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PDBsum entry 2j5b

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protein ligands Protein-protein interface(s) links
Ligase PDB id
2j5b
Jmol
Contents
Protein chains
322 a.a. *
Ligands
TYE ×2
Waters ×330
* Residue conservation analysis
PDB id:
2j5b
Name: Ligase
Title: Structure of the tyrosyl tRNA synthetase from acanthamoeba polyphaga mimivirus complexed with tyrosynol
Structure: Tyrosyl-tRNA synthetase. Chain: a, b. Fragment: residues 2-346. Synonym: tyrosine-tRNA ligase, tyrrs, tyrosyl-tRNA syntheta engineered: yes
Source: Acanthamoeba polyphaga mimivirus. Organism_taxid: 212035. Expressed in: escherichia coli. Expression_system_taxid: 469008. Expression_system_variant: plyss.
Resolution:
2.20Å     R-factor:   0.216     R-free:   0.248
Authors: C.Abergel,J.Rudinger-Thirion,R.Giege,J.M.Claverie
Key ref: C.Abergel et al. (2007). Virus-encoded aminoacyl-tRNA synthetases: structural and functional characterization of mimivirus TyrRS and MetRS. J Virol, 81, 12406-12417. PubMed id: 17855524
Date:
13-Sep-06     Release date:   25-Sep-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q5UPJ7  (SYY_MIMIV) -  Tyrosine--tRNA ligase
Seq:
Struc:
346 a.a.
322 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.6.1.1.1  - Tyrosine--tRNA ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + L-tyrosyl-tRNA(Tyr)
ATP
+
L-tyrosine
Bound ligand (Het Group name = TYE)
matches with 92.31% similarity
+ tRNA(Tyr)
= AMP
+ diphosphate
+ L-tyrosyl-tRNA(Tyr)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     translation   2 terms 
  Biochemical function     nucleotide binding     6 terms  

 

 
    reference    
 
 
J Virol 81:12406-12417 (2007)
PubMed id: 17855524  
 
 
Virus-encoded aminoacyl-tRNA synthetases: structural and functional characterization of mimivirus TyrRS and MetRS.
C.Abergel, J.Rudinger-Thirion, R.Giegé, J.M.Claverie.
 
  ABSTRACT  
 
Aminoacyl-tRNA synthetases are pivotal in determining how the genetic code is translated in amino acids and in providing the substrate for protein synthesis. As such, they fulfill a key role in a process universally conserved in all cellular organisms from their most complex to their most reduced parasitic forms. In contrast, even complex viruses were not found to encode much translation machinery, with the exception of isolated components such as tRNAs. In this context, the discovery of four aminoacyl-tRNA synthetases encoded in the genome of mimivirus together with a full set of translation initiation, elongation, and termination factors appeared to blur what was once a clear frontier between the cellular and viral world. Functional studies of two mimivirus tRNA synthetases confirmed the MetRS specificity for methionine and the TyrRS specificity for tyrosine and conformity with the identity rules for tRNA(Tyr) for archea/eukarya. The atomic structure of the mimivirus tyrosyl-tRNA synthetase in complex with tyrosinol exhibits the typical fold and active-site organization of archaeal-type TyrRS. However, the viral enzyme presents a unique dimeric conformation and significant differences in its anticodon binding site. The present work suggests that mimivirus aminoacyl-tRNA synthetases function as regular translation enzymes in infected amoebas. Their phylogenetic classification does not suggest that they have been acquired recently by horizontal gene transfer from a cellular host but rather militates in favor of an intricate evolutionary relationship between large DNA viruses and ancestral eukaryotes.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20360389 M.Legendre, S.Audic, O.Poirot, P.Hingamp, V.Seltzer, D.Byrne, A.Lartigue, M.Lescot, A.Bernadac, J.Poulain, C.Abergel, and J.M.Claverie (2010).
mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus.
  Genome Res, 20, 664-674.  
20102337 R.W.Smith, and N.K.Gray (2010).
Poly(A)-binding protein (PABP): a common viral target.
  Biochem J, 426, 1.  
19403753 D.Byrne, R.Grzela, A.Lartigue, S.Audic, S.Chenivesse, S.Encinas, J.M.Claverie, and C.Abergel (2009).
The polyadenylation site of Mimivirus transcripts obeys a stringent 'hairpin rule'.
  Genome Res, 19, 1233-1242.  
19653859 J.M.Claverie, and C.Abergel (2009).
Mimivirus and its virophage.
  Annu Rev Genet, 43, 49-66.  
18926919 N.Wegner, R.Wait, and P.J.Venables (2009).
Evolutionarily conserved antigens in autoimmune disease: implications for an infective aetiology.
  Int J Biochem Cell Biol, 41, 390-397.  
19439473 S.Jeudy, A.Lartigue, J.M.Claverie, and C.Abergel (2009).
Dissecting the unique nucleotide specificity of mimivirus nucleoside diphosphate kinase.
  J Virol, 83, 7142-7150.
PDB codes: 2b8p 2b8q 3b6b 3ddi 3dkd 3ee3 3eic 3ejm 3elh 3em1 3emt 3ena 3etm 3evm 3evo 3evw 3fbb 3fbc 3fbe 3fbf 3fc9 3fcv 3fcw 3g2x 3gp9 3gpa
  18215256 A.Monier, J.B.Larsen, R.A.Sandaa, G.Bratbak, J.M.Claverie, and H.Ogata (2008).
Marine mimivirus relatives are probably large algal viruses.
  Virol J, 5, 12.  
18400173 D.Benarroch, P.Smith, and S.Shuman (2008).
Characterization of a trifunctional mimivirus mRNA capping enzyme and crystal structure of the RNA triphosphatase domain.
  Structure, 16, 501-512.
PDB codes: 2qy2 2qze
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 codes are shown on the right.