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PDBsum entry 1wdw

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protein ligands Protein-protein interface(s) links
Lyase PDB id
1wdw
Jmol
Contents
Protein chains
(+ 0 more) 241 a.a. *
(+ 0 more) 385 a.a. *
Ligands
PLP ×6
Waters ×221
* Residue conservation analysis
PDB id:
1wdw
Name: Lyase
Title: Structural basis of mutual activation of the tryptophan synt complex from a hyperthermophile, pyrococcus furiosus
Structure: Tryptophan synthase alpha chain. Chain: a, c, e, g, i, k. Synonym: tryptophan synthase alpha subunit. Engineered: yes. Tryptophan synthase beta chain 1. Chain: b, d, f, h, j, l. Synonym: tryptophan synthase beta subunit. Engineered: yes
Source: Pyrococcus furiosus. Organism_taxid: 2261. Gene: trpa. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: trpb.
Biol. unit: Tetramer (from PQS)
Resolution:
3.00Å     R-factor:   0.196     R-free:   0.231
Authors: S.J.Lee,K.Ogasahara,J.Ma,K.Nishio,M.Ishida,Y.Yamagata,T.Tsuk K.Yutani,Riken Structural Genomics/proteomics Initiative (R
Key ref:
S.J.Lee et al. (2005). Conformational Changes in the tryptophan synthase from a hyperthermophile upon alpha2beta2 complex formation: crystal structure of the complex. Biochemistry, 44, 11417-11427. PubMed id: 16114878 DOI: 10.1021/bi050317h
Date:
19-May-04     Release date:   12-Jul-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q8U094  (TRPA_PYRFU) -  Tryptophan synthase alpha chain
Seq:
Struc:
248 a.a.
241 a.a.
Protein chains
Pfam   ArchSchema ?
Q8U093  (TRPB1_PYRFU) -  Tryptophan synthase beta chain 1
Seq:
Struc:
388 a.a.
385 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E, F, G, H, I, J, K, L: E.C.4.2.1.20  - Tryptophan synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Tryptophan Biosynthesis
      Reaction: L-serine + 1-C-(indol-3-yl)glycerol 3-phosphate = L-tryptophan + D-glyceraldehyde 3-phosphate + H2O
L-serine
+ 1-C-(indol-3-yl)glycerol 3-phosphate
= L-tryptophan
+ D-glyceraldehyde 3-phosphate
+ H(2)O
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Bound ligand (Het Group name = PLP) matches with 93.75% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   5 terms 
  Biochemical function     catalytic activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi050317h Biochemistry 44:11417-11427 (2005)
PubMed id: 16114878  
 
 
Conformational Changes in the tryptophan synthase from a hyperthermophile upon alpha2beta2 complex formation: crystal structure of the complex.
S.J.Lee, K.Ogasahara, J.Ma, K.Nishio, M.Ishida, Y.Yamagata, T.Tsukihara, K.Yutani.
 
  ABSTRACT  
 
The three-dimensional structure of the bifunctional tryptophan synthase alpha(2)beta(2) complex from Pyrococcus furiosus was determined by crystallographic analysis. This crystal structure, with the structures of an alpha subunit monomer and a beta(2) subunit dimer that have already been reported, is the first structural set in which changes in structure that occur upon the association of the individual tryptophan synthase subunits were observed. To elucidate the structural basis of the stimulation of the enzymatic activity of each of the alpha and beta(2) subunits upon alpha(2)beta(2) complex formation, the conformational changes due to complex formation were analyzed in detail compared with the structures of the alpha monomer and beta(2) subunit dimer. The major conformational changes due to complex formation occurred in the region correlated with the catalytic function of the enzyme as follows. (1) Structural changes in the beta subunit were greater than those in the alpha subunit. (2) Large movements of A46 and L165 in the alpha subunit due to complex formation caused a more open conformation favoring the entry of the substrate at the alpha active site. (3) The major changes in the beta subunit were the broadening of a long tunnel through which the alpha subunit product (indole) is transferred to the beta active site and the opening of an entrance at the beta active site. (4) The changes in the conformations of both the alpha and beta subunits due to complex formation contributed to the stabilization of the subunit association, which is critical for the stimulation of the enzymatic activities.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20370823 K.Nishio, K.Ogasahara, Y.Morimoto, T.Tsukihara, S.J.Lee, and K.Yutani (2010).
Large conformational changes in the Escherichia coli tryptophan synthase beta(2) subunit upon pyridoxal 5'-phosphate binding.
  FEBS J, 277, 2157-2170.
PDB codes: 2dh5 2dh6
19640845 M.Goto, T.Yamauchi, N.Kamiya, I.Miyahara, T.Yoshimura, H.Mihara, T.Kurihara, K.Hirotsu, and N.Esaki (2009).
Crystal structure of a homolog of mammalian serine racemase from Schizosaccharomyces pombe.
  J Biol Chem, 284, 25944-25952.
PDB codes: 1wtc 2zr8
17425797 R.Merkl (2007).
Modelling the evolution of the archeal tryptophan synthase.
  BMC Evol Biol, 7, 59.  
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.