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PDBsum entry 2hz7

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protein links
Ligase PDB id
2hz7
Jmol
Contents
Protein chain
556 a.a. *
Waters ×160
* Residue conservation analysis
PDB id:
2hz7
Name: Ligase
Title: Crystal structure of the glutaminyl-tRNA synthetase from deinococcus radiodurans
Structure: Glutaminyl-tRNA synthetase. Chain: a. Synonym: glutamine-tRNA ligase, glnrs. Engineered: yes
Source: Deinococcus radiodurans. Organism_taxid: 1299. Gene: glns. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.30Å     R-factor:   0.200     R-free:   0.242
Authors: M.Deniziak,C.Sauter,H.D.Becker,C.Paulus,R.Giege,D.Kern
Key ref: M.Deniziak et al. (2007). Deinococcus glutaminyl-tRNA synthetase is a chimer between proteins from an ancient and the modern pathways of aminoacyl-tRNA formation. Nucleic Acids Res, 35, 1421-1431. PubMed id: 17284460
Date:
08-Aug-06     Release date:   24-Apr-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P56926  (SYQ_DEIRA) -  Glutamine--tRNA ligase
Seq:
Struc:
 
Seq:
Struc:
852 a.a.
556 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.6.1.1.18  - Glutamine--tRNA ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + L-glutamine + tRNA(Gln) = AMP + diphosphate + L-glutaminyl- tRNA(Gln)
ATP
+ L-glutamine
+ tRNA(Gln)
= AMP
+ diphosphate
+ L-glutaminyl- tRNA(Gln)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     translation   5 terms 
  Biochemical function     nucleotide binding     7 terms  

 

 
    reference    
 
 
Nucleic Acids Res 35:1421-1431 (2007)
PubMed id: 17284460  
 
 
Deinococcus glutaminyl-tRNA synthetase is a chimer between proteins from an ancient and the modern pathways of aminoacyl-tRNA formation.
M.Deniziak, C.Sauter, H.D.Becker, C.A.Paulus, R.Giegé, D.Kern.
 
  ABSTRACT  
 
Glutaminyl-tRNA synthetase from Deinococcus radiodurans possesses a C-terminal extension of 215 residues appending the anticodon-binding domain. This domain constitutes a paralog of the Yqey protein present in various organisms and part of it is present in the C-terminal end of the GatB subunit of GatCAB, a partner of the indirect pathway of Gln-tRNA(Gln) formation. To analyze the peculiarities of the structure-function relationship of this GlnRS related to the Yqey domain, a structure of the protein was solved from crystals diffracting at 2.3 A and a docking model of the synthetase complexed to tRNA(Gln) constructed. The comparison of the modeled complex with the structure of the E. coli complex reveals that all residues of E. coli GlnRS contacting tRNA(Gln) are conserved in D. radiodurans GlnRS, leaving the functional role of the Yqey domain puzzling. Kinetic investigations and tRNA-binding experiments of full length and Yqey-truncated GlnRSs reveal that the Yqey domain is involved in tRNA(Gln) recognition. They demonstrate that Yqey plays the role of an affinity-enhancer of GlnRS for tRNA(Gln) acting only in cis. However, the presence of Yqey in free state in organisms lacking GlnRS, suggests that this domain may exert additional cellular functions.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19906721 A.Nakamura, K.Sheppard, J.Yamane, M.Yao, D.Söll, and I.Tanaka (2010).
Two distinct regions in Staphylococcus aureus GatCAB guarantee accurate tRNA recognition.
  Nucleic Acids Res, 38, 672-682.
PDB code: 3ip4
20717102 M.Blaise, M.Bailly, M.Frechin, M.A.Behrens, F.Fischer, C.L.Oliveira, H.D.Becker, J.S.Pedersen, S.Thirup, and D.Kern (2010).
Crystal structure of a transfer-ribonucleoprotein particle that promotes asparagine formation.
  EMBO J, 29, 3118-3129.
PDB code: 3kfu
20601684 O.Nureki, P.O'Donoghue, N.Watanabe, A.Ohmori, H.Oshikane, Y.Araiso, K.Sheppard, D.Söll, and R.Ishitani (2010).
Structure of an archaeal non-discriminating glutamyl-tRNA synthetase: a missing link in the evolution of Gln-tRNAGln formation.
  Nucleic Acids Res, 38, 7286-7297.
PDB code: 3aii
19520089 J.Wu, W.Bu, K.Sheppard, M.Kitabatake, S.T.Kwon, D.Söll, and J.L.Smith (2009).
Insights into tRNA-dependent amidotransferase evolution and catalysis from the structure of the Aquifex aeolicus enzyme.
  J Mol Biol, 391, 703-716.
PDB codes: 3h0l 3h0m 3h0r
18604446 J.Yuan, K.Sheppard, and D.Söll (2008).
Amino acid modifications on tRNA.
  Acta Biochim Biophys Sin (Shanghai), 40, 539-553.  
18279892 K.Sheppard, and D.Söll (2008).
On the evolution of the tRNA-dependent amidotransferases, GatCAB and GatDE.
  J Mol Biol, 377, 831-844.  
18252769 K.Sheppard, J.Yuan, M.J.Hohn, B.Jester, K.M.Devine, and D.Söll (2008).
From one amino acid to another: tRNA-dependent amino acid biosynthesis.
  Nucleic Acids Res, 36, 1813-1825.  
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. Where a reference describes a PDB structure, the PDB code is shown on the right.