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PDBsum entry 1vbm

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protein ligands Protein-protein interface(s) links
Ligase PDB id
1vbm
Jmol
Contents
Protein chains
318 a.a. *
Ligands
SO4 ×4
YSA ×2
Waters ×88
* Residue conservation analysis
PDB id:
1vbm
Name: Ligase
Title: Crystal structure of the escherichia coli tyrosyl-tRNA synthetase complexed with tyr-ams
Structure: Tyrosyl-tRNA synthetase. Chain: a, b. Fragment: residues 5-322. Synonym: tyrosine--tRNA ligase, tyrrs. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
Resolution:
2.70Å     R-factor:   0.246     R-free:   0.284
Authors: T.Kobayashi,K.Sakamoto,T.Takimura,K.Kamata,R.Sekine, S.Nishimura,S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref:
T.Kobayashi et al. (2005). Structural snapshots of the KMSKS loop rearrangement for amino acid activation by bacterial tyrosyl-tRNA synthetase. J Mol Biol, 346, 105-117. PubMed id: 15663931 DOI: 10.1016/j.jmb.2004.11.034
Date:
27-Feb-04     Release date:   25-Jan-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0AGJ9  (SYY_ECOLI) -  Tyrosine--tRNA ligase
Seq:
Struc:
424 a.a.
318 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
+ tRNA(Tyr)
=
AMP
Bound ligand (Het Group name = YSA)
matches with 48.00% similarity
+ 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     tRNA aminoacylation for protein translation   2 terms 
  Biochemical function     nucleotide binding     4 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2004.11.034 J Mol Biol 346:105-117 (2005)
PubMed id: 15663931  
 
 
Structural snapshots of the KMSKS loop rearrangement for amino acid activation by bacterial tyrosyl-tRNA synthetase.
T.Kobayashi, T.Takimura, R.Sekine, V.P.Kelly, K.Vincent, K.Kamata, K.Sakamoto, S.Nishimura, S.Yokoyama.
 
  ABSTRACT  
 
Tyrosyl-tRNA synthetase (TyrRS) has been studied extensively by mutational and structural analyses to elucidate its catalytic mechanism. TyrRS has the HIGH and KMSKS motifs that catalyze the amino acid activation with ATP. In the present study, the crystal structures of the Escherichia coli TyrRS catalytic domain, in complexes with l-tyrosine and a l-tyrosyladenylate analogue, Tyr-AMS, were solved at 2.0A and 2.7A resolution, respectively. In the Tyr-AMS-bound structure, the 2'-OH group and adenine ring of the Tyr-AMS are strictly recognized by hydrogen bonds. This manner of hydrogen-bond recognition is conserved among the class I synthetases. Moreover, a comparison between the two structures revealed that the KMSKS loop is rearranged in response to adenine moiety binding and hydrogen-bond formation, and the KMSKS loop adopts the more compact ("semi-open") form, rather than the flexible, open form. The HIGH motif initially recognizes the gamma-phosphate, and then the alpha and gamma-phosphates of ATP, with a slight rearrangement of the residues. The other residues around the substrate also accommodate the Tyr-AMS. This induced-fit form presents a novel "snapshot" of the amino acid activation step in the aminoacylation reaction by TyrRS. The present structures and the T.thermophilus TyrRS ATP-free and bound structures revealed that the extensive induced-fit conformational changes of the KMSKS loop and the local conformational changes within the substrate binding site form the basis for driving the amino acid activation step: the KMSKS loop adopts the open form, transiently shifts to the semi-open conformation according to the adenosyl moiety binding, and finally assumes the rigid ATP-bound, closed form. After the amino acid activation, the KMSKS loop adopts the semi-open form again to accept the CCA end of tRNA for the aminoacyl transfer reaction.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. The Tyr-AMP binding sites of the TyrRSs. (a) The Tyr-AMP-binding site of the E. coli TyrRS·Tyr-AMS complex. (b) The corresponding view of the B. stearothermophilus TyrRS·Tyr-AMP complex5 (PDB ID: 3TS1). The carbon atoms of Tyr-AMS/Tyr-AMP are shown in light blue, and the hydrogen bonds are indicated by green broken lines. A phosphate atom is shown in green.
Figure 8.
Figure 8. Conformational changes of the KMSKS loop. (a) Open conformation of the KMSKS loop in the E. coli TyrRS·L-tyrosine structure. (b) Semi-open conformation of the KMSKS loop in the E. coil TyrRS·Tyr-AMS structure. The superposition of the open-form KMSKS loop is also shown by a pink translucent tube. (c) Closed conformation of the KMSKS loop in the T. thermophilus TyrRS·ATP·L-tyrosinol·tRNA^Tyr structure13 (PDB ID: 1H3E). The KMSKS loops are shown by orange tubes. The carbon atoms of L-tyrosine and L-tyrosinol are shown in pink, and those of Tyr-AMS are shown in light blue, respectively. (d) The bottleneck of the catalytic site in the T. thermophilus TyrRS closed form. The surface model of Tyr-AMP phosphate, which is a landmark of the aminoacyl transfer center, is shown by a stick model. (e) The 3'-adenosine of the tRNA cannot pass through the bottleneck of (d). The adenosine moiety is shown by a CPK model. (f) The exposed catalytic site in the E. coli TyrRS semi-open form. Tyr-AMS is shown by a stick model. The molecular surfaces were produced using the program MSMS (http://www.scripps.edu/mb/olson/people/sanner/html/msms_home.html).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 346, 105-117) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22683997 A.Palencia, T.Crépin, M.T.Vu, T.L.Lincecum, S.A.Martinis, and S.Cusack (2012).
Structural dynamics of the aminoacylation and proofreading functional cycle of bacterial leucyl-tRNA synthetase.
  Nat Struct Mol Biol, 19, 677-684.
PDB codes: 4aq7 4arc 4ari 4as1
20217843 I.T.Yonemoto, and E.M.Tippmann (2010).
The juggernauts of biology.
  Bioessays, 32, 314-321.  
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.  
20482517 X.L.Zhou, M.Wang, M.Tan, Q.Huang, G.Eriani, and E.D.Wang (2010).
Functional characterization of leucine-specific domain 1 from eukaryal and archaeal leucyl-tRNA synthetases.
  Biochem J, 429, 505-513.  
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.  
19668857 J.K.Takimoto, K.L.Adams, Z.Xiang, and L.Wang (2009).
Improving orthogonal tRNA-synthetase recognition for efficient unnatural amino acid incorporation and application in mammalian cells.
  Mol Biosyst, 5, 931-934.  
19783652 J.Lee, J.Johnson, Z.Ding, M.Paetzel, and R.B.Cornell (2009).
Crystal structure of a mammalian CTP: phosphocholine cytidylyltransferase catalytic domain reveals novel active site residues within a highly conserved nucleotidyltransferase fold.
  J Biol Chem, 284, 33535-33548.
PDB code: 3hl4
19278648 K.Sakamoto, K.Murayama, K.Oki, F.Iraha, M.Kato-Murayama, M.Takahashi, K.Ohtake, T.Kobayashi, S.Kuramitsu, M.Shirouzu, and S.Yokoyama (2009).
Genetic encoding of 3-iodo-L-tyrosine in Escherichia coli for single-wavelength anomalous dispersion phasing in protein crystallography.
  Structure, 17, 335-344.
PDB codes: 2z0z 2z10 2zxv
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.  
18180246 N.Shen, M.Zhou, B.Yang, Y.Yu, X.Dong, and J.Ding (2008).
Catalytic mechanism of the tryptophan activation reaction revealed by crystal structures of human tryptophanyl-tRNA synthetase in different enzymatic states.
  Nucleic Acids Res, 36, 1288-1299.
PDB codes: 2quh 2qui 2quj 2quk
18784368 T.L.Hendrickson (2008).
Proofreading optimizes iodotyrosine insertion into the genetic code.
  Proc Natl Acad Sci U S A, 105, 13699-13700.  
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.  
17690095 D.Thompson, C.Lazennec, P.Plateau, and T.Simonson (2007).
Ammonium scanning in an enzyme active site. The chiral specificity of aspartyl-tRNA synthetase.
  J Biol Chem, 282, 30856-30868.  
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.  
17510965 M.E.Budiman, M.H.Knaggs, J.S.Fetrow, and R.W.Alexander (2007).
Using molecular dynamics to map interaction networks in an aminoacyl-tRNA synthetase.
  Proteins, 68, 670-689.  
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
17948002 T.A.Cropp, J.C.Anderson, and J.W.Chin (2007).
Reprogramming the amino-acid substrate specificity of orthogonal aminoacyl-tRNA synthetases to expand the genetic code of eukaryotic cells.
  Nat Protoc, 2, 2590-2600.  
16689635 L.Wang, J.Xie, and P.G.Schultz (2006).
Expanding the genetic code.
  Annu Rev Biophys Biomol Struct, 35, 225-249.  
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
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.