PDBsum entry 2hdh

Oxidoreductase

PDB id: 2hdh

Contents

Protein chain

293 a.a. *

Ligands

NAD ×2

Waters ×253

* Residue conservation analysis

PDB id:

2hdh

Name:

Oxidoreductase

Title:

Biochemical characterization and structure determination of human heart short chain l-3-hydroxyacyl coa dehydrogenase provide insight into catalytic mechanism

Structure:

L-3-hydroxyacyl coa dehydrogenase. Chain: a, b. Synonym: schad. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Organ: heart. Organelle: mitochondrial. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: expressed as selenomethionine-substituted protein. Protein was expressed with a c-terminal hexameric histidine tag.

Biol. unit:

Dimer (from PQS)

Resolution:

2.20Å R-factor: 0.198 R-free: 0.251

Authors:

J.J.Barycki,J.M.Bratt,L.J.Banaszak

Key ref:

J.J.Barycki et al. (1999). Biochemical characterization and crystal structure determination of human heart short chain L-3-hydroxyacyl-CoA dehydrogenase provide insights into catalytic mechanism. Biochemistry, 38, 5786-5798. PubMed id: 10231530 DOI: 10.1021/bi9829027

Date:

04-Dec-98 Release date: 12-May-99

Protein chains

Q16836  (HCDH_HUMAN) -  Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial from Homo sapiens

Seq: 314 a.a.

Struc: 293 a.a.*

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

Enzyme reactions

• Enzyme class: 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 + NAD(+) (Bound ligand (Het Group name = NAD) corresponds exactly) = 3-oxoacyl-CoA + NADH + H(+)

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

reference

DOI no: 10.1021/bi9829027

Biochemistry 38:5786-5798 (1999)

PubMed id: 10231530

Biochemical characterization and crystal structure determination of human heart short chain L-3-hydroxyacyl-CoA dehydrogenase provide insights into catalytic mechanism.

J.J.Barycki, L.K.O'Brien, J.M.Bratt, R.Zhang, R.Sanishvili, A.W.Strauss, L.J.Banaszak.

ABSTRACT

Human heart short chain L-3-hydroxyacyl-CoA dehydrogenase (SCHAD) catalyzes the oxidation of the hydroxyl group of L-3-hydroxyacyl-CoA to a keto group, concomitant with the reduction of NAD+ to NADH, as part of the beta-oxidation pathway. The homodimeric enzyme has been overexpressed in Escherichia coli, purified to homogeneity, and studied using biochemical and crystallographic techniques. The dissociation constants of NAD+ and NADH have been determined over a broad pH range and indicate that SCHAD binds reduced cofactor preferentially. Examination of apparent catalytic constants reveals that SCHAD displays optimal enzymatic activity near neutral pH, with catalytic efficiency diminishing rapidly toward pH extremes. The crystal structure of SCHAD complexed with NAD+ has been solved using multiwavelength anomalous diffraction techniques and a selenomethionine-substituted analogue of the enzyme. The subunit structure is comprised of two domains. The first domain is similar to other alpha/beta dinucleotide folds but includes an unusual helix-turn-helix motif which extends from the central beta-sheet. The second, or C-terminal, domain is primarily alpha-helical and mediates subunit dimerization and, presumably, L-3-hydroxyacyl-CoA binding. Molecular modeling studies in which L-3-hydroxybutyryl-CoA was docked into the enzyme-NAD+ complex suggest that His 158 serves as a general base, abstracting a proton from the 3-OH group of the substrate. Furthermore, the ability of His 158 to perform such a function may be enhanced by an electrostatic interaction with Glu 170, consistent with previous biochemical observations. These studies provide further understanding of the molecular basis of several inherited metabolic disease states correlated with L-3-hydroxyacyl-CoA dehydrogenase deficiencies.