PDBsum entry 4zdb

Isomerase

PDB id: 4zdb

Contents

Protein chains

267 a.a.

Ligands

SO4 ×8

CAA ×3

GOL ×7

Waters ×411

PDB id:

4zdb

Name:

Isomerase

Title:

Yeast enoyl-coa isomerase (sceci2) complexed with acetoacetyl-coa

Structure:

3,2-trans-enoyl-coa isomerase. Chain: a, b, c. Synonym: delta(3),delta(2)-enoyl-coa isomerase,d3,d2-enoyl-coa isomerase,dodecenoyl-coa isomerase. Engineered: yes. Other_details: cysteine 212 was oxidized to cme (s,s-(2- hydroxyethyl)thiocysteine) in the structure due to the presence of beta-mecarptoethanol.

Source:

Saccharomyces cerevisiae (strain atcc 204508 / s288c). Baker's yeast. Organism_taxid: 559292. Gene: eci1, ylr284c. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.14Å R-factor: 0.166 R-free: 0.190

Authors:

G.U.Onwukwe,M.K.Koski,R.K.Wierenga

Key ref:

G.U.Onwukwe et al. (2015). Structures of yeast peroxisomal Δ(3),Δ(2)-enoyl-CoA isomerase complexed with acyl-CoA substrate analogues: the importance of hydrogen-bond networks for the reactivity of the catalytic base and the oxyanion hole. Acta Crystallogr D Biol Crystallogr, 71, 2178-2191. PubMed id: 26527136 DOI: 10.1107/S139900471501559X

Date:

17-Apr-15 Release date: 11-Nov-15

Protein chains

Q05871  (ECI1_YEAST) -  3,2-trans-enoyl-CoA isomerase from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 280 a.a.

Struc: 267 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.5.3.3.8 - Delta(3)-Delta(2)-enoyl-CoA isomerase.
• Reaction:
  1. a (3Z)-enoyl-CoA = a 4-saturated (2E)-enoyl-CoA
  2. a (3E)-enoyl-CoA = a 4-saturated (2E)-enoyl-CoA

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

Added reference

DOI no: 10.1107/S139900471501559X

Acta Crystallogr D Biol Crystallogr 71:2178-2191 (2015)

PubMed id: 26527136

Structures of yeast peroxisomal Δ(3),Δ(2)-enoyl-CoA isomerase complexed with acyl-CoA substrate analogues: the importance of hydrogen-bond networks for the reactivity of the catalytic base and the oxyanion hole.

G.U.Onwukwe, M.K.Koski, P.Pihko, W.Schmitz, R.K.Wierenga.

ABSTRACT

Δ(3),Δ(2)-Enoyl-CoA isomerases (ECIs) catalyze the shift of a double bond from 3Z- or 3E-enoyl-CoA to 2E-enoyl-CoA. ECIs are members of the crotonase superfamily. The crotonase framework is used by many enzymes to catalyze a wide range of reactions on acyl-CoA thioesters. The thioester O atom is bound in a conserved oxyanion hole. Here, the mode of binding of acyl-CoA substrate analogues to peroxisomal Saccharomyces cerevisiae ECI (ScECI2) is described. The best defined part of the bound acyl-CoA molecules is the 3',5'-diphosphate-adenosine moiety, which interacts with residues of loop 1 and loop 2, whereas the pantetheine part is the least well defined. The catalytic base, Glu158, is hydrogen-bonded to the Asn101 side chain and is further hydrogen-bonded to the side chain of Arg100 in the apo structure. Arg100 is completely buried in the apo structure and a conformational change of the Arg100 side chain appears to be important for substrate binding and catalysis. The oxyanion hole is formed by the NH groups of Ala70 (loop 2) and Leu126 (helix 3). The O atoms of the corresponding peptide units, Gly69 O and Gly125 O, are both part of extensive hydrogen-bond networks. These hydrogen-bond networks are a conserved feature of the crotonase oxyanion hole and their importance for catalysis is discussed.