spacer
spacer

PDBsum entry 1y2q

Go to PDB code: 
protein links
Ligase PDB id
1y2q
Jmol
Contents
Protein chain
143 a.a. *
Waters ×176
* Residue conservation analysis
PDB id:
1y2q
Name: Ligase
Title: Crystal structure of the editing domain of threonyl-tRNA synthetase from pyrococcus abyssi
Structure: Threonyl-tRNA synthetase. Chain: a. Fragment: editing domain. Synonym: threonine--tRNA ligase, thrrs. Engineered: yes
Source: Pyrococcus abyssi. Organism_taxid: 29292. Gene: thrs. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PDB file)
Resolution:
1.95Å     R-factor:   0.209     R-free:   0.272
Authors: S.Dwivedi,S.P.Kruparani,R.Sankaranarayanan
Key ref:
S.Dwivedi et al. (2005). A D-amino acid editing module coupled to the translational apparatus in archaea. Nat Struct Mol Biol, 12, 556-557. PubMed id: 15908961 DOI: 10.1038/nsmb943
Date:
23-Nov-04     Release date:   14-Jun-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9UZ14  (SYT_PYRAB) -  Threonine--tRNA ligase
Seq:
Struc:
 
Seq:
Struc:
625 a.a.
143 a.a.
Key:    PfamA domain  Secondary structure

 Enzyme reactions 
   Enzyme class: E.C.6.1.1.3  - Threonine--tRNA ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + L-threonine + tRNA(Thr) = AMP + diphosphate + L-threonyl-tRNA(Thr)
ATP
+ L-threonine
+ tRNA(Thr)
= AMP
+ diphosphate
+ L-threonyl-tRNA(Thr)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biochemical function     threonine-tRNA ligase activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1038/nsmb943 Nat Struct Mol Biol 12:556-557 (2005)
PubMed id: 15908961  
 
 
A D-amino acid editing module coupled to the translational apparatus in archaea.
S.Dwivedi, S.P.Kruparani, R.Sankaranarayanan.
 
  ABSTRACT  
 
We report the crystal structure of an archaea-specific editing domain of threonyl-tRNA synthetase that reveals a marked structural similarity to D-amino acid deacylases found in eubacteria and eukaryotes. The domain can bind D-amino acids despite a low sequence identity to other D-amino acid deacylases. These results together indicate the presence of these deacylases in all three kingdoms of life. This underlines an important role they may have played in enforcing homochirality during translation.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Crystal structure of Pab-NTD and a comparison with DTD. (a) Ribbon diagram of Pab-NTD. (b) Structural superposition of Pab-NTD (cyan) and DTD (pink).
Figure 2.
Figure 2. Amino acid -binding studies using Bis-ANS fluorescence. (a -d) The change in fluorescence was monitored by titrating a premix of Pab-NTD (0.1 mg ml-1) and Bis-ANS (10 M) against L-serine (a), L-threonine (b), D-serine (c), and D-threonine (d). Titration curves with 0 mM, 5 mM and 10 mM amino acid are shown.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2005, 12, 556-557) copyright 2005.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21098258 T.Hussain, V.Kamarthapu, S.P.Kruparani, M.V.Deshmukh, and R.Sankaranarayanan (2010).
Mechanistic insights into cognate substrate discrimination during proofreading in translation.
  Proc Natl Acad Sci U S A, 107, 22117-22121.
PDB codes: 3pd2 3pd3 3pd4 3pd5
20007323 T.K.Bhatt, M.Yogavel, S.Wydau, R.Berwal, and A.Sharma (2010).
Ligand-bound structures provide atomic snapshots for the catalytic mechanism of D-amino acid deacylase.
  J Biol Chem, 285, 5917-5930.
PDB codes: 3knf 3knp 3ko3 3ko4 3ko5 3ko7 3ko9 3kob 3koc 3kod
19379069 J.Ling, N.Reynolds, and M.Ibba (2009).
Aminoacyl-tRNA synthesis and translational quality control.
  Annu Rev Microbiol, 63, 61-78.  
20042123 T.K.Bhatt, C.Kapil, S.Khan, M.A.Jairajpuri, V.Sharma, D.Santoni, F.Silvestrini, E.Pizzi, and A.Sharma (2009).
A genomic glimpse of aminoacyl-tRNA synthetases in malaria parasite Plasmodium falciparum.
  BMC Genomics, 10, 644.  
17185419 J.Ling, H.Roy, and M.Ibba (2007).
Mechanism of tRNA-dependent editing in translational quality control.
  Proc Natl Acad Sci U S A, 104, 72-77.  
17283340 J.SternJohn, S.Hati, P.G.Siliciano, and K.Musier-Forsyth (2007).
Restoring species-specific posttransfer editing activity to a synthetase with a defunct editing domain.
  Proc Natl Acad Sci U S A, 104, 2127-2132.  
17264083 M.Kemp, B.Bae, J.P.Yu, M.Ghosh, M.Leffak, and S.K.Nair (2007).
Structure and function of the c-myc DNA-unwinding element-binding protein DUE-B.
  J Biol Chem, 282, 10441-10448.
PDB code: 2okv
17027500 T.Crepin, A.Yaremchuk, M.Tukalo, and S.Cusack (2006).
Structures of two bacterial prolyl-tRNA synthetases with and without a cis-editing domain.
  Structure, 14, 1511-1525.
PDB codes: 2i4l 2i4m 2i4n 2i4o 2j3l 2j3m
16902403 T.Hussain, S.P.Kruparani, B.Pal, A.C.Dock-Bregeon, S.Dwivedi, M.R.Shekar, K.Sureshbabu, and R.Sankaranarayanan (2006).
Post-transfer editing mechanism of a D-aminoacyl-tRNA deacylase-like domain in threonyl-tRNA synthetase from archaea.
  EMBO J, 25, 4152-4162.
PDB codes: 2hkz 2hl0 2hl1 2hl2
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.