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PDBsum entry 1jij

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Ligase PDB id
1jij
Jmol
Contents
Protein chain
319 a.a. *
Ligands
629
* Residue conservation analysis
PDB id:
1jij
Name: Ligase
Title: Crystal structure of s. Aureus tyrrs in complex with sb-2396
Structure: Tyrosyl-tRNA synthetase. Chain: a. Synonym: tyrosine--tRNA ligase. Tyrrs. Tyrosyl-transfer RNA synthetase. Engineered: yes
Source: Staphylococcus aureus. Organism_taxid: 1280. Variant: aureus n315. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PDB file)
Resolution:
3.20Å     R-factor:   0.257     R-free:   0.305
Authors: X.Qiu,C.A.Janson,W.W.Smith,R.L.Jarvest
Key ref:
X.Qiu et al. (2001). Crystal structure of Staphylococcus aureus tyrosyl-tRNA synthetase in complex with a class of potent and specific inhibitors. Protein Sci, 10, 2008-2016. PubMed id: 11567092 DOI: 10.1110/ps.18001
Date:
02-Jul-01     Release date:   26-Oct-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
A6QHR2  (SYY_STAAE) -  Tyrosine--tRNA ligase
Seq:
Struc:
420 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 = 629)
matches with 40.00% 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!
  Cellular component     cytoplasm   1 term 
  Biological process     translation   3 terms 
  Biochemical function     nucleotide binding     6 terms  

 

 
    reference    
 
 
DOI no: 10.1110/ps.18001 Protein Sci 10:2008-2016 (2001)
PubMed id: 11567092  
 
 
Crystal structure of Staphylococcus aureus tyrosyl-tRNA synthetase in complex with a class of potent and specific inhibitors.
X.Qiu, C.A.Janson, W.W.Smith, S.M.Green, P.McDevitt, K.Johanson, P.Carter, M.Hibbs, C.Lewis, A.Chalker, A.Fosberry, J.Lalonde, J.Berge, P.Brown, C.S.Houge-Frydrych, R.L.Jarvest.
 
  ABSTRACT  
 
SB-219383 and its analogues are a class of potent and specific inhibitors of bacterial tyrosyl-tRNA synthetases. Crystal structures of these inhibitors have been solved in complex with the tyrosyl-tRNA synthetase from Staphylococcus aureus, the bacterium that is largely responsible for hospital-acquired infections. The full-length enzyme yielded crystals that diffracted to 2.8 A resolution, but a truncated version of the enzyme allowed the resolution to be extended to 2.2 A. These inhibitors not only occupy the known substrate binding sites in unique ways, but also reveal a butyl binding pocket. It was reported that the Bacillus stearothermophilus TyrRS T51P mutant has much increased catalytic activity. The S. aureus enzyme happens to have a proline at position 51. Therefore, our structures may contribute to the understanding of the catalytic mechanism and provide the structural basis for designing novel antimicrobial agents.
 
  Selected figure(s)  
 
Figure 7.
Fig. 7. The binding of SB-284485 to YRS. (A) Schematic diagram showing all the hydrogen bonding interactions (dashed lines) between the inhibitor and YRS. The hydrogen bonding distances are labeled. (B) Stereoview of the fucose binding mode. Hydrogen bonds are shown in dashed lines. SB-243545 is included for comparison. Protein carbons are in yellow, SB-284485 carbons are in purple, and SB-243545 carbons are in grey. Oxygen is red and nitrogen is cyan. (C) Stereoview of the superposition of SB-284485 (purple) and tyrosyl adenylate (green). The latter is shown with ribose hydrogen bonds and is modeled based on bsTyrRS structures.
Figure 8.
Fig. 8. Stereoviews of the Electron Density (2Fo-Fc) Maps for the YRS Inhibitors. (A) The density for SB-219383 contoured at 1 . (B) The density of SB239629 contoured at 1 . (C) The density for SB-243545 contoured at 1 . (D) The density for SB-284485 contoured at 1.5 .
 
  The above figures are reprinted by permission from the Protein Society: Protein Sci (2001, 10, 2008-2016) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
17200839 G.Koczyk, L.S.Wyrwicz, and L.Rychlewski (2007).
LigProf: a simple tool for in silico prediction of ligand-binding sites.
  J Mol Model, 13, 445-455.  
17299750 I.Kufareva, L.Budagyan, E.Raush, M.Totrov, and R.Abagyan (2007).
PIER: protein interface recognition for structural proteomics.
  Proteins, 67, 400-417.  
  17401211 L.Bonnefond, M.Frugier, E.Touzé, B.Lorber, C.Florentz, R.Giegé, J.Rudinger-Thirion, and C.Sauter (2007).
Tyrosyl-tRNA synthetase: the first crystallization of a human mitochondrial aminoacyl-tRNA synthetase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 338-341.  
17882381 M.Torchala, and M.Hoffmann (2007).
IA, database of known ligands of aminoacyl-tRNA synthetases.
  J Comput Aided Mol Des, 21, 523-525.  
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
16545112 K.A.Snyder, H.J.Feldman, M.Dumontier, J.J.Salama, and C.W.Hogue (2006).
Domain-based small molecule binding site annotation.
  BMC Bioinformatics, 7, 152.  
15840810 L.Bonnefond, M.Frugier, R.Giegé, and J.Rudinger-Thirion (2005).
Human mitochondrial TyrRS disobeys the tyrosine identity rules.
  RNA, 11, 558-562.  
15671170 T.Kobayashi, K.Sakamoto, T.Takimura, R.Sekine, V.P.Kelly, K.Vincent, K.Kamata, S.Nishimura, and S.Yokoyama (2005).
Structural basis of nonnatural amino acid recognition by an engineered aminoacyl-tRNA synthetase for genetic code expansion.
  Proc Natl Acad Sci U S A, 102, 1366-1371.
PDB codes: 1vbn 1wq3 1wq4
15372084 M.B.Schmid (2004).
Seeing is believing: the impact of structural genomics on antimicrobial drug discovery.
  Nat Rev Microbiol, 2, 739-746.  
12754495 T.Kobayashi, O.Nureki, R.Ishitani, A.Yaremchuk, M.Tukalo, S.Cusack, K.Sakamoto, and S.Yokoyama (2003).
Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion.
  Nat Struct Biol, 10, 425-432.
PDB code: 1j1u
14671330 X.L.Yang, F.J.Otero, R.J.Skene, D.E.McRee, P.Schimmel, and L.Ribas de Pouplana (2003).
Crystal structures that suggest late development of genetic code components for differentiating aromatic side chains.
  Proc Natl Acad Sci U S A, 100, 15376-15380.
PDB codes: 1q11 1r6t
12110594 A.Yaremchuk, I.Kriklivyi, M.Tukalo, and S.Cusack (2002).
Class I tyrosyl-tRNA synthetase has a class II mode of cognate tRNA recognition.
  EMBO J, 21, 3829-3840.
PDB codes: 1h3e 1h3f
12427973 X.L.Yang, R.J.Skene, D.E.McRee, and P.Schimmel (2002).
Crystal structure of a human aminoacyl-tRNA synthetase cytokine.
  Proc Natl Acad Sci U S A, 99, 15369-15374.
PDB code: 1n3l
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 code is shown on the right.