PDBsum entry 5y8h

Oxidoreductase

PDB id: 5y8h

Contents

Protein chains

292 a.a.

Ligands

NAD ×2

AKR ×3

GOL ×2

9ON ×2

Metals

_MG

Waters ×581

PDB id:

5y8h

Name:

Oxidoreductase

Title:

Mycobacterium tuberculosis 3-hydroxyisobutyrate dehydrogenase (mthibadh) + NAD+

Structure:

Probable 3-hydroxyisobutyrate dehydrogenase. Chain: a, b. Synonym: hibadh. Engineered: yes

Source:

Mycobacterium tuberculosis (strain atcc 25618 / h37rv). Organism_taxid: 83332. Strain: atcc 25618 / h37rv. Gene: mmsb, rv0751c, mtv041.25c. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.10Å R-factor: 0.162 R-free: 0.211

Authors:

R.Srikalaivani,A.Singh,A.Surolia,M.Vijayan

Key ref:

R.Srikalaivani et al. (2018). Structure, interactions and action of Mycobacterium tuberculosis 3-hydroxyisobutyric acid dehydrogenase. Biochem J, 475, 2457-2471. PubMed id: 29959185 DOI: 10.1042/BCJ20180271

Date:

21-Aug-17 Release date: 11-Jul-18

Protein chains

P9WNY5  (MMSB_MYCTU) -  Probable 3-hydroxyisobutyrate dehydrogenase from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Seq: 294 a.a.

Struc: 292 a.a.

Enzyme reactions

• Enzyme class: E.C.1.1.1.31 - 3-hydroxyisobutyrate dehydrogenase.
• Reaction: 3-hydroxy-2-methylpropanoate + NAD⁺ = 2-methyl-3-oxopropanoate + NADH + H⁺

3-hydroxy-2-methylpropanoate (Bound ligand (Het Group name = 9ON) matches with 54.55% similarity) + NAD(+) (Bound ligand (Het Group name = NAD) corresponds exactly) = 2-methyl-3-oxopropanoate + NADH + H(+)

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

reference

DOI no: 10.1042/BCJ20180271

Biochem J 475:2457-2471 (2018)

PubMed id: 29959185

Structure, interactions and action of Mycobacterium tuberculosis 3-hydroxyisobutyric acid dehydrogenase.

R.Srikalaivani, A.Singh, M.Vijayan, A.Surolia.

ABSTRACT

Biochemical and crystallographic studies on Mycobacterium tuberculosis 3-hydroxyisobutyric acid dehydrogenase (MtHIBADH), a member of the 3-hydroxyacid dehydrogenase superfamily, have been carried out. Gel filtration and blue native PAGE of MtHIBADH show that the enzyme is a dimer. The enzyme preferentially uses NAD⁺ as the cofactor and is specific to S-hydroxyisobutyric acid (HIBA). It can also use R-HIBA, l-serine and 3-hydroxypropanoic acid (3-HP) as substrates, but with much less efficiency. The pH optimum for activity is ∼11. Structures of the native enzyme, the holoenzyme, binary complexes with NAD⁺, S-HIBA, R-HIBA, l-serine and 3-HP and ternary complexes involving the substrates and NAD⁺ have been determined. None of the already known structures of HIBADH contain a substrate molecule at the binding site. The structures reported here provide for the first time, among other things, a clear indication of the location and interactions of the substrates at the active site. They also define the entrance of the substrates to the active site region. The structures provide information on the role of specific residues at the active site and the entrance. The results obtained from crystal structures are consistent with solution studies including mutational analysis. They lead to the proposal of a plausible mechanism of the action of the enzyme.