spacer
spacer

PDBsum entry 1q11

Go to PDB code: 
protein ligands metals links
Ligase PDB id
1q11
Jmol
Contents
Protein chain
329 a.a. *
Ligands
PO4
TYE
GOL ×2
Metals
__K
Waters ×348
* Residue conservation analysis
PDB id:
1q11
Name: Ligase
Title: Crystal structure of an active fragment of human tyrosyl-trn synthetase with tyrosinol
Structure: Tyrosyl-tRNA synthetase. Chain: a. Fragment: mini tyrrs. Synonym: tyrosyl--tRNA ligase, tyrrs. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
Resolution:
1.60Å     R-factor:   0.197     R-free:   0.217
Authors: X.-L.Yang,P.Schimmel,L.Ribas De Pouplana
Key ref:
X.L.Yang et al. (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. PubMed id: 14671330 DOI: 10.1073/pnas.2136794100
Date:
18-Jul-03     Release date:   06-Jan-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P54577  (SYYC_HUMAN) -  Tyrosine--tRNA ligase, cytoplasmic
Seq:
Struc:
 
Seq:
Struc:
528 a.a.
329 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 = TYE)
matches with 92.31% similarity
+ tRNA(Tyr)
= AMP
+
diphosphate
Bound ligand (Het Group name = PO4)
matches with 55.56% similarity
+ 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: 10.1073/pnas.2136794100 Proc Natl Acad Sci U S A 100:15376-15380 (2003)
PubMed id: 14671330  
 
 
Crystal structures that suggest late development of genetic code components for differentiating aromatic side chains.
X.L.Yang, F.J.Otero, R.J.Skene, D.E.McRee, P.Schimmel, L.Ribas de Pouplana.
 
  ABSTRACT  
 
Early forms of the genetic code likely generated "statistical" proteins, with similar side chains occupying the same sequence positions at different ratios. In this scenario, groups of related side chains were treated by aminoacyl-tRNA synthetases as a single molecular species until a discrimination mechanism developed that could separate them. The aromatic amino acids tryptophan, tyrosine, and phenylalanine likely constituted one of these groups. A crystal structure of human tryptophanyl-tRNA synthetase was solved at 2.1 A with a tryptophanyl-adenylate bound at the active site. A cocrystal structure of an active fragment of human tyrosyl-tRNA synthetase with its cognate amino acid analog was also solved at 1.6 A. The two structures enabled active site identifications and provided the information for structure-based sequence alignments of approximately 45 orthologs of each enzyme. Two critical positions shared by all tyrosyl-tRNA synthetases and tryptophanyl-tRNA synthetases for amino acid discrimination were identified. The variations at these two positions and phylogenetic analyses based on the structural information suggest that, in contrast to many other amino acids, discrimination of tyrosine from tryptophan occurred late in the development of the genetic code.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Classification of aminoacyl-tRNA synthetases adapted from ref. 5. The 20 synthetases are divided into 2 classes of 10 enzymes each. The exceptional class I LysRS is shown in gray. Highlighted with a yellow box, TyrRS and TrpRS from class Ic are paired with PheRS from class IIc.
Figure 2.
Fig. 2. Structure of the dimeric human TrpRS with one monomer shown in color. The circled CP1 insertion of the Rossmann fold domain forms the dimerization interface. All three domains [N-terminal appended domain (blue), Rossmann fold catalytic domain (yellow), and anticodon recognition domain (green)] were resolved in one monomer of the dimer with a disordered linker of 21 residues connecting the N-domain and the Rossmann fold domain. However, in the other monomer, the first 96 residues, which include the N-terminal domain, the linker region, and part of the Rossmann fold catalytic domain, were completely disordered. A bound Trp-AMP was found only in the monomer with the resolved N-domain.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21224416 A.K.Antonczak, Z.Simova, I.T.Yonemoto, M.Bochtler, A.Piasecka, H.Czapinska, A.Brancale, and E.M.Tippmann (2011).
Importance of single molecular determinants in the fidelity of expanded genetic codes.
  Proc Natl Acad Sci U S A, 108, 1320-1325.
PDB code: 3prh
  20944229 G.W.Han, X.L.Yang, D.McMullan, Y.E.Chong, S.S.Krishna, C.L.Rife, D.Weekes, S.M.Brittain, P.Abdubek, E.Ambing, T.Astakhova, H.L.Axelrod, D.Carlton, J.Caruthers, H.J.Chiu, T.Clayton, L.Duan, J.Feuerhelm, J.C.Grant, S.K.Grzechnik, L.Jaroszewski, K.K.Jin, H.E.Klock, M.W.Knuth, A.Kumar, D.Marciano, M.D.Miller, A.T.Morse, E.Nigoghossian, L.Okach, J.Paulsen, R.Reyes, H.van den Bedem, A.White, G.Wolf, Q.Xu, K.O.Hodgson, J.Wooley, A.M.Deacon, A.Godzik, S.A.Lesley, M.A.Elsliger, P.Schimmel, and I.A.Wilson (2010).
Structure of a tryptophanyl-tRNA synthetase containing an iron-sulfur cluster.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 1326-1334.
PDB code: 2g36
19932696 M.Guo, P.Schimmel, and X.L.Yang (2010).
Functional expansion of human tRNA synthetases achieved by structural inventions.
  FEBS Lett, 584, 434-442.  
20700144 M.Guo, X.L.Yang, and P.Schimmel (2010).
New functions of aminoacyl-tRNA synthetases beyond translation.
  Nat Rev Mol Cell Biol, 11, 668-674.  
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
20010843 Q.Zhou, M.Kapoor, M.Guo, R.Belani, X.Xu, W.B.Kiosses, M.Hanan, C.Park, E.Armour, M.H.Do, L.A.Nangle, P.Schimmel, and X.L.Yang (2010).
Orthogonal use of a human tRNA synthetase active site to achieve multifunctionality.
  Nat Struct Mol Biol, 17, 57-61.  
20571084 R.A.Hughes, and A.D.Ellington (2010).
Rational design of an orthogonal tryptophanyl nonsense suppressor tRNA.
  Nucleic Acids Res, 38, 6813-6830.  
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.  
19386587 F.Charrière, P.O'Donoghue, S.Helgadóttir, L.Maréchal-Drouard, M.Cristodero, E.K.Horn, D.Söll, and A.Schneider (2009).
Dual targeting of a tRNAAsp requires two different aspartyl-tRNA synthetases in Trypanosoma brucei.
  J Biol Chem, 284, 16210-16217.  
19267673 I.A.Vasil'eva, E.A.Semenova, and N.A.Moor (2009).
Interaction of human phenylalanyl-tRNA synthetase with specific tRNA according to thiophosphate footprinting.
  Biochemistry (Mosc), 74, 175-185.  
19477417 M.Kapoor, F.J.Otero, B.M.Slike, K.L.Ewalt, and X.L.Yang (2009).
Mutational separation of aminoacylation and cytokine activities of human tyrosyl-tRNA synthetase.
  Chem Biol, 16, 531-539.  
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
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
17704131 E.Jakó, P.Ittzés, A.Szenes, A.Kun, E.Szathmáry, and G.Pál (2007).
In silico detection of tRNA sequence features characteristic to aminoacyl-tRNA synthetase class membership.
  Nucleic Acids Res, 35, 5593-5609.  
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.  
17726052 L.T.Guo, X.L.Chen, B.T.Zhao, Y.Shi, W.Li, H.Xue, and Y.X.Jin (2007).
Human tryptophanyl-tRNA synthetase is switched to a tRNA-dependent mode for tryptophan activation by mutations at V85 and I311.
  Nucleic Acids Res, 35, 5934-5943.  
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
17545306 W.Xie, L.A.Nangle, W.Zhang, P.Schimmel, and X.L.Yang (2007).
Long-range structural effects of a Charcot-Marie-Tooth disease-causing mutation in human glycyl-tRNA synthetase.
  Proc Natl Acad Sci U S A, 104, 9976-9981.
PDB codes: 2pme 2pmf
17637340 X.L.Yang, M.Guo, M.Kapoor, K.L.Ewalt, F.J.Otero, R.J.Skene, D.E.McRee, and P.Schimmel (2007).
Functional and crystal structure analysis of active site adaptations of a potent anti-angiogenic human tRNA synthetase.
  Structure, 15, 793-805.
PDB code: 1r6u
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.  
16798914 N.Shen, L.Guo, B.Yang, Y.Jin, and J.Ding (2006).
Structure of human tryptophanyl-tRNA synthetase in complex with tRNATrp reveals the molecular basis of tRNA recognition and specificity.
  Nucleic Acids Res, 34, 3246-3258.
PDB codes: 2ake 2dr2
16724112 X.L.Yang, F.J.Otero, K.L.Ewalt, J.Liu, M.A.Swairjo, C.Köhrer, U.L.RajBhandary, R.J.Skene, D.E.McRee, and P.Schimmel (2006).
Two conformations of a crystalline human tRNA synthetase-tRNA complex: implications for protein synthesis.
  EMBO J, 25, 2919-2929.
PDB code: 2azx
15723076 M.R.Buddha, and B.R.Crane (2005).
Structure and activity of an aminoacyl-tRNA synthetase that charges tRNA with nitro-tryptophan.
  Nat Struct Mol Biol, 12, 274-275.
PDB codes: 1yi8 1yia
15520379 M.R.Buddha, K.M.Keery, and B.R.Crane (2004).
An unusual tryptophanyl tRNA synthetase interacts with nitric oxide synthase in Deinococcus radiodurans.
  Proc Natl Acad Sci U S A, 101, 15881-15886.  
15148387 P.C.Zamecnik, M.K.Raychowdhury, D.R.Tabatadze, and H.F.Cantiello (2004).
Reversal of cystic fibrosis phenotype in a cultured Delta508 cystic fibrosis transmembrane conductance regulator cell line by oligonucleotide insertion.
  Proc Natl Acad Sci U S A, 101, 8150-8155.  
15489861 S.Hauenstein, C.M.Zhang, Y.M.Hou, and J.J.Perona (2004).
Shape-selective RNA recognition by cysteinyl-tRNA synthetase.
  Nat Struct Mol Biol, 11, 1134-1141.
PDB code: 1u0b
15189139 T.L.Hendrickson, V.de Crécy-Lagard, and P.Schimmel (2004).
Incorporation of nonnatural amino acids into proteins.
  Annu Rev Biochem, 73, 147-176.  
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.