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PDBsum entry 1d2r

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protein Protein-protein interface(s) links
Ligase PDB id
1d2r
Jmol
Contents
Protein chains
(+ 0 more) 326 a.a. *
* Residue conservation analysis
PDB id:
1d2r
Name: Ligase
Title: 2.9 a crystal structure of ligand-free tryptophanyl-tRNA synthetase: domain movements fragment the adenine nucleotide binding site.
Structure: Protein (tryptophanyl tRNA synthetase). Chain: a, b, c, d, e, f. Synonym: trprs. Ec: 6.1.1.2
Source: Geobacillus stearothermophilus. Organism_taxid: 1422
Biol. unit: Dimer (from PQS)
Resolution:
2.90Å     R-factor:   0.237     R-free:   0.262
Authors: V.A.Ilyin,C.W.Carter Jr.
Key ref: V.A.Ilyin et al. (2000). 2.9 A crystal structure of ligand-free tryptophanyl-tRNA synthetase: domain movements fragment the adenine nucleotide binding site. Protein Sci, 9, 218-231. PubMed id: 10716174 DOI: 10.1110/ps.9.2.218
Date:
27-Sep-99     Release date:   05-Apr-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00953  (SYW_GEOSE) -  Tryptophan--tRNA ligase
Seq:
Struc:
328 a.a.
326 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.6.1.1.2  - Tryptophan--tRNA ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + L-tryptophan + tRNA(Trp) = AMP + diphosphate + L-tryptophyl- tRNA(Trp)
ATP
+ L-tryptophan
+ tRNA(Trp)
= AMP
+ diphosphate
+ L-tryptophyl- tRNA(Trp)
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: 10.1110/ps.9.2.218 Protein Sci 9:218-231 (2000)
PubMed id: 10716174  
 
 
2.9 A crystal structure of ligand-free tryptophanyl-tRNA synthetase: domain movements fragment the adenine nucleotide binding site.
V.A.Ilyin, B.Temple, M.Hu, G.Li, Y.Yin, P.Vachette, C.W.Carter.
 
  ABSTRACT  
 
The crystal structure of ligand-free tryptophanyl-tRNA synthetase (TrpRS) was solved at 2.9 A using a combination of molecular replacement and maximum-entropy map/phase improvement. The dimeric structure (R = 23.7, Rfree = 26.2) is asymmetric, unlike that of the TrpRS tryptophanyl-5'AMP complex (TAM; DoubliƩ S, Bricogne G, Gilmore CJ, Carter CW Jr, 1995, Structure 3:17-31). In agreement with small-angle solution X-ray scattering experiments, unliganded TrpRS has a conformation in which both monomers open, leaving only the tryptophan-binding regions of their active sites intact. The amino terminal alphaA-helix, TIGN, and KMSKS signature sequences, and the distal helical domain rotate as a single rigid body away from the dinucleotide-binding fold domain, opening the AMP binding site, seen in the TAM complex, into two halves. Comparison of side-chain packing in ligand-free TrpRS and the TAM complex, using identification of nonpolar nuclei (Ilyin VA, 1994, Protein Eng 7:1189-1195), shows that significant repacking occurs between three relatively stable core regions, one of which acts as a bearing between the other two. These domain rearrangements provide a new structural paradigm that is consistent in detail with the "induced-fit" mechanism proposed for TyrRS by Fersht et al. (Fersht AR, Knill-Jones JW, Beduelle H, Winter G, 1988, Biochemistry 27:1581-1587). Coupling of ATP binding determinants associated with the two catalytic signature sequences to the helical domain containing the presumptive anticodon-binding site provides a mechanism to coordinate active-site chemistry with relocation of the major tRNA binding determinants.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
  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
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.  
19174517 P.Laowanapiban, M.Kapustina, C.Vonrhein, M.Delarue, P.Koehl, and C.W.Carter (2009).
Independent saturation of three TrpRS subsites generates a partially assembled state similar to those observed in molecular simulations.
  Proc Natl Acad Sci U S A, 106, 1790-1795.
PDB codes: 3fhj 3fi0
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
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.  
17937916 M.Kapustina, V.Weinreb, L.Li, B.Kuhlman, and C.W.Carter (2007).
A conformational transition state accompanies tryptophan activation by B. stearothermophilus tryptophanyl-tRNA synthetase.
  Structure, 15, 1272-1284.  
17428498 P.Retailleau, V.Weinreb, M.Hu, and C.W.Carter (2007).
Crystal structure of tryptophanyl-tRNA synthetase complexed with adenosine-5' tetraphosphate: evidence for distributed use of catalytic binding energy in amino acid activation by class I aminoacyl-tRNA synthetases.
  J Mol Biol, 369, 108-128.
PDB code: 2ov4
17378584 S.W.Lue, and S.O.Kelley (2007).
A single residue in leucyl-tRNA synthetase affecting amino acid specificity and tRNA aminoacylation.
  Biochemistry, 46, 4466-4472.  
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
16373473 J.H.Brown (2006).
Breaking symmetry in protein dimers: designs and functions.
  Protein Sci, 15, 1.  
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
  16511069 J.Jeyakanthan, E.Inagaki, C.Kuroishi, and T.H.Tahirov (2005).
Structure of PIN-domain protein PH0500 from Pyrococcus horikoshii.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 463-468.
PDB codes: 1v96 1ye5
15856481 J.Roach, S.Sharma, M.Kapustina, and C.W.Carter (2005).
Structure alignment via Delaunay tetrahedralization.
  Proteins, 60, 66-81.  
15840835 Y.Zhang, L.Wang, P.G.Schultz, and I.A.Wilson (2005).
Crystal structures of apo wild-type M. jannaschii tyrosyl-tRNA synthetase (TyrRS) and an engineered TyrRS specific for O-methyl-L-tyrosine.
  Protein Sci, 14, 1340-1349.
PDB codes: 1u7d 1u7x
15187228 Z.Zhang, L.Alfonta, F.Tian, B.Bursulaya, S.Uryu, D.S.King, and P.G.Schultz (2004).
Selective incorporation of 5-hydroxytryptophan into proteins in mammalian cells.
  Proc Natl Acad Sci U S A, 101, 8882-8887.  
14674776 M.Acchione, J.G.Guillemette, S.M.Twine, C.W.Hogue, B.Rajendran, and A.G.Szabo (2003).
Fluorescence based structural analysis of tryptophan analogue-AMP formation in single tryptophan mutants of Bacillus stearothermophilus tryptophanyl-tRNA synthetase.
  Biochemistry, 42, 14994-15002.  
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
12021441 R.C.Noonan, C.W.Carter CW, and C.K.Bagdassarian (2002).
Enzymatic conformational fluctuations along the reaction coordinate of cytidine deaminase.
  Protein Sci, 11, 1424-1434.  
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
11420434 K.O.Alper, M.Singla, J.L.Stone, and C.K.Bagdassarian (2001).
Correlated conformational fluctuations during enzymatic catalysis: Implications for catalytic rate enhancement.
  Protein Sci, 10, 1319-1330.  
12762019 O.Nureki, S.Fukai, S.Sekine, A.Shimada, T.Terada, T.Nakama, M.Shirouzu, D.G.Vassylyev, and S.Yokoyama (2001).
Structural basis for amino acid and tRNA recognition by class I aminoacyl-tRNA synthetases.
  Cold Spring Harb Symp Quant Biol, 66, 167-173.  
11679724 P.Retailleau, Y.Yin, M.Hu, J.Roach, G.Bricogne, C.Vonrhein, P.Roversi, E.Blanc, R.M.Sweet, and C.W.Carter (2001).
High-resolution experimental phases for tryptophanyl-tRNA synthetase (TrpRS) complexed with tryptophanyl-5'AMP.
  Acta Crystallogr D Biol Crystallogr, 57, 1595-1608.
PDB codes: 1i6k 1i6l 1i6m
11052665 M.Praetorius-Ibba, N.Stange-Thomann, M.Kitabatake, K.Ali, I.Söll, C.W.Carter, M.Ibba, and D.Söll (2000).
Ancient adaptation of the active site of tryptophanyl-tRNA synthetase for tryptophan binding.
  Biochemistry, 39, 13136-13143.  
10811626 S.Cusack, A.Yaremchuk, and M.Tukalo (2000).
The 2 A crystal structure of leucyl-tRNA synthetase and its complex with a leucyl-adenylate analogue.
  EMBO J, 19, 2351-2361.
PDB code: 1h3n
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.