Crystal structure of YbaK protein fromHaemophilus influenzae (HI1434) at 1.8 ? resolution: Functional implications
2000; Wiley; Volume: 40; Issue: 1 Linguagem: Inglês
10.1002/(sici)1097-0134(20000701)40
ISSN1097-0134
AutoresHong Zhang, Kui Huang, Zhong Li, Linda Banerjei, Kathryn E. Fisher, Nick V. Grishin, Edward Eisenstein, Osnat Herzberg,
Tópico(s)Enzyme Structure and Function
ResumoProteins: Structure, Function, and BioinformaticsVolume 40, Issue 1 p. 86-97 Research Article Crystal structure of YbaK protein from Haemophilus influenzae (HI1434) at 1.8 Å resolution: Functional implications Hong Zhang, Hong Zhang Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, MarylandSearch for more papers by this authorKui Huang, Kui Huang Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, MarylandSearch for more papers by this authorZhong Li, Zhong Li Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, MarylandSearch for more papers by this authorLinda Banerjei, Linda Banerjei The Institute for Genomic Research, Rockville, MarylandSearch for more papers by this authorKathryn E. Fisher, Kathryn E. Fisher Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, MarylandSearch for more papers by this authorNick V. Grishin, Nick V. Grishin National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MarylandSearch for more papers by this authorEdward Eisenstein, Edward Eisenstein Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, Maryland The National Institute of Standard and Technology, Gaithersburg, MarylandSearch for more papers by this authorOsnat Herzberg, Corresponding Author Osnat Herzberg osnat@carb.nist.gov Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, MarylandCenter for Advanced Research in Biotechnology and University of Maryland Biotechnology Institute, 9600 Gudelsky Dr., Rockville MD 20850===Search for more papers by this author Hong Zhang, Hong Zhang Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, MarylandSearch for more papers by this authorKui Huang, Kui Huang Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, MarylandSearch for more papers by this authorZhong Li, Zhong Li Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, MarylandSearch for more papers by this authorLinda Banerjei, Linda Banerjei The Institute for Genomic Research, Rockville, MarylandSearch for more papers by this authorKathryn E. Fisher, Kathryn E. Fisher Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, MarylandSearch for more papers by this authorNick V. Grishin, Nick V. Grishin National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MarylandSearch for more papers by this authorEdward Eisenstein, Edward Eisenstein Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, Maryland The National Institute of Standard and Technology, Gaithersburg, MarylandSearch for more papers by this authorOsnat Herzberg, Corresponding Author Osnat Herzberg osnat@carb.nist.gov Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, MarylandCenter for Advanced Research in Biotechnology and University of Maryland Biotechnology Institute, 9600 Gudelsky Dr., Rockville MD 20850===Search for more papers by this author First published: 11 May 2000 https://doi.org/10.1002/(SICI)1097-0134(20000701)40:1 3.0.CO;2-YCitations: 39Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Abstract Structural genomics of proteins of unknown function most straightforwardly assists with assignment of biochemical activity when the new structure resembles that of proteins whose functions are known. When a new fold is revealed, the universe of known folds is enriched, and once the function is determined by other means, novel structure-function relationships are established. The previously unannotated protein HI1434 from H. influenzae provides a hybrid example of these two paradigms. It is a member of a microbial protein family, labeled in SwissProt as YbaK and ebsC. The crystal structure at 1.8 Å resolution reported here reveals a fold that is only remotely related to the C-lectin fold, in particular to endostatin, and thus is not sufficiently similar to imply that YbaK proteins are saccharide binding proteins. However, a crevice that may accommodate a small ligand is evident. The putative binding site contains only one invariant residue, Lys46, which carries a functional group that could play a role in catalysis, indicating that YbaK is probably not an enzyme. Detailed sequence analysis, including a number of newly sequenced microbial organisms, highlights sequence homology to an insertion domain in prolyl-tRNA synthetases (proRS) from prokaryote, a domain whose function is unknown. A HI1434-based model of the insertion domain shows that it should also contain the putative binding site. Being part of a tRNA synthetases, the insertion domain is likely to be involved in oligonucleotide binding, with possible roles in recognition/discrimination or editing of prolyl-tRNA. By analogy, YbaK may also play a role in nucleotide or oligonucleotide binding, the nature of which is yet to be determined. Proteins 2000;40:86–97. © 2000 Wiley-Liss, Inc. Citing Literature Volume40, Issue11 July 2000Pages 86-97 RelatedInformation
Referência(s)