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PDBsum entry 1ujp

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Lyase PDB id
1ujp
Jmol
Contents
Protein chain
243 a.a. *
Ligands
CIT
Waters ×303
* Residue conservation analysis
PDB id:
1ujp
Name: Lyase
Title: Crystal structure of tryptophan synthase a-subunit from ther thermophilus hb8
Structure: Tryptophan synthase alpha chain. Chain: a. Synonym: tryptophan synthase a-subunit. Engineered: yes
Source: Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.34Å     R-factor:   0.203     R-free:   0.221
Authors: Y.Asada,S.Yokoyama,S.Kuramitsu,M.Miyano,N.Kunishima,Riken St Genomics/proteomics Initiative (Rsgi)
Key ref: Y.Asada et al. (2005). Stabilization mechanism of the tryptophan synthase alpha-subunit from Thermus thermophilus HB8: X-ray crystallographic analysis and calorimetry. J Biochem, 138, 343-353. PubMed id: 16272128 DOI: 10.1093/jb/mvi133
Date:
08-Aug-03     Release date:   26-Aug-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P16608  (TRPA_THET2) -  Tryptophan synthase alpha chain
Seq:
Struc:
271 a.a.
243 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 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
Bound ligand (Het Group name = CIT)
matches with 42.86% similarity
+ 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!
  Biological process     metabolic process   5 terms 
  Biochemical function     catalytic activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1093/jb/mvi133 J Biochem 138:343-353 (2005)
PubMed id: 16272128  
 
 
Stabilization mechanism of the tryptophan synthase alpha-subunit from Thermus thermophilus HB8: X-ray crystallographic analysis and calorimetry.
Y.Asada, M.Sawano, K.Ogasahara, J.Nakamura, M.Ota, C.Kuroishi, M.Sugahara, K.Yutani, N.Kunishima.
 
  ABSTRACT  
 
In order to elucidate the thermo-stabilization mechanism of the tryptophan synthase alpha-subunit from the extreme thermophile Thermus thermophilus HB8 (Tt-alpha-subunit), its crystal structure was determined and its stability was examined using DSC. The results were compared to those of other orthologs from mesophilic and hyperthermophilic organisms. The denaturation temperature of the Tt-alpha-subunit was higher than that of the alpha-subunit from S. typhimurium (St-alpha-subunit) but lower than that of the alpha-subunit from P. furiosus (Pf-alpha-subunit). Specific denaturation enthalpy and specific denaturation heat capacity values of the Tt-alpha-subunit were the lowest among the three proteins, suggesting that entropy effects are responsible for the stabilization of the Tt-alpha-subunit. Based on a structural comparison with the St-alpha-subunit, two deletions in loop regions, an increase in the number of ion pairs and a decrease in cavity volume seem to be responsible for the stabilization of the Tt-alpha-subunit. The results of structural comparison suggest that the native structure of the Tt-alpha-subunit is better adapted to an ideally stable structure than that of the St-alpha-subunit, but worse than that of the Pf-alpha-subunit. The results of calorimetry suggest that the residual structure of the Tt-alpha-subunit in the denatured state contributes to the stabilization.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21085641 M.Q.Fatmi, and C.E.Chang (2010).
The role of oligomerization and cooperative regulation in protein function: the case of tryptophan synthase.
  PLoS Comput Biol, 6, e1000994.  
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