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PDBsum entry 1evl

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protein ligands metals Protein-protein interface(s) links
Ligase PDB id
1evl
Jmol
Contents
Protein chains
401 a.a. *
Ligands
TSB ×4
Metals
_ZN ×4
Waters ×1544
* Residue conservation analysis
PDB id:
1evl
Name: Ligase
Title: Crystal structure of a truncated form of threonyl-tRNA synthetase with a threonyl adenylate analog
Structure: Threonyl-tRNA synthetase. Chain: a, b, c, d. Fragment: catalytic and anticodon binding domains (residues 242-642). Engineered: yes. Other_details: truncated form
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
1.55Å     R-factor:   0.215     R-free:   0.226
Authors: R.Sankaranarayanan,A.C.Dock-Bregeon,B.Rees,D.Moras
Key ref:
R.Sankaranarayanan et al. (2000). Zinc ion mediated amino acid discrimination by threonyl-tRNA synthetase. Nat Struct Biol, 7, 461-465. PubMed id: 10881191 DOI: 10.1038/75856
Date:
20-Apr-00     Release date:   19-Jul-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A8M3  (SYT_ECOLI) -  Threonine--tRNA ligase
Seq:
Struc:
 
Seq:
Struc:
642 a.a.
401 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 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
Bound ligand (Het Group name = TSB)
matches with 55.00% similarity
+ 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 
  Biological process     tRNA aminoacylation for protein translation   2 terms 
  Biochemical function     nucleotide binding     4 terms  

 

 
    reference    
 
 
DOI no: 10.1038/75856 Nat Struct Biol 7:461-465 (2000)
PubMed id: 10881191  
 
 
Zinc ion mediated amino acid discrimination by threonyl-tRNA synthetase.
R.Sankaranarayanan, A.C.Dock-Bregeon, B.Rees, M.Bovee, J.Caillet, P.Romby, C.S.Francklyn, D.Moras.
 
  ABSTRACT  
 
Accurate translation of the genetic code depends on the ability of aminoacyl-tRNA synthetases to distinguish between similar amino acids. In order to investigate the basis of amino acid recognition and to understand the role played by the zinc ion present in the active site of threonyl-tRNA synthetase, we have determined the crystal structures of complexes of an active truncated form of the enzyme with a threonyl adenylate analog or threonine. The zinc ion is directly involved in threonine recognition, forming a pentacoordinate intermediate with both the amino group and the side chain hydroxyl. Amino acid activation experiments reveal that the enzyme shows no activation of isosteric valine, and activates serine at a rate 1,000-fold less than that of cognate threonine. This study demonstrates that the zinc ion is neither strictly catalytic nor structural and suggests how the zinc ion ensures that only amino acids that possess a hydroxyl group attached to the beta-position are activated.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. The active site of N-ThrRS with Thr-AMS ligand. a, Stereo view of the dimeric core of ThrRS with the Thr-AMS molecules in the active site. The two monomers are represented in blue and red and the Thr-AMS molecule is in a CPK representation. b, View of the active site showing the interactions with the zinc ion. The class-specific motifs 2 and 3 are colored red and green, respectively. The zinc ion and water molecule are represented as pink and cyan spheres. c, The interaction network of the Thr-AMS molecule with the metal ion and the protein residues. d, Schematic representation showing the geometry of the zinc ion before and after the amino acid binding. In the square-based pyramidal state, the metal ion is displaced from the mean plane of the square towards His 511 by 0.6 . Figs 1ab and 2 were made using SETOR29.
Figure 2.
Figure 2. Comparison of threonine, Thr-AMS and Ser-AMS ligands as seen bound to their respective aaRS a, N-ThrRS -threonine structure: stereo view of an annealed omit map30 showing the electron density of the threonine substrate and water molecules, which were removed from the model before annealing (contour 3 ). Water molecules, shown as pink balls, occupy the positions of the phosphate and the ribose oxygens of Thr-AMS. b, N-ThrRS -Thr-AMS structure: stereo view of an annealed omit map showing the Thr-AMS molecule, omitted from the model (contour 2.5 ). c, Comparison of the orientations of the Ser-AMS and Thr-AMS molecules in the active sites of SerRS17 and ThrRS, respectively.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2000, 7, 461-465) copyright 2000.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21222438 A.Minajigi, B.Deng, and C.S.Francklyn (2011).
Fidelity escape by the unnatural amino acid β-hydroxynorvaline: an efficient substrate for Escherichia coli threonyl-tRNA synthetase with toxic effects on growth.
  Biochemistry, 50, 1101-1109.  
21285375 M.H.Nawaz, E.Merriman, X.L.Yang, and P.Schimmel (2011).
p23H implicated as cis/trans regulator of AlaXp-directed editing for mammalian cell homeostasis.
  Proc Natl Acad Sci U S A, 108, 2723-2728.  
21149735 D.Moras (2010).
Proofreading in translation: dynamics of the double-sieve model.
  Proc Natl Acad Sci U S A, 107, 21949-21950.  
20160114 J.Ling, and D.Söll (2010).
Severe oxidative stress induces protein mistranslation through impairment of an aminoacyl-tRNA synthetase editing site.
  Proc Natl Acad Sci U S A, 107, 4028-4033.  
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
19703275 A.Y.Mulkidjanian, and M.Y.Galperin (2009).
On the origin of life in the Zinc world. 2. Validation of the hypothesis on the photosynthesizing zinc sulfide edifices as cradles of life on Earth.
  Biol Direct, 4, 27.  
19379069 J.Ling, N.Reynolds, and M.Ibba (2009).
Aminoacyl-tRNA synthesis and translational quality control.
  Annu Rev Microbiol, 63, 61-78.  
19221587 K.Chen, and L.Kurgan (2009).
Investigation of atomic level patterns in protein--small ligand interactions.
  PLoS ONE, 4, e4473.  
20010690 M.Guo, Y.E.Chong, R.Shapiro, K.Beebe, X.L.Yang, and P.Schimmel (2009).
Paradox of mistranslation of serine for alanine caused by AlaRS recognition dilemma.
  Nature, 462, 808-812.
PDB codes: 3hxu 3hxv 3hxw 3hxx 3hxy 3hxz 3hy0 3hy1
19549823 M.Sokabe, T.Ose, A.Nakamura, K.Tokunaga, O.Nureki, M.Yao, and I.Tanaka (2009).
The structure of alanyl-tRNA synthetase with editing domain.
  Proc Natl Acad Sci U S A, 106, 11028-11033.
PDB codes: 2zze 2zzf 2zzg
18997014 A.Minajigi, and C.S.Francklyn (2008).
RNA-assisted catalysis in a protein enzyme: The 2'-hydroxyl of tRNA(Thr) A76 promotes aminoacylation by threonyl-tRNA synthetase.
  Proc Natl Acad Sci U S A, 105, 17748-17753.  
18172502 K.Beebe, M.Mock, E.Merriman, and P.Schimmel (2008).
Distinct domains of tRNA synthetase recognize the same base pair.
  Nature, 451, 90-93.  
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
  18931432 S.Shimizu, E.C.Juan, Y.I.Miyashita, Y.Sato, M.M.Hoque, K.Suzuki, M.Yogiashi, M.Tsunoda, A.C.Dock-Bregeon, D.Moras, T.Sekiguchi, and A.Takénaka (2008).
Crystallization and preliminary crystallographic studies of putative threonyl-tRNA synthetases from Aeropyrum pernix and Sulfolobus tokodaii.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 903-910.  
17644600 J.Caillet, M.Graffe, F.Eyermann, P.Romby, and M.Springer (2007).
Mutations in residues involved in zinc binding in the catalytic site of Escherichia coli threonyl-tRNA synthetase confer a dominant lethal phenotype.
  J Bacteriol, 189, 6839-6848.  
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.  
17785455 M.Saravanan, K.Vasu, S.Ghosh, and V.Nagaraja (2007).
Dual role for Zn2+ in maintaining structural integrity and inducing DNA sequence specificity in a promiscuous endonuclease.
  J Biol Chem, 282, 32320-32326.  
16675947 S.Bilokapic, T.Maier, D.Ahel, I.Gruic-Sovulj, D.Söll, I.Weygand-Durasevic, and N.Ban (2006).
Structure of the unusual seryl-tRNA synthetase reveals a distinct zinc-dependent mode of substrate recognition.
  EMBO J, 25, 2498-2509.
PDB codes: 2cim 2cj9 2cja 2cjb
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
15507440 B.Ruan, M.L.Bovee, M.Sacher, C.Stathopoulos, K.Poralla, C.S.Francklyn, and D.Söll (2005).
A unique hydrophobic cluster near the active site contributes to differences in borrelidin inhibition among threonyl-tRNA synthetases.
  J Biol Chem, 280, 571-577.  
15775966 M.W.Zhao, B.Zhu, R.Hao, M.G.Xu, G.Eriani, and E.D.Wang (2005).
Leucyl-tRNA synthetase from the ancestral bacterium Aquifex aeolicus contains relics of synthetase evolution.
  EMBO J, 24, 1430-1439.  
16338408 O.Kotik-Kogan, N.Moor, D.Tworowski, and M.Safro (2005).
Structural basis for discrimination of L-phenylalanine from L-tyrosine by phenylalanyl-tRNA synthetase.
  Structure, 13, 1799-1807.
PDB codes: 2akw 2aly 2amc
16087664 S.An, and K.Musier-Forsyth (2005).
Cys-tRNA(Pro) editing by Haemophilus influenzae YbaK via a novel synthetase.YbaK.tRNA ternary complex.
  J Biol Chem, 280, 34465-34472.  
15908961 S.Dwivedi, S.P.Kruparani, and R.Sankaranarayanan (2005).
A D-amino acid editing module coupled to the translational apparatus in archaea.
  Nat Struct Mol Biol, 12, 556-557.
PDB code: 1y2q
15525705 D.J.Rigden (2004).
Archaea recruited D-Tyr-tRNATyr deacylase for editing in Thr-tRNA synthetase.
  RNA, 10, 1845-1851.  
15240874 D.Korencic, I.Ahel, J.Schelert, M.Sacher, B.Ruan, C.Stathopoulos, P.Blum, M.Ibba, and D.Söll (2004).
A freestanding proofreading domain is required for protein synthesis quality control in Archaea.
  Proc Natl Acad Sci U S A, 101, 10260-10265.  
15079065 K.Beebe, E.Merriman, L.Ribas De Pouplana, and P.Schimmel (2004).
A domain for editing by an archaebacterial tRNA synthetase.
  Proc Natl Acad Sci U S A, 101, 5958-5963.  
14764088 R.Banerjee, D.Y.Dubois, J.Gauthier, S.X.Lin, S.Roy, and J.Lapointe (2004).
The zinc-binding site of a class I aminoacyl-tRNA synthetase is a SWIM domain that modulates amino acid binding via the tRNA acceptor arm.
  Eur J Biochem, 271, 724-733.  
15322138 S.An, and K.Musier-Forsyth (2004).
Trans-editing of Cys-tRNAPro by Haemophilus influenzae YbaK protein.
  J Biol Chem, 279, 42359-42362.  
15333948 S.Dwivedi, S.P.Kruparani, and R.Sankaranarayanan (2004).
Cloning, expression, purification, crystallization and preliminary X-ray crystallographic investigations of a unique editing domain from archaebacteria.
  Acta Crystallogr D Biol Crystallogr, 60, 1662-1664.  
12581659 A.R.Ferré-D'Amaré (2003).
RNA-modifying enzymes.
  Curr Opin Struct Biol, 13, 49-55.  
14530268 F.C.Wong, P.J.Beuning, C.Silvers, and K.Musier-Forsyth (2003).
An isolated class II aminoacyl-tRNA synthetase insertion domain is functional in amino acid editing.
  J Biol Chem, 278, 52857-52864.  
12581352 J.Caillet, T.Nogueira, B.Masquida, F.Winter, M.Graffe, A.C.Dock-Brégeon, A.Torres-Larios, R.Sankaranarayanan, E.Westhof, B.Ehresmann, C.Ehresmann, P.Romby, and M.Springer (2003).
The modular structure of Escherichia coli threonyl-tRNA synthetase as both an enzyme and a regulator of gene expression.
  Mol Microbiol, 47, 961-974.  
12554667 K.Beebe, L.Ribas De Pouplana, and P.Schimmel (2003).
Elucidation of tRNA-dependent editing by a class II tRNA synthetase and significance for cell viability.
  EMBO J, 22, 668-675.  
14690420 M.L.Bovee, M.A.Pierce, and C.S.Francklyn (2003).
Induced fit and kinetic mechanism of adenylation catalyzed by Escherichia coli threonyl-tRNA synthetase.
  Biochemistry, 42, 15102-15113.  
12486031 M.Ryckelynck, R.Giegé, and M.Frugier (2003).
Yeast tRNA(Asp) charging accuracy is threatened by the N-terminal extension of aspartyl-tRNA synthetase.
  J Biol Chem, 278, 9683-9690.  
12615010 P.Romby, and M.Springer (2003).
Bacterial translational control at atomic resolution.
  Trends Genet, 19, 155-161.  
11953757 A.Torres-Larios, A.C.Dock-Bregeon, P.Romby, B.Rees, R.Sankaranarayanan, J.Caillet, M.Springer, C.Ehresmann, B.Ehresmann, and D.Moras (2002).
Structural basis of translational control by Escherichia coli threonyl tRNA synthetase.
  Nat Struct Biol, 9, 343-347.
PDB code: 1kog
12392560 I.Gruic-Sovulj, I.Landeka, D.Söll, and I.Weygand-Durasevic (2002).
tRNA-dependent amino acid discrimination by yeast seryl-tRNA synthetase.
  Eur J Biochem, 269, 5271-5279.  
12032090 K.J.Newberry, Y.M.Hou, and J.J.Perona (2002).
Structural origins of amino acid selection without editing by cysteinyl-tRNA synthetase.
  EMBO J, 21, 2778-2787.
PDB codes: 1li5 1li7
11864608 T.L.Hendrickson, T.K.Nomanbhoy, V.de Crécy-Lagard, S.Fukai, O.Nureki, S.Yokoyama, and P.Schimmel (2002).
Mutational separation of two pathways for editing by a class I tRNA synthetase.
  Mol Cell, 9, 353-362.  
  11375928 M.Ibba, and D.Söll (2001).
The renaissance of aminoacyl-tRNA synthesis.
  EMBO Rep, 2, 382-387.  
11553770 M.T.Hilgers, and M.L.Ludwig (2001).
Crystal structure of the quorum-sensing protein LuxS reveals a catalytic metal site.
  Proc Natl Acad Sci U S A, 98, 11169-11174.
PDB code: 1ie0
11166571 M.V.Rodnina, and W.Wintermeyer (2001).
Ribosome fidelity: tRNA discrimination, proofreading and induced fit.
  Trends Biochem Sci, 26, 124-130.  
11412966 T.K.Nomanbhoy, and P.Schimmel (2001).
Active site of an aminoacyl-tRNA synthetase dissected by energy-transfer-dependent fluorescence.
  Bioorg Med Chem Lett, 11, 1485-1491.  
10922054 P.J.Beuning, and K.Musier-Forsyth (2000).
Hydrolytic editing by a class II aminoacyl-tRNA synthetase.
  Proc Natl Acad Sci U S A, 97, 8916-8920.  
11112538 T.A.Keating, C.G.Marshall, and C.T.Walsh (2000).
Reconstitution and characterization of the Vibrio cholerae vibriobactin synthetase from VibB, VibE, VibF, and VibH.
  Biochemistry, 39, 15522-15530.  
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.