4680. DOI: 10.1093/nar/22.22.4673
27. Jensen RB, Jensen KL, Jespersen HM, Skriver K: Widespread occurrence of a highly conserved RING-H2 zinc finger motif in the model plant Arabidopsis thaliana. FEBS Lett. 1998, 436: 283-287. 10.1016/S0014-5793(98)01143-0. DOI: 10.1016/S0014-5793(98)01143-0
28. Salinas-Mondragon RE, Garciduenas-Pina C, Guzman P: Early elicitor induction in members of a novel multigene family coding for highly related RING-H2 proteins in Arabidopsis thaliana. Plant Mol Biol. 1999, 40: 579-590. 10.1023/A:1006267201855. DOI: 10.1023/A:1006267201855
29. Matsuda N, Suzuki T, Tanaka K, Nakano A: Rma1, a novel type of RING finger protein conserved from Arabidopsis to human, is a membrane-bound ubiquitin ligase. J Cell Sci. 2001, 114: 1949-1957.
30. Kurup S, Jones HD, Holdsworth MJ: Interactions of the developmental regulator ABI3 with proteins identified from developing Arabidopsis seeds. Plant J. 2000, 21: 143-155. 10.1046/j.1365-313x.2000.00663.x. DOI: 10.1046/j.1365-313x.2000.00663.x
31. Torii KU, Stoop-Myer CD, Okamoto H, Coleman JE, Matsui M, Deng XW: The RING finger motif of photomorphogenic repressor COP1 specifically interacts with the RING-H2 motif of a novel Arabidopsis protein. J Biol Chem. 1999, 274: 27674-27681. 10.1074/jbc.274.39.27674. DOI: 10.1074/jbc.274.39.27674
32. Hardtke CS, Okamoto H, Stoop-Myer C, Deng XW: Biochemical evidence for ubiquitin ligase activity of the Arabidopsis COP1 interacting protein 8 (CIP8). Plant J. 2002,
33. Bouche N, Bouchez D: Arabidopsis gene knockout: phenotypes wanted. Curr Opin Plant Biol. 2001, 4: 111-117. 10.1016/S1369-5266(00)00145-X. DOI: 10.1016/S1369-5266(00)00145-X
34. Deng XW, Matsui M, Wei N, Wagner D, Chu AM, Feldmann KA, Quail PH: COP1, an Arabidopsis regulatory gene, encodes a protein with both a zinc-binding motif and a G beta homologous domain. Cell. 1992, 71: 791-801. DOI: 10.1016/0092-8674(92)90555-Q
35. Potuschak T, Stary S, Schlogelhofer P, Becker F, Nejinskaia V, Bachmair A: PRT1 of Arabidopsis thaliana encodes a component of the plant N-end rule pathway. Proc Natl Acad Sci USA. 1998, 95: 7904-7908. 10.1073/pnas.95.14.7904. DOI: 10.1073/pnas.95.14.7904
36. Lee H, Xiong L, Gong Z, Ishitani M, Stevenson B, Zhu JK: The Arabidopsis HOS1 gene negatively regulates cold signal transduction and encodes a RING finger protein that displays cold-regulated nucleo-cytoplasmic partitioning. Genes Dev. 2001, 15: 912-924. 10.1101/gad.866801. DOI: 10.1101/gad.866801
37. MIPS Arabidopsis thaliana genome project. [http://mips.gsf.de/proj/thal]
38. ClustalW. [http://www.ebi.ac.uk/clustalw/]
39. Osterlund MT, Hardtke CS, Wei N, Deng XW: Targeted destabilization of HY5 during light-regulated development of Arabidopsis. Nature. 2000, 405: 462-466. 10.1038/35013076. DOI: 10.1038/35013076