Crystal Structure of YbaK Protein from Haemophilus Influenzae (HI1434) at 1.8 Angstrom Resolution: Functional Implications

Published

July 1, 2000

Author(s)

Huan Zhang, K Huang, Z Li, L Banerjei, K E. Fisher, N V. Grishin, Edward Eisenstein, O Herzberg

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 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.

Citation

Proteins-Structure Function And Genetics

Pub Type

Journals

Keywords

c-lectin fold, circular permutation, hypothetical proteins, structural genomics, x-ray crystallography

Citation

Zhang, H. , Huang, K. , Li, Z. , Banerjei, L. , Fisher, K. , Grishin, N. , Eisenstein, E. and Herzberg, O. (2000), Crystal Structure of YbaK Protein from Haemophilus Influenzae (HI1434) at 1.8 Angstrom Resolution: Functional Implications, Proteins-Structure Function And Genetics (Accessed October 14, 2025)