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PDBsum entry 1jal

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protein Protein-protein interface(s) links
Structural genomics, unknown function PDB id
1jal
Jmol
Contents
Protein chains
348 a.a. *
Waters ×484
* Residue conservation analysis
PDB id:
1jal
Name: Structural genomics, unknown function
Title: Ychf protein (hi0393)
Structure: Ychf protein. Chain: a, b. Synonym: hi0393, probable gtp-binding protein hi0393. Engineered: yes
Source: Haemophilus influenzae. Organism_taxid: 727. Gene: ychf. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.40Å     R-factor:   0.208     R-free:   0.247
Authors: A.Teplyakov,G.L.Gilliland,Structure 2 Function Project (S2f)
Key ref: A.Teplyakov et al. (2003). Crystal structure of the YchF protein reveals binding sites for GTP and nucleic acid. J Bacteriol, 185, 4031-4037. PubMed id: 12837776
Date:
30-May-01     Release date:   25-Mar-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P44681  (ENGD_HAEIN) -  Ribosome-binding ATPase YchF
Seq:
Struc:
363 a.a.
348 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     ATP catabolic process   1 term 
  Biochemical function     nucleotide binding     7 terms  

 

 
J Bacteriol 185:4031-4037 (2003)
PubMed id: 12837776  
 
 
Crystal structure of the YchF protein reveals binding sites for GTP and nucleic acid.
A.Teplyakov, G.Obmolova, S.Y.Chu, J.Toedt, E.Eisenstein, A.J.Howard, G.L.Gilliland.
 
  ABSTRACT  
 
The bacterial protein encoded by the gene ychF is 1 of 11 universally conserved GTPases and the only one whose function is unknown. The crystal structure determination of YchF was sought to help with the functional assignment of the protein. The YchF protein from Haemophilus influenzae was cloned and expressed, and the crystal structure was determined at 2.4 A resolution. The polypeptide chain is folded into three domains. The N-terminal domain has a mononucleotide binding fold typical for the P-loop NTPases. An 80-residue domain next to it has a pronounced alpha-helical coiled coil. The C-terminal domain features a six-stranded half-barrel that curves around an alpha-helix. The crablike three-domain structure of YchF suggests the binding site for a double-stranded nucleic acid in the cleft between the domains. The structure of the putative GTP-binding site is consistent with the postulated guanine specificity of the protein. Fluorescence measurements have demonstrated the ability of YchF to bind a double-stranded nucleic acid and GTP. Taken together with other experimental data and genomic analysis, these results suggest that YchF may be part of a nucleoprotein complex and may function as a GTP-dependent translation factor.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21265745 F.Blombach, S.J.Brouns, and J.van der Oost (2011).
Assembling the archaeal ribosome: roles for translation-factor-related GTPases.
  Biochem Soc Trans, 39, 45-50.  
20217845 L.Delaye, and A.Moya (2010).
Evolution of reduced prokaryotic genomes and the minimal cell concept: variations on a theme.
  Bioessays, 32, 281-287.  
18423011 J.Fernebro, C.Blomberg, E.Morfeldt, H.Wolf-Watz, S.Normark, and B.H.Normark (2008).
The influence of in vitro fitness defects on pneumococcal ability to colonize and to cause invasive disease.
  BMC Microbiol, 8, 65.  
16890423 D.J.Rigden (2006).
Understanding the cell in terms of structure and function: insights from structural genomics.
  Curr Opin Biotechnol, 17, 457-464.  
16333325 E.D.Brown (2005).
Conserved P-loop GTPases of unknown function in bacteria: an emerging and vital ensemble in bacterial physiology.
  Biochem Cell Biol, 83, 738-746.  
15036155 A.F.Yakunin, A.A.Yee, A.Savchenko, A.M.Edwards, and C.H.Arrowsmith (2004).
Structural proteomics: a tool for genome annotation.
  Curr Opin Chem Biol, 8, 42-48.  
15479782 M.Y.Galperin, and E.V.Koonin (2004).
'Conserved hypothetical' proteins: prioritization of targets for experimental study.
  Nucleic Acids Res, 32, 5452-5463.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.