1XX4

Crystal Structure of Rat Mitochondrial 3,2-Enoyl-CoA

Summary for 1XX4

• Entry DOI: 10.2210/pdb1xx4/pdb
• Related: 1DUB 1HZD 1PJH
• Descriptor: 3,2-trans-enoyl-CoA isomerase, mitochondrial, PHOSPHATE ION, ZINC ION, ... (5 entities in total)
• Functional Keywords: crotonase superfamily, domain swapped, isomerase
• Biological source: Rattus norvegicus (Norway rat)
• Cellular location: Mitochondrion matrix: P23965
• Total number of polymer chains: 1
• Total formula weight: 30202.55

Authors

Hubbard, P.A.,Yu, W.,Schulz, H.,Kim, J.-J. (deposition date: 2004-11-03, release date: 2004-11-23, Last modification date: 2024-04-03)

Primary citation

Hubbard, P.A.,Yu, W.,Schulz, H.,Kim, J.J.
Domain swapping in the low-similarity isomerase/hydratase superfamily: the crystal structure of rat mitochondrial Delta3, Delta2-enoyl-CoA isomerase.
Protein Sci., 14:1545-1555, 2005

PubMed Abstract: Two monofunctional Delta(3), Delta(2)-enoyl-CoA isomerases, one in mitochondria (mECI) and the other in both mitochondria and peroxisomes (pECI), belong to the low-similarity isomerase/hydratase superfamily. Both enzymes catalyze the movement of a double bond from C3 to C2 of an unsaturated acyl-CoA substrate for re-entry into the beta-oxidation pathway. Mutagenesis has shown that Glu165 of rat mECI is involved in catalysis; however, the putative catalytic residue in yeast pECI, Glu158, is not conserved in mECI. To elucidate whether Glu165 of mECI is correctly positioned for catalysis, the crystal structure of rat mECI has been solved. Crystal packing suggests the enzyme is trimeric, in contrast to other members of the superfamily, which appear crystallographically to be dimers of trimers. The polypeptide fold of mECI, like pECI, belongs to a subset of this superfamily in which the C-terminal domain of a given monomer interacts with its own N-terminal domain. This differs from that of crotonase and 1,4-dihydroxy-2-naphtoyl-CoA synthase, whose C-terminal domains are involved in domain swapping with an adjacent monomer. The structure confirms Glu165 as the putative catalytic acid/base, positioned to abstract the pro-R proton from C2 and reprotonate at C4 of the acyl chain. The large tunnel-shaped active site cavity observed in the mECI structure explains the relative substrate promiscuity in acyl-chain length and stereochemistry. Comparison with the crystal structure of pECI suggests the catalytic residues from both enzymes are spatially conserved but not in their primary structures, providing a powerful reminder of how catalytic residues cannot be determined solely by sequence alignments.

PubMed: 15883186
DOI: 10.1110/ps.041303705

Experimental method

X-RAY DIFFRACTION (2.2 Å)