PDBsum entry 1tpc

Isomerase(intramolecular oxidoreductase)

PDB id: 1tpc

Contents

Protein chains

245 a.a. *

Ligands

PGH ×2

Waters ×234

* Residue conservation analysis

PDB id:

1tpc

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)

Resolution:

1.90Å R-factor: 0.182

Authors:

Z.Zhang,S.Sugio,E.A.Komives,K.D.Liu,J.R.Knowles,G.A.Petsko,D.Ringe

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

Date:

03-Feb-94 Release date: 14-Feb-95

Protein chains

P00940  (TPIS_CHICK) -  Triosephosphate isomerase from Gallus gallus

Seq: 248 a.a.

Struc: 245 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: E.C.4.2.3.3 - methylglyoxal synthase.
• Reaction: dihydroxyacetone phosphate = methylglyoxal + phosphate

dihydroxyacetone phosphate (Bound ligand (Het Group name = PGH) matches with 66.67% similarity) = methylglyoxal + phosphate

• Enzyme class 3: E.C.5.3.1.1 - triose-phosphate isomerase.
• Reaction: D-glyceraldehyde 3-phosphate = dihydroxyacetone phosphate

D-glyceraldehyde 3-phosphate (Bound ligand (Het Group name = PGH) matches with 66.67% similarity) = dihydroxyacetone phosphate

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

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.

ABSTRACT

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.