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

Proteins. 2000 Jul 1;40(1):86-97. doi: 10.1002/(sici)1097-0134(20000701)40:1<86::aid-prot100>;2-y.


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.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Amino Acyl-tRNA Synthetases / chemistry
  • Bacterial Proteins*
  • Carbon-Oxygen Lyases
  • Carrier Proteins / chemistry*
  • Carrier Proteins / isolation & purification
  • Crystallography, X-Ray
  • Haemophilus influenzae / chemistry*
  • Lectins / chemistry
  • Models, Molecular
  • Molecular Sequence Data
  • Protein Folding
  • Protein Structure, Tertiary
  • Sequence Homology, Amino Acid


  • Bacterial Proteins
  • Carrier Proteins
  • Lectins
  • Carbon-Oxygen Lyases
  • HI1434 protein, Haemophilus influenzae
  • Amino Acyl-tRNA Synthetases
  • prolyl T RNA synthetase

Associated data

  • PDB/1DBU
  • PDB/1DBX