4U1A

Crystal structure of human peroxisomal delta3,delta2, enoyl-CoA isomerase helix-10 deletion mutant (ISOB-ECI2)

Summary for 4U1A

• Entry DOI: 10.2210/pdb4u1a/pdb
• Descriptor: Enoyl-CoA delta isomerase 2, CHLORIDE ION (3 entities in total)
• Functional Keywords: peci, crotonase, beta-oxidation, isomerase
• Biological source: Homo sapiens (Human)
• Cellular location: Isoform 1: Mitochondrion . Isoform 2: Peroxisome matrix: O75521
• Total number of polymer chains: 3
• Total formula weight: 89647.54

Authors

Onwukwe, G.U.,Koski, M.K.,Wierenga, R.K. (deposition date: 2014-07-15, release date: 2014-12-24, Last modification date: 2024-05-08)

Primary citation

Onwukwe, G.U.,Kursula, P.,Koski, M.K.,Schmitz, W.,Wierenga, R.K.
Human Delta (3) , Delta (2) -enoyl-CoA isomerase, type 2: a structural enzymology study on the catalytic role of its ACBP domain and helix-10.
Febs J., 282:746-768, 2015

PubMed Abstract: The catalytic domain of the trimeric human Δ(3),Δ(2)-enoyl-CoA isomerase, type 2 (HsECI2), has the typical crotonase fold. In the active site of this fold two main chain NH groups form an oxyanion hole for binding the thioester oxygen of the 3E- or 3Z-enoyl-CoA substrate molecules. A catalytic glutamate is essential for the proton transfer between the substrate C2 and C4 atoms for forming the product 2E-enoyl-CoA, which is a key intermediate in the β-oxidation pathway. The active site is covered by the C-terminal helix-10. In HsECI2, the isomerase domain is extended at its N terminus by an acyl-CoA binding protein (ACBP) domain. Small angle X-ray scattering analysis of HsECI2 shows that the ACBP domain protrudes out of the central isomerase trimer. X-ray crystallography of the isomerase domain trimer identifies the active site geometry. A tunnel, shaped by loop-2 and extending from the catalytic site to bulk solvent, suggests a likely mode of binding of the fatty acyl chains. Calorimetry data show that the separately expressed ACBP and isomerase domains bind tightly to fatty acyl-CoA molecules. The truncated isomerase variant (without ACBP domain) has significant enoyl-CoA isomerase activity; however, the full-length isomerase is more efficient. Structural enzymological studies of helix-10 variants show the importance of this helix for efficient catalysis. Its hydrophobic side chains, together with residues from loop-2 and loop-4, complete a hydrophobic cluster that covers the active site, thereby fixing the thioester moiety in a mode of binding competent for efficient catalysis.

PubMed: 25515061
DOI: 10.1111/febs.13179

Experimental method

X-RAY DIFFRACTION (2.85 Å)