TY - JOUR
T1 - Crystal structure of YbaK protein from Haemophilus influenzae (HI1434) at 1.8 Å resolution
T2 - Functional implications
AU - Zhang, Hong
AU - Huang, Kui
AU - Li, Zhong
AU - Banerjei, Linda
AU - Fisher, Kathryn E.
AU - Grishin, Nick V.
AU - Eisenstein, Edward
AU - Herzberg, Osnat
N1 - Copyright:
Copyright 2007 Elsevier B.V., All rights reserved.
PY - 2000/7/1
Y1 - 2000/7/1
N2 - 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. (C) 2000 Wiley-Liss, Inc.
AB - 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. (C) 2000 Wiley-Liss, Inc.
KW - C-lectin fold
KW - Circular permutation
KW - Hypothetical proteins
KW - Structural genomics
KW - X-ray crystallography
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U2 - 10.1002/(SICI)1097-0134(20000701)40:1<86::AID-PROT100>3.0.CO;2-Y
DO - 10.1002/(SICI)1097-0134(20000701)40:1<86::AID-PROT100>3.0.CO;2-Y
M3 - Article
C2 - 10813833
AN - SCOPUS:0034237733
SN - 0887-3585
VL - 40
SP - 86
EP - 97
JO - Proteins: Structure, Function and Genetics
JF - Proteins: Structure, Function and Genetics
IS - 1
ER -