PDBsum entry 2e1b

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Ligase, hydrolase PDB id
Protein chain
216 a.a. *
* Residue conservation analysis
PDB id:
Name: Ligase, hydrolase
Title: Crystal structure of the alax-m trans-editing enzyme from pyrococcus horikoshii
Structure: 216aa long hypothetical alanyl-tRNA synthetase. Chain: a. Synonym: ph0108. Engineered: yes
Source: Pyrococcus horikoshii. Organism_taxid: 53953. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
2.70Å     R-factor:   0.227     R-free:   0.313
Authors: R.Fukunaga,S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref:
R.Fukunaga and S.Yokoyama (2007). Structure of the AlaX-M trans-editing enzyme from Pyrococcus horikoshii. Acta Crystallogr D Biol Crystallogr, 63, 390-400. PubMed id: 17327676 DOI: 10.1107/S090744490605640X
20-Oct-06     Release date:   06-Mar-07    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
O57848  (ALAXM_PYRHO) -  Alanyl-tRNA editing protein AlaX-M
216 a.a.
216 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     regulation of translational fidelity   3 terms 
  Biochemical function     aminoacyl-tRNA editing activity     7 terms  


DOI no: 10.1107/S090744490605640X Acta Crystallogr D Biol Crystallogr 63:390-400 (2007)
PubMed id: 17327676  
Structure of the AlaX-M trans-editing enzyme from Pyrococcus horikoshii.
R.Fukunaga, S.Yokoyama.
The editing domain of alanyl-tRNA synthetase (AlaRS) contributes to high-fidelity aminoacylation by hydrolyzing (editing) the incorrect products Ser-tRNA(Ala) and Gly-tRNA(Ala) (cis-editing). The AlaX protein shares sequence homology to the editing domain of AlaRS. There are three types of AlaX proteins, with different numbers of amino-acid residues (AlaX-S, AlaX-M and AlaX-L). In this report, AlaX-M from Pyrococcus horikoshii is shown to deacylate Ser-tRNA(Ala) and Gly-tRNA(Ala) (trans-editing). The crystal structure of P. horikoshii AlaX-M has been determined at 2.7 A resolution. AlaX-M consists of an N-terminal domain (N-domain) and a C-terminal domain (C-domain). A zinc ion is coordinated by the conserved zinc-binding cluster in the C-domain, which is expected to be the enzymatic active site. The glycine-rich motif, consisting of successive conserved glycine residues in the N-domain, forms a loop (the 'glycine-rich loop'). The glycine-rich loop is located near the active site and may be involved in substrate recognition and/or catalysis.
  Selected figure(s)  
Figure 9.
Figure 9 tRNA-binding model. (a) tRNA-binding model (orange) on a surface electropotential model of AlaX-M. Only the tRNA acceptor arm is shown. (b) The N-domain is coloured pink and the glycine-rich loop is coloured violet. The zinc-binding residues and the zinc ion are shown as yellow ball-and-stick models and as a magenta sphere, respectively. The tRNA model is shown in orange. The third base pair in the acceptor stem, corresponding to the G3-U70 wobble base pair in tRNA^Ala, is coloured cyan.
Figure 10.
Figure 10 Comparison of substrate-recognition sites. (a) The putative substrate-recognition site in AlaX-M (stereoview). The zinc-binding residues are coloured yellow. The glycine-rich loop is coloured violet. (b) Serine recognition in AlaX-S. (c) The recognition of a Ser-Ade76 analogue in the ThrRS editing domain.
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2007, 63, 390-400) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19661429 M.Guo, Y.E.Chong, K.Beebe, R.Shapiro, X.L.Yang, and P.Schimmel (2009).
The C-Ala domain brings together editing and aminoacylation functions on one tRNA.
  Science, 325, 744-747.
PDB code: 3g98
19423669 M.Naganuma, S.Sekine, R.Fukunaga, and S.Yokoyama (2009).
Unique protein architecture of alanyl-tRNA synthetase for aminoacylation, editing, and dimerization.
  Proc Natl Acad Sci U S A, 106, 8489-8494.
PDB codes: 2ztg 2zvf
19549823 M.Sokabe, T.Ose, A.Nakamura, K.Tokunaga, O.Nureki, M.Yao, and I.Tanaka (2009).
The structure of alanyl-tRNA synthetase with editing domain.
  Proc Natl Acad Sci U S A, 106, 11028-11033.
PDB codes: 2zze 2zzf 2zzg
18522650 C.D.Hausmann, and M.Ibba (2008).
Aminoacyl-tRNA synthetase complexes: molecular multitasking revealed.
  FEMS Microbiol Rev, 32, 705-721.  
18172502 K.Beebe, M.Mock, E.Merriman, and P.Schimmel (2008).
Distinct domains of tRNA synthetase recognize the same base pair.
  Nature, 451, 90-93.  
18723508 Y.E.Chong, X.L.Yang, and P.Schimmel (2008).
Natural Homolog of tRNA Synthetase Editing Domain Rescues Conditional Lethality Caused by Mistranslation.
  J Biol Chem, 283, 30073-30078.  
  17329819 R.Fukunaga, and S.Yokoyama (2007).
Crystallization and preliminary X-ray crystallographic study of alanyl-tRNA synthetase from the archaeon Archaeoglobus fulgidus.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 224-228.  
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