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PDBsum entry 1v7y

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protein ligands Protein-protein interface(s) links
Lyase PDB id
1v7y
Jmol
Contents
Protein chains
248 a.a. *
Ligands
SO4 ×2
Waters ×87
* Residue conservation analysis
PDB id:
1v7y
Name: Lyase
Title: Crystal structure of tryptophan synthase alpha-subunit from escherichia coli at room temperature
Structure: Tryptophan synthase alpha chain. Chain: a, b. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.50Å     R-factor:   0.218     R-free:   0.271
Authors: K.Nishio,Y.Morimoto,M.Ishizuka,K.Ogasahara,K.Yutani,T.Tsukih Structural Genomics/proteomics Initiative (Rsgi)
Key ref:
K.Nishio et al. (2005). Conformational changes in the alpha-subunit coupled to binding of the beta 2-subunit of tryptophan synthase from Escherichia coli: crystal structure of the tryptophan synthase alpha-subunit alone. Biochemistry, 44, 1184-1192. PubMed id: 15667212 DOI: 10.1021/bi047927m
Date:
25-Dec-03     Release date:   15-Feb-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A877  (TRPA_ECOLI) -  Tryptophan synthase alpha chain
Seq:
Struc:
268 a.a.
248 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: 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
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     metabolic process   5 terms 
  Biochemical function     catalytic activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi047927m Biochemistry 44:1184-1192 (2005)
PubMed id: 15667212  
 
 
Conformational changes in the alpha-subunit coupled to binding of the beta 2-subunit of tryptophan synthase from Escherichia coli: crystal structure of the tryptophan synthase alpha-subunit alone.
K.Nishio, Y.Morimoto, M.Ishizuka, K.Ogasahara, T.Tsukihara, K.Yutani.
 
  ABSTRACT  
 
When the tryptophan synthase alpha- and beta(2)-subunits combine to form the alpha(2)beta(2)-complex, the enzymatic activity of each subunit is stimulated by 1-2 orders of magnitude. To elucidate the structural basis of this mutual activation, it is necessary to determine the structures of the alpha- and beta-subunits alone and together with the alpha(2)beta(2)-complex. The crystal structures of the tryptophan synthase alpha(2)beta(2)-complex from Salmonella typhimurium (Stalpha(2)beta(2)-complex) have already been reported. However, the structures of the subunit alone from mesophiles have not yet been determined. The structure of the tryptophan synthase alpha-subunit alone from Escherichia coli (Ecalpha-subunit) was determined by an X-ray crystallographic analysis at 2.3 A, which is the first report on the subunits alone from the mesophiles. The biggest difference between the structures of the Ecalpha-subunit alone and the alpha-subunit in the Stalpha(2)beta(2)-complex (Stalpha-subunit) was as follows. Helix 2' in the Stalpha-subunit, including an active site residue (Asp60), was changed to a flexible loop in the Ecalpha-subunit alone. The conversion of the helix to a loop resulted in the collapse of the correct active site conformation. This region is also an important part for the mutual activation in the Stalpha(2)beta(2)-complex and interaction with the beta-subunit. These results suggest that the formation of helix 2'that is essential for the stimulation of the enzymatic activity of the alpha-subunit is constructed by the induced-fit mode involved in conformational changes upon interaction between the alpha- and beta-subunits. This also confirms the prediction of the conformational changes based on the thermodynamic analysis for the association between the alpha- and beta-subunits.
 

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
19626709 H.Fu, G.R.Grimsley, A.Razvi, J.M.Scholtz, and C.N.Pace (2009).
Increasing protein stability by improving beta-turns.
  Proteins, 77, 491-498.  
17586773 X.Yang, R.Vadrevu, Y.Wu, and C.R.Matthews (2007).
Long-range side-chain-main-chain interactions play crucial roles in stabilizing the (betaalpha)8 barrel motif of the alpha subunit of tryptophan synthase.
  Protein Sci, 16, 1398-1409.  
17222865 Y.Wu, R.Vadrevu, S.Kathuria, X.Yang, and C.R.Matthews (2007).
A tightly packed hydrophobic cluster directs the formation of an off-pathway sub-millisecond folding intermediate in the alpha subunit of tryptophan synthase, a TIM barrel protein.
  J Mol Biol, 366, 1624-1638.  
15691828 S.Raboni, S.Bettati, and A.Mozzarelli (2005).
Identification of the geometric requirements for allosteric communication between the alpha- and beta-subunits of tryptophan synthase.
  J Biol Chem, 280, 13450-13456.  
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.