PDBsum entry 1tpb

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Isomerase(intramolecular oxidoreductase) PDB id
Protein chains
245 a.a. *
PGH ×2
Waters ×253
* Residue conservation analysis
PDB id:
Name: Isomerase(intramolecular oxidoreductase)
Title: Offset of a catalytic lesion by a bound water soluble
Structure: Triosephosphate isomerase. Chain: 1, 2. Engineered: yes
Source: Gallus gallus. Chicken. Organism_taxid: 9031
Biol. unit: Dimer (from PQS)
1.90Å     R-factor:   0.182    
Authors: Z.Zhang,S.Sugio,E.A.Komives,K.D.Liu,J.R.Knowles,G.A.Petsko,D
Key ref:
E.A.Komives et al. (1995). The structural basis for pseudoreversion of the E165D lesion by the secondary S96P mutation in triosephosphate isomerase depends on the positions of active site water molecules. Biochemistry, 34, 13612-13621. PubMed id: 7577950 DOI: 10.1021/bi00041a041
03-Feb-94     Release date:   14-Feb-95    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P00940  (TPIS_CHICK) -  Triosephosphate isomerase
248 a.a.
245 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - Triose-phosphate isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: D-glyceraldehyde 3-phosphate = glycerone phosphate
D-glyceraldehyde 3-phosphate
Bound ligand (Het Group name = PGH)
matches with 66.67% similarity
= glycerone phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular space   4 terms 
  Biological process     metabolic process   9 terms 
  Biochemical function     catalytic activity     3 terms  


    Added reference    
DOI no: 10.1021/bi00041a041 Biochemistry 34:13612-13621 (1995)
PubMed id: 7577950  
The structural basis for pseudoreversion of the E165D lesion by the secondary S96P mutation in triosephosphate isomerase depends on the positions of active site water molecules.
E.A.Komives, J.C.Lougheed, K.Liu, S.Sugio, Z.Zhang, G.A.Petsko, D.Ringe.
The structural basis for the improvement in catalytic efficiency of the mutant E165D chicken triosephosphate isomerase by the secondary mutation, S96P, has been analyzed using a combination of X-ray crystallography and Fourier transform infrared spectroscopy. All X-ray structures were of the complex of phosphoglycolohydroxamate (PGH), an intermediate analog, with the isomerase, and each was solved to a resolution of 1.9 A. Comparison of the structure of the double mutant, E165D.S96P, with that of the single mutant, E165D, as well as with the wild-type isomerase shows only insignificant differences in the positions of the side chains in all of the mutants when compared with the wild-type isomerase, except that in both the E165D and E165D.S96P mutants, the aspartate side chain was approximately 0.7 A further away from the substrate analog than the glutamate side chain. Significant differences were observed in the crystal structure of the E165D.S96P double mutant in the positions of ordered water molecules bound at the active site. The loss of two water molecules located near the side chain at position 165 was observed in isomerases containing the S96P mutation. The resulting increase in hydrophobicity of the pocket probably causes an increase in the pKa of the catalytic base, D165, thereby improving its basicity. A new ordered water molecule was observed underneath the bound PGH in the E165D.S96P structure, which likely decreases the pKa's of the substrate protons, thereby increasing their acidity. An enzyme derived carbonyl stretch at 1746 cm-1 that is only observed in the IR spectrum of the E165D.S96P double mutant isomerase with bound substrates has been assigned to a stable ground state protonated D165-enediol(ate) intermediate complex. Thus, the gain in activity resulting from the S96P second site change probably results from a combination of improving the basicity of the enzyme, improving the acidity of the substrate protons, and stabilization of a reaction intermediate. All three of these effects seem to be caused by changes in bound water molecules.

Literature references that cite this PDB file's key reference

  PubMed id Reference
12509510 G.Jogl, S.Rozovsky, A.E.McDermott, and L.Tong (2003).
Optimal alignment for enzymatic proton transfer: structure of the Michaelis complex of triosephosphate isomerase at 1.2-A resolution.
  Proc Natl Acad Sci U S A, 100, 50-55.
PDB codes: 1ney 1nf0
10398928 D.Ringe, and C.Mattos (1999).
Analysis of the binding surfaces of proteins.
  Med Res Rev, 19, 321-331.  
9435218 S.Shaltiel, S.Cox, and S.S.Taylor (1998).
Conserved water molecules contribute to the extensive network of interactions at the active site of protein kinase A.
  Proc Natl Acad Sci U S A, 95, 484-491.  
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