Deep trefoil knot implicated in RNA binding found in an archaebacterial protein

Proteins: Structure, Function and Genetics

Volumn 50, Issue 2, 2003, Pages 177-183

  Zarembinski, Thomas I ^a   Kim, Youngchang ^a   Peterson, Kelly ^a   Christendat, Dinesh ^b   Dharamsi, Akil ^b   Arrowsmith, Cheryl H ^b   Edwards, Aled M ^b   Joachimiak, Andrzej ^a  

^a ARGONNE NATIONAL LABORATORY   (United States)

^b UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; RNA; TREFOIL PEPTIDE;

AMINO TERMINAL SEQUENCE; ARCHAEBACTERIUM; ARTICLE; CARBOXY TERMINAL SEQUENCE; CATALYSIS; CRYSTALLIZATION; GENE; GENE OVEREXPRESSION; MT1 GENE; PRIORITY JOURNAL; RNA BINDING;

AMINO ACID SEQUENCE; ARCHAEAL PROTEINS; BACTERIAL PROTEINS; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; RNA; RNA-BINDING PROTEINS;

ARCHAEA; BACTERIA (MICROORGANISMS); LOTUS; PROKARYOTA;

EID: 0037297693     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10311     Document Type: Article

References (32)

1. Wierenga RK. The TIM-barrel fold: A versatile framework for efficient enzymes. FEBS Lett 2001;492:193-198.
2. Jansen R, Gerstein M. Analysis of the yeast transcriptome with structural and functional categories: Characterizing highly expressed proteins. Nucleic Acids Res 2000;28:1481-1488.
3. Hegyi H, Gerstein M. The relationship between protein structure and function: A comprehensive survey with application to the yeast genome. J Mol Biol 1999;288:147-164.
4. Hennig M, Schlesier B, Dauter Z, Pfeffer S, Betzel C, Höhne WE, Wilson KS. A TIM barrel protein without enzymatic activity? Crystal-structure of narbonin at 1.8 Å resolution. FEBS Lett 1992;306:80-84.
5. Farber GK, Petsko GA. The evolution of α/β enzymes. Trends Biochem Sci 1990;15:228-234.
6. Nagano N, Hutchinson EG, Thornton JM. Barrel structures in proteins: Automatic identification and classification including a sequence analysis of TIM barrels. Protein Sci 1999;8:2072-2084.
7. Taylor WR. A deeply knotted protein structure and how it might fold. Nature 2000;406:916-919.
8. Nureki O, Shirouzu M, Hashimoto K, Ishitani R, Terada T, Tamakoshi M, Oshima T, Chijimatsu M, Takio K, Vassylyev DG, Shibata T, Inoue Y, Kuramitsu S, Yokoyama S. An enzyme with a deep trefoil knot for the active-site architecture. Acta Crystallogr D Biol Crystallogr 2002;58:1129-1137.
9. Takusagawa F, Kamitori K, A real knot in protein. J Am Chem Soc 1996;118:8945-8946.
10. Arndt E, Kromer W, Hatakeyama T. Organization and nucleotide sequence of a gene cluster coding for eight ribosomal proteins in the archaebacterium Halobacterium marismortui. J Biol Chem 1990;265:3034-3039.
11. Walsh MA, Dementieva I, Evans G, Sanishvili R, Joachimiak A. Taking MAD to the extreme: ultrafast protein structure determination. Acta Crystallogr 1999;D55:1168-1173.
12. Otwinowski Z, Minor W. Processing of x-ray diffraction data collected in oscillation mode. Methods Enzymol 1997;276:307326.
13. Miller R, Gallo SM, Khalak HG, Weeks CM. SnB: Crystal structure determination via Shake-and-Bake. J Appl Crystallogr 1994;27:613-621.
14. de la Fortelle E, Bricogne G. Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods. Methods Enzymol 1997;276:472-494.
15. Number 4 Collaborative Computational Project. The CCP4 Suite: Programs for protein crystallography. Acta Crystallogr 1994;D50:760-763.
16. Kleywegt GJ, Jones TA. xdl MAPMAN and xdl DATAMAN - Programs for reformatting, analysis, and manipulation of biomacromolecular electron-density maps and reflection data sets. Acta Crystallogr 1996;D52:826-828.
17. Jones TA, Kjeldgaard M. Electron-density map interpretation. Methods Enzymol 1997;277:173-207.
18. Brünger, AT. CNS, Crystallography and NMR System. Version 0.5. New Haven, CT: Yale University; 1998.
19. Holm L, Sander C. Protein structure comparison by alignment of distance matrices. J Mol Biol 1993;233:123-128.
20. 8-barrel enzyme into two folded halves. Nat Struct Biol 2001;8:32-36.
21. 8-barrel enzymes: A hidden homology? Protein Sci 1996;5:1136-1143.
22. Song H, Parsons MR, Rowsell S, Leonard G, Phillips SEV. Crystal structure of intact elongation factor EF-Tu from Escherichia coli in GDP conformation at 2.05 Å resolution. J Mol Biol 1999;285:1245-1256.
23. Schindelin H, Jiang W, Inouye M, Heinemann U. Crystal structure of CspA, the major cold shock protein of Escherichia coli. Proc Natl Acad Sci USA 1994;91:5119-5123.
24. Nicholls A, Sharp KA, Honig B. Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 1991;11:281-296.
25. Jiang W, Hou Y, Inouye M. CspA, the major cold-shock protein of Escherichia coli, is an RNA chaperone. J Biol Chem 1997;272:196-202.
26. Bae W, Xia B, Inouye M, Severinov K. Escherichia coli CspAfamily RNA chaperones are transcription antiterminators. Proc Natl Acad Sci USA 2000;97:7784-7789.
27. Bycroft M, Hubbard TJP, Proctor M, Freund SMV, Murzin AG. The solution structure of the S1 RNA binding domain: A member of an ancient nucleic acid-binding fold. Cell 1997;88:235-242.
28. Yang H, Jeffrey PD, Miller J, Kinnucan E, Sun Y, Thomä NH, Zheng N, Chen PL, Lee WH, Pavletich NP. BRCA2 function in DNA binding and recombination from a BRCA2-DSS1-ssDNA structure. Science 2002;297:1837-1848.
29. 2+, K+, and pyruvate. Biochemistry 1994;33:6301-6309.
30. Mikami B, Adachi M, Kage T, Sarikaya E, Nanmori T, Shinke R, Utsumi S. Structure of raw starch-digesting Bacillus cereus beta-amylase complexed with maltose. Biochemistry 1999;38:7050-7061.
31. 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.
32. Kraulis JP. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 1991;24:946-950.