1DBU

Crystal structure of cysteinyl-tRNA(Pro) deacylase protein from H. influenzae (HI1434)

Summary for 1DBU

• Entry DOI: 10.2210/pdb1dbu/pdb
• Related: 1DBX
• Descriptor: cysteinyl-tRNA(Pro) deacylase, MERCURY (II) ION (3 entities in total)
• Functional Keywords: structural genomics, ybak, structure 2 function project, s2f, hydrolase
• Biological source: Haemophilus influenzae
• Total number of polymer chains: 1
• Total formula weight: 17474.20

Authors

Zhang, H.,Huang, K.,Li, Z.,Herzberg, O.,Structure 2 Function Project (S2F) (deposition date: 1999-11-03, release date: 2000-06-14, Last modification date: 2024-11-13)

Primary citation

Zhang, H.,Huang, K.,Li, Z.,Banerjei, L.,Fisher, K.E.,Grishin, N.V.,Eisenstein, E.,Herzberg, O.
Crystal structure of YbaK protein from Haemophilus influenzae (HI1434) at 1.8 A resolution: functional implications.
Proteins, 40:86-97, 2000

PubMed 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 A 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.

PubMed: 10813833
DOI: 10.1002/(SICI)1097-0134(20000701)40:1<86::AID-PROT100>3.0.CO;2-Y

Experimental method

X-RAY DIFFRACTION (1.8 Å)