Crystal structure of YbaK protein from Haemophilus influenzae (HI1434) at 1.8 Å resolution: Functional implications

Proteins: Structure, Function and Genetics

Volumn 40, Issue 1, 2000, Pages 86-97

  Zhang, Hong ^a   Huang, Kui ^a   Li, Zhong ^a   Banerjei, Linda ^b   Fisher, Kathryn E ^a   Grishin, Nick V ^c   Eisenstein, Edward ^a,d,e   Herzberg, Osnat ^a  

^a UNIVERSITY OF MARYLAND BIOTECHNOLOGY INSTITUTE   (United States)

^b J CRAIG VENTER INSTITUTE   (United States)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

^d UNIVERSITY OF MARYLAND BALTIMORE COUNTY   (United States)

^e NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY   (United States)

Author keywords

C lectin fold; Circular permutation; Hypothetical proteins; Structural genomics; X ray crystallography

Indexed keywords

BACTERIAL PROTEIN; CARBOHYDRATE BINDING PROTEIN; ENDOSTATIN; LECTIN; LYSINE; NUCLEOTIDE; OLIGONUCLEOTIDE; PROLINE TRANSFER RNA; SYNTHETASE;

ARTICLE; BINDING SITE; CONTROLLED STUDY; CRYSTAL STRUCTURE; HAEMOPHILUS INFLUENZAE; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; AMINO ACYL-TRNA SYNTHETASES; BACTERIAL PROTEINS; CARRIER PROTEINS; CRYSTALLOGRAPHY, X-RAY; HAEMOPHILUS INFLUENZAE; LECTINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; SEQUENCE HOMOLOGY, AMINO ACID;

BACTERIA (MICROORGANISMS); HAEMOPHILUS INFLUENZAE; PROKARYOTA;

EID: 0034237733     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(20000701)40:1<86::AID-PROT100>3.0.CO;2-Y     Document Type: Article

References (58)

1. Fleischmann RD, Adams MD, White O, et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 1995;269:496-512.
2. Jancarik J, Kim S-H. Sparse matrix sampling: a screening method for crystallization of proteins. J Appl Crystallogr 1991;24:409-411.
3. Hendrickson WA. Determination of macromolecular structures from anomalous diffraction of synchrotron radiation. Science 1991;254:51-58.
4. Smith JL. Determination of three-dimensional structure by multiwavelength anomalous diffraction. Curr Opin Struct Biol 1991;1: 1002-1011.
5. Terwilliger TC, Berendzen J. Automated MAD and MIR structure solution. Acta Crystallogr D 1999;55:849-861.
6. Lamzin VS, Wilson KS. Automated refinement of protein models. Acta Crystallogr D 1993;49:129-149.
7. Perrakis A, Morris R, Lamzin VS. Automated protein model building combined with iterative structure refinement. Nat Struct Biol 1999;6:458-463.
8. Brünger AT, Adams PD, Clore GM, et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D 1998;54:905-921.
9. Hwang KY, Chung JH, Kim SH, Han YS, Cho Y. Structure-based identification of a novel NTPase from Methanococcus jannaschii. Nat Struct Biol 1999;6:691-696.
10. Colovos C, Cascio D, Yeates TO. The 1.8 Å crystal structure of the ycaC gene product from Escherichia coli reveals an octameric hydrolase of unknown specificity. Structure 1998;6:1329-1337.
11. Zarembinski TI, Hung LW, Mueller-Dieckmann HJ, et al. Structure-based assignment of the biochemical function of a hypothetical protein: a test case of structural genomics. Proc Natl Acad Sci USA 1998;95:15189-15193.
12. Eswaramoorthy S, Kycia H, Gerchman S, Graziano V, Studier W, Swaminathan S. Crystal structure of a yeast hypothetical protein. (PDB code 1b54). 1999.
13. Kasuya A, Thornton JM. Three-dimensional structure analysis of PROSITE patterns. J Mol Biol 1999;286:1673-1691.
14. Casari G, Andrade MA, Bork P, et al. Challenging times for bioinformatics. Nature 1995;376:647-648.
15. Tatusov RL, Mushegian AR, Bork P, et al. Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli. Curr Biol 1996;6:279-291.
16. 0) in Salmonella typhimurium. J Mol Biol 1986;192:163-175.
17. Bensing BA, Dunny GM. Cloning and molecular analysis of genes affecting expression of binding substance, the recipient-encoded receptor(s) mediating mating aggregate formation in Enterococcus faecalis. J Bacteriol 1993;175:7421-7429.
18. Messerschmidt A, Pflugrath JW. Crystal orientaion and X-ray pattern prediction routines for area detector diffractometer system in macromolecular crystallography. J Appl Crystallogr 1987; 20:306-315.
19. Sweet RM, Skinner J. An integrated graphical user interface for synchrotron beamline control and data collection. In: American Crystallographic Association Annual Meeting Abstracts; 1995. p 42.
20. Otwinowski Z, Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 1997;276:307-326.
21. Ramakrishnan V, Biou V. Treatment of multiwavelength anomalous diffraction data as a special case of multiple isomorphous replacement. Methods Enzymol 1997;276:538-557.
22. 4 CCPN. The CCP4 Suite: programs for protein crystallography. Acta Crystallogr D 1994;50:760-763.
23. Otwinowski Z. Maximum likelihood refinement of heavy atom parameters. In: Wolf W, Evans PR, Leslie AGW, editors. Isomorphous replacement and anomalous scattering. Warrington, UK: Daresbury Laboratory; 1991. p 80-86.
24. Cowtan K. "DM": an automated procedure for phase improvement by density modification. Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography 1994;31:34-38.
25. Jones TA, Zou J-Y, Cowan SW, Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A 1991;47:110-119.
26. Murshudov GN, Vagin AA, Dodson EJ. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D 1997;53:240-255.
27. Brünger AT. Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 1992;355:472-475.
28. Navaza J. AMoRe: an automated package for molecular replacement. Acta Crystallogr A 1994;50:157-163.
29. Altschul SF, Madden TL, Schaffer AA, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25:3389-3402.
30. 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.
31. Perrakis A, Sixma TK, Wilson KS, Lamzin VS. wARP: improvement and extension of crystallographic phases by weighted averaging of multiple refined dummy atomic models. Acta Crystallogr D 1997;53:448-455.
32. Holm L, Sander C. Dali: a network tool for protein structure comparison. Trends Biochem Sci 1995;20:478-480.
33. Gibrat JF, Madej T, Bryant SH. Surprising similarities in structure comparison. Curr Opin Struct Biol 1996;6:377-385.
34. Murzin AG. Structure classification-based assessment of CASP3 predictions for the fold recognition targets. Proteins 1999;Supp 3:88-103.
35. Hohenester E, Sasaki T, Olsen BR, Timpl R. Crystal structure of the angiogenesis inhibitor endostatin at 1.5 Å resolution. EMBO J 1998;17:1656-1664.
36. Ding YH, Javaherian K, Lo KM, et al. Zinc-dependent dimers observed in crystals of human endostatin. Proc Natl Acad Sci USA 1998;95:10443-10448.
37. Boehm T, Folkman J, Browder T, O'Reilly MS. Antiangiogenic therapy of experimental cancer does not induce acquired drug resistance. Nature 1997;390:404-407.
38. O'Reilly MS, Boehm T, Shing Y, et al. Endostatin: an endogenous inhibitor of angiogenesis and tumor growth. Cell 1997;88:277-285.
39. Carrington DM, Auffret A, Hanke DE. Polypeptide ligation occurs during post-translational modification of concanavalin A. Nature 1985;313:64-67.
40. Brown KJ, Parish CR. Histidine-rich glycoprotein and platelet factor 4 mask heparan sulfate proteoglycans recognized by acidic and basic fibroblast growth factor. Biochemistry 1994;33:13918-13927.
41. Lobsanov YD, Gitt MA, Leffler H, Barondes SH, Rini JM. X-ray crystal structure of the human dimeric S-Lac lectin, L-14-II, in complex with lactose at 2.9-Å resolution. J Biol Chem 1993;268: 27034-27038.
42. Liao DI, Kapadia G, Ahmed H, Vasta GR, Herzberg O. Structure of S-lectin, a developmentally regulated vertebrate β-galactoside-binding protein. Proc Natl Acad Sci USA 1994;91: 1428-1432.
43. Emsley J, White HE, O'Hara BP, et al. Structure of pentameric human serum amyloid P component. Nature 1994;367:338-345.
44. Vyas NK. Atomic features of protein-carbohydrate interactions. Curr Opin Struct Biol 1991;1:732-740.
45. Burns DM, Burger MJ, Beacham IR. Silent genes in bacteria: the previously designated "cryptic" ilvHI locus of "Salmonella typhimurium LT2" is active in natural isolates. FEMS Microbiol Lett 1995;131:167-172.
46. Eriani G, Delarue M, Poch O, Gangloff J, Moras D. Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature 1990;347:203-206.
47. Wolf YI, Aravind L, Grishin NV, Koonin EV. Evolution of aminoacyl-tRNA synthetases-analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res 1999;9:689-710.
48. Kunst F, Ogasawara N, Moszer I, et al. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 1997;390:249-256.
49. Pro. Biochemistry 1998;37:8605-8613.
50. Pro identity. Nucleic Acids Res 1994;22:522-529.
51. Ruff M, Krishnaswamy S, Boeglin M, et al. Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNA(Asp). Science 1991;252: 1682-1689.
52. Sankaranarayanan R, Dock-Bregeon AC, Romby P, et al. The structure of threonyl-tRNA synthetase-tRNA(Thr) complex enlightens its repressor activity and reveals an essential zinc ion in the active site. Cell 1999;97:371-381.
53. Fersht AR. Enzymic editing mechanisms and the genetic code. Proc R Soc Lond B Biol Sci 1981;212:351-379.
54. Murzin AG. OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences. EMBO J 1993;12:861-867.
55. Kraulis PJ. Molscript: a program to produce both detailed and schematic plots structures. J Appl Crystallogr 1991;24:946-950.
56. Nicholls A. GRASP: graphical representation and analysis of surface properties. NY: Columbia University; 1992.
57. Mizuno H, Fujimoto Z, Koizumi M, Kano H, Atoda H, Morita T. Structure of coagulation factors IX/X-binding protein, a heterodimer of C-type lectin domains. Nat Struct Biol 1997;4:438-441.
58. Rost B, Sander C, Schneider R. PHD - an automatic mail server for protein secondary structure prediction. Comput Appl Biosci 1994;10:53-60.