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PDBsum entry 2e7y

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
2e7y
Jmol
Contents
Protein chains
272 a.a. *
Ligands
SO4 ×2
PGO ×4
Metals
_ZN ×4
Waters ×325
* Residue conservation analysis
PDB id:
2e7y
Name: Hydrolase
Title: High resolution structure of t. Maritima trnase z
Structure: Trnase z. Chain: a, b. Engineered: yes
Source: Thermotoga maritima. Organism_taxid: 2336. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.97Å     R-factor:   0.204     R-free:   0.249
Authors: R.Ishii,S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref:
R.Ishii et al. (2007). The structure of the flexible arm of Thermotoga maritima tRNase Z differs from those of homologous enzymes. Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 637-641. PubMed id: 17671357 DOI: 10.1107/S1744309107033623
Date:
15-Jan-07     Release date:   11-Sep-07    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9WZW8  (Q9WZW8_THEMA) -  Ribonuclease Z
Seq:
Struc:
280 a.a.
272 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.1.26.11  - Ribonuclease Z.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endonucleolytic cleavage of RNA, removing extra 3' nucleotides from tRNA precursor, generating 3' termini of tRNAs. A 3'-hydroxy group is left at the tRNA terminus and a 5'-phosphoryl group is left at the trailer molecule.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   1 term 
  Biochemical function     hydrolase activity     2 terms  

 

 
DOI no: 10.1107/S1744309107033623 Acta Crystallogr Sect F Struct Biol Cryst Commun 63:637-641 (2007)
PubMed id: 17671357  
 
 
The structure of the flexible arm of Thermotoga maritima tRNase Z differs from those of homologous enzymes.
R.Ishii, A.Minagawa, H.Takaku, M.Takagi, M.Nashimoto, S.Yokoyama.
 
  ABSTRACT  
 
tRNA 3'-processing endoribonuclease (tRNase Z) is one of the enzymes involved in the 3'-end processing of precursor tRNAs and is a member of the metallo-beta-lactamase superfamily. tRNase Z crystal structures have revealed that the enzyme forms a dimer and has a characteristic domain, named a flexible arm or an exosite, which protrudes from the metallo-beta-lactamase core and is involved in tRNA binding. The refined structure of Thermotoga maritima tRNase Z has been determined at 1.97 A resolution, revealing the structure of the flexible arm and the zinc-bound active site. The structure of the flexible arm of T. maritima tRNase Z is distinct from those of the Bacillus subtilis and Escherichia coli tRNase Zs. A comparison of the three tRNase Z structures revealed differences in the dimer orientation, which may be related to the unique cleavage-site specificity of T. maritima tRNase Z.
 
  Selected figure(s)  
 
Figure 3.
Stereoview of the active site of T. maritima tRNase Z. The side chains interacting with the zinc ions in subunit A are depicted as ball-and-stick models. The zinc ions and the water are depicted as grey and red spheres, respectively. The anomalous difference map (contoured at the 3[sigma] level) calculated from the data collected at the zinc peak wavelength (1.279 A) is also superimposed (black). Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 August 1; 63(Pt 8): 637–641. Published online 2007 July 21. doi: 10.1107/S1744309107033623. Copyright [copyright] International Union of Crystallography 2007
Figure 4.
Comparison of the structure of the T. maritima tRNase Z dimer with that of the B. subtilis tRNase Z dimer complexed with tRNA. (a) Superposition of the T. maritima tRNase Z dimer (red) and the B. subtilis tRNase Z dimer (blue). The right subunits of the dimers were superimposed using the Secondary Structure Matching server (Krissinel & Henrick, 2004[triangle]). The black line indicates the screw axis to superimpose one protomer of T. maritima tRNase Z onto that of B. subtilis tRNase Z and the green dashed line indicates the pseudo-twofold axis of the T. maritima tRNase Z dimer. The pseudo-twofold axis is parallel (top panel) and perpendicular (bottom panel) to the paper. (b) The dimer interface of T. maritima tRNase Z and (c) that of B. subtilis tRNase Z. The two subunits are coloured green and pink, respectively. Zn ions are depicted as grey spheres. The loop connecting [beta]1 and [beta]2 is coloured cyan. The orientation of tRNase Z is the same as in the top panel of (a). Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 August 1; 63(Pt 8): 637–641. Published online 2007 July 21. doi: 10.1107/S1744309107033623. Copyright [copyright] International Union of Crystallography 2007
 
  The above figures are reprinted from an Open Access publication published by the IUCr: Acta Crystallogr Sect F Struct Biol Cryst Commun (2007, 63, 637-641) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20810645 E.M.Phizicky, and A.K.Hopper (2010).
tRNA biology charges to the front.
  Genes Dev, 24, 1832-1860.  
20819227 W.Zhao, H.Yu, S.Li, and Y.Huang (2010).
Identification and analysis of candidate fungal tRNA 3'-end processing endonucleases tRNase Zs, homologs of the putative prostate cancer susceptibility protein ELAC2.
  BMC Evol Biol, 10, 272.  
19351879 L.Levinger, A.Hopkinson, R.Desetty, and C.Wilson (2009).
Effect of changes in the flexible arm on tRNase Z processing kinetics.
  J Biol Chem, 284, 15685-15691.  
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