PDBsum entry 5mgb

Oxidoreductase

PDB id: 5mgb

Contents

Protein chains

725 a.a.

Ligands

SO4 ×4

CAA ×2

NAD ×2

GOL ×2

Waters ×96

PDB id:

5mgb

Name:

Oxidoreductase

Title:

Crystal structure of rat peroxisomal multifunctional enzyme type-1 (rpmfe1) complexed with acetoacetyl-coa and NAD

Structure:

Peroxisomal bifunctional enzyme. Chain: a, b. Synonym: pbfe. Engineered: yes

Source:

Rattus norvegicus. Rat. Organism_taxid: 10116. Gene: ehhadh. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.80Å R-factor: 0.212 R-free: 0.261

Authors:

P.Kasaragod,T.-R.Kiema,W.Schmitz,J.K.Hiltunen,R.K.Wierenga

Key ref:

P.Kasaragod et al. (2017). Structural enzymology comparisons of multifunctional enzyme, type-1 (MFE1): the flexibility of its dehydrogenase part. FEBS Open Bio, 7, 1830-1842. PubMed id: 29226071

Date:

21-Nov-16 Release date: 21-Dec-16

Supersedes:

5aak

Protein chains

P07896  (ECHP_RAT) -  Peroxisomal bifunctional enzyme from Rattus norvegicus

Seq: 722 a.a.

Struc: 725 a.a.

Enzyme reactions

• Enzyme class 2: E.C.1.1.1.35 - 3-hydroxyacyl-CoA dehydrogenase.
• Reaction: a (3S)-3-hydroxyacyl-CoA + NAD⁺ = a 3-oxoacyl-CoA + NADH + H⁺

(3S)-3-hydroxyacyl-CoA (Bound ligand (Het Group name = CAA) matches with 96.36% similarity) + NAD(+) (Bound ligand (Het Group name = NAD) corresponds exactly) = 3-oxoacyl-CoA + NADH + H(+)

• Enzyme class 3: E.C.4.2.1.17 - enoyl-CoA hydratase.
• Reaction:
  1. a 4-saturated-(3S)-3-hydroxyacyl-CoA = a (3E)-enoyl-CoA + H2O
  2. a (3S)-3-hydroxyacyl-CoA = a (2E)-enoyl-CoA + H2O

(3S)-3-hydroxyacyl-CoA (Bound ligand (Het Group name = CAA) matches with 96.36% similarity) = (2E)-enoyl-CoA + H2O

• Enzyme class 4: 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

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

FEBS Open Bio 7:1830-1842 (2017)

PubMed id: 29226071

Structural enzymology comparisons of multifunctional enzyme, type-1 (MFE1): the flexibility of its dehydrogenase part.

P.Kasaragod, G.B.Midekessa, S.Sridhar, W.Schmitz, T.R.Kiema, J.K.Hiltunen, R.K.Wierenga.

ABSTRACT

Multifunctional enzyme, type-1 (MFE1) is a monomeric enzyme with a 2E-enoyl-CoA hydratase and a 3S-hydroxyacyl-CoA dehydrogenase (HAD) active site. Enzyme kinetic data of rat peroxisomal MFE1 show that the catalytic efficiencies for converting the short-chain substrate 2E-butenoyl-CoA into acetoacetyl-CoA are much lower when compared with those of the homologous monofunctional enzymes. The mode of binding of acetoacetyl-CoA (to the hydratase active site) and the very similar mode of binding of NAD⁺and NADH (to the HAD part) are described and compared with those of their monofunctional counterparts. Structural comparisons suggest that the conformational flexibility of the HAD and hydratase parts of MFE1 are correlated. The possible importance of the conformational flexibility of MFE1 for its biocatalytic properties is discussed.