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PDBsum entry 2cyb

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protein ligands Protein-protein interface(s) links
Ligase PDB id
2cyb
Jmol
Contents
Protein chains
319 a.a. *
Ligands
TYR ×2
Waters ×314
* Residue conservation analysis
PDB id:
2cyb
Name: Ligase
Title: Crystal structure of tyrosyl-tRNA synthetase complexed with l-tyrosine from archaeoglobus fulgidus
Structure: Tyrosyl-tRNA synthetase. Chain: a, b. Synonym: tyrosine--tRNA ligase, tyrrs. Engineered: yes
Source: Archaeoglobus fulgidus. Organism_taxid: 2234. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Trimer (from PQS)
Resolution:
1.80Å     R-factor:   0.202     R-free:   0.240
Authors: M.Kuratani,H.Sakai,M.Takahashi,T.Yanagisawa,T.Kobayashi, T.Terada,M.Shirouzu,S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref:
M.Kuratani et al. (2006). Crystal structures of tyrosyl-tRNA synthetases from Archaea. J Mol Biol, 355, 395-408. PubMed id: 16325203 DOI: 10.1016/j.jmb.2005.10.073
Date:
06-Jul-05     Release date:   22-Nov-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O29482  (SYY_ARCFU) -  Tyrosine--tRNA ligase
Seq:
Struc:
323 a.a.
319 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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 = TYR)
corresponds exactly
+ 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!
  Cellular component     cytoplasm   1 term 
  Biological process     translation   3 terms 
  Biochemical function     nucleotide binding     5 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2005.10.073 J Mol Biol 355:395-408 (2006)
PubMed id: 16325203  
 
 
Crystal structures of tyrosyl-tRNA synthetases from Archaea.
M.Kuratani, H.Sakai, M.Takahashi, T.Yanagisawa, T.Kobayashi, K.Murayama, L.Chen, Z.J.Liu, B.C.Wang, C.Kuroishi, S.Kuramitsu, T.Terada, Y.Bessho, M.Shirouzu, S.Sekine, S.Yokoyama.
 
  ABSTRACT  
 
Tyrosyl-tRNA synthetase (TyrRS) catalyzes the tyrosylation of tRNA(Tyr) in a two-step reaction. TyrRS has the "HIGH" and "KMSKS" motifs, which play essential roles in the formation of the tyrosyl-adenylate from tyrosine and ATP. Here, we determined the crystal structures of Archaeoglobus fulgidus and Pyrococcus horikoshii TyrRSs in the l-tyrosine-bound form at 1.8A and 2.2A resolutions, respectively, and that of Aeropyrum pernix TyrRS in the substrate-free form at 2.2 A. The conformation of the KMSKS motif differs among the three TyrRSs. In the A.pernix TyrRS, the KMSKS loop conformation corresponds to the ATP-bound "closed" form. In contrast, the KMSKS loop of the P.horikoshii TyrRS forms a novel 3(10) helix, which appears to correspond to the "semi-closed" form. This conformation enlarges the entrance to the tyrosine-binding pocket, which facilitates the pyrophosphate ion release after the tyrosyl-adenylate formation, and probably is involved in the initial tRNA binding. The KMSSS loop of the A.fulgidus TyrRS is somewhat farther from the active site and is stabilized by hydrogen bonds. Based on the three structures, possible structural changes of the KMSKS motif during the tyrosine activation reaction are discussed. We suggest that the insertion sequence just before the KMSKS motif, which exists in some archaeal species, enhances the binding affinity of the TyrRS for its cognate tRNA. In addition, a non-proline cis peptide bond, which is involved in the tRNA binding, is conserved among the archaeal TyrRSs.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. HIGH signature motif. (a) The structure of the HIGH motif of the T. thermophilus TyrRS (PDB: 1H3E). The His52 and His55 residues, and the ATP are shown in a stick model. The NH groups of the two histidine residues form hydrogen bonds with the oxygen atoms of the a and g-phosphate moieties of the ATP. (b) Superposition of the HIGH motifs based on the C^a atoms of the a3 helices (Figure 2). The C^a atoms of the A. fulgidus (Af), A. pernix (Ap), and P. horikoshii (Ph) TyrRSs are shown in stick models and are colored purple, green, and pink, respectively. The side-chain atoms are colored in the same manner as in Figure 3. (c) A sulfate ion is coordinated in the A. pernix TyrRS. The residues involved in hydrogen bond interactions are shown in a stick model, and the hydrogen bond interactions are shown as broken lines.
Figure 5.
Figure 5. The conformation of the insertion sequence. (a) The hydrophobic interaction between the insertion sequence (blue; residues 230-250, including helix a12) and the C-terminal domain (red) in the P. horikoshii TyrRS. The insertion sequence and the C-terminal domain in the P. horikoshii TyrRS are shown as tube models. Residues involved in this interaction are shown in stick models. The hydrogen bonding distance (Å) is shown. The atoms are colored in the same manner as in Figure 3. (b) Superposition of the insertion residues of the P. horikoshii TyrRS and the corresponding residues of the M. jannaschii TyrRS and tRNA complex. As the KMSSS residues are disordered in the M. jannaschii TyrRS, their coordinates were supplemented with those of the A. fulgidus TyrRS by superimposition. The residue numbers of the tRNA anticodon are indicated. Lys234 and Trp235 are shown in stick models. Lys234, which is located near the tRNA, is colored green.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 355, 395-408) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20123733 M.Zhou, X.Dong, N.Shen, C.Zhong, and J.Ding (2010).
Crystal structures of Saccharomyces cerevisiae tryptophanyl-tRNA synthetase: new insights into the mechanism of tryptophan activation and implications for anti-fungal drug design.
  Nucleic Acids Res, 38, 3399-3413.
PDB codes: 3kt0 3kt3 3kt6 3kt8
19942682 X.Dong, M.Zhou, C.Zhong, B.Yang, N.Shen, and J.Ding (2010).
Crystal structure of Pyrococcus horikoshii tryptophanyl-tRNA synthetase and structure-based phylogenetic analysis suggest an archaeal origin of tryptophanyl-tRNA synthetase.
  Nucleic Acids Res, 38, 1401-1412.  
19098308 G.Sharma, and E.A.First (2009).
Thermodynamic Analysis Reveals a Temperature-dependent Change in the Catalytic Mechanism of Bacillus stearothermophilus Tyrosyl-tRNA Synthetase.
  J Biol Chem, 284, 4179-4190.  
19386777 S.Kamijo, A.Fujii, K.Onodera, and K.Wakabayashi (2009).
Analyses of conditions for KMSSS loop in tyrosyl-tRNA synthetase by building a mutant library.
  J Biochem, 146, 241-250.  
19053270 L.W.Tremblay, F.Fan, M.W.Vetting, and J.S.Blanchard (2008).
The 1.6 A crystal structure of Mycobacterium smegmatis MshC: the penultimate enzyme in the mycothiol biosynthetic pathway.
  Biochemistry, 47, 13326-13335.
PDB code: 3c8z
  18259057 P.Bahti, S.Chen, Y.Li, N.Shaw, X.Zhang, M.Zhang, C.Cheng, G.Song, J.Yin, H.Zhang, D.Che, A.Abbas, H.Xu, B.C.Wang, and Z.J.Liu (2008).
Purification, crystallization and preliminary crystallographic analysis of the non-Pfam protein AF1514 from Archeoglobus fulgidus DSM 4304.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 91-93.  
18560823 T.Li, M.Froeyen, and P.Herdewijn (2008).
Comparative structural dynamics of Tyrosyl-tRNA synthetase complexed with different substrates explored by molecular dynamics.
  Eur Biophys J, 38, 25-35.  
17855524 C.Abergel, J.Rudinger-Thirion, R.Giegé, and J.M.Claverie (2007).
Virus-encoded aminoacyl-tRNA synthetases: structural and functional characterization of mimivirus TyrRS and MetRS.
  J Virol, 81, 12406-12417.
PDB code: 2j5b
17407263 M.T.Vu, and S.A.Martinis (2007).
A unique insert of leucyl-tRNA synthetase is required for aminoacylation and not amino acid editing.
  Biochemistry, 46, 5170-5176.  
17576676 M.Tsunoda, Y.Kusakabe, N.Tanaka, S.Ohno, M.Nakamura, T.Senda, T.Moriguchi, N.Asai, M.Sekine, T.Yokogawa, K.Nishikawa, and K.T.Nakamura (2007).
Structural basis for recognition of cognate tRNA by tyrosyl-tRNA synthetase from three kingdoms.
  Nucleic Acids Res, 35, 4289-4300.
PDB code: 2dlc
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.