PDBsum entry 3vl3

Oxidoreductase

PDB id: 3vl3

Contents

Protein chain

364 a.a.

Ligands

IPM

Metals

_CL

_CA

Waters ×275

PDB id:

3vl3

Name:

Oxidoreductase

Title:

3-isopropylmalate dehydrogenase from shewanella oneidensis mr-1 at 340 mpa

Structure:

3-isopropylmalate dehydrogenase. Chain: a. Synonym: 3-ipm-dh, beta-ipm dehydrogenase, imdh. Engineered: yes

Source:

Shewanella oneidensis. Organism_taxid: 211586. Strain: mr-1. Gene: leub, so_4235. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.80Å R-factor: 0.159 R-free: 0.202

Authors:

T.Nagae,N.Watanabe

Key ref:

T.Nagae et al. (2012). High-pressure-induced water penetration into 3-isopropylmalate dehydrogenase. Acta Crystallogr D Biol Crystallogr, 68, 300-309. PubMed id: 22349232

Date:

29-Nov-11 Release date: 29-Feb-12

Protein chain

Q8E9N3  (LEU3_SHEON) -  3-isopropylmalate dehydrogenase from Shewanella oneidensis (strain MR-1)

Seq: 364 a.a.

Struc: 364 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.1.1.1.85 - 3-isopropylmalate dehydrogenase.
• Pathway: Leucine Biosynthesis
• Reaction: (2R,3S)-3-isopropylmalate + NAD⁺ = 4-methyl-2-oxopentanoate + CO2 + NADH

(2R,3S)-3-isopropylmalate (Bound ligand (Het Group name = IPM) corresponds exactly) + NAD(+) = 4-methyl-2-oxopentanoate + CO2 + NADH

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

reference

Acta Crystallogr D Biol Crystallogr 68:300-309 (2012)

PubMed id: 22349232

High-pressure-induced water penetration into 3-isopropylmalate dehydrogenase.

T.Nagae, T.Kawamura, L.M.Chavas, K.Niwa, M.Hasegawa, C.Kato, N.Watanabe.

ABSTRACT

Hydrostatic pressure induces structural changes in proteins, including denaturation, the mechanism of which has been attributed to water penetration into the protein interior. In this study, structures of 3-isopropylmalate dehydrogenase (IPMDH) from Shewanella oneidensis MR-1 were determined at about 2 Å resolution under pressures ranging from 0.1 to 650 MPa using a diamond anvil cell (DAC). Although most of the protein cavities are monotonically compressed as the pressure increases, the volume of one particular cavity at the dimer interface increases at pressures over 340 MPa. In parallel with this volume increase, water penetration into the cavity could be observed at pressures over 410 MPa. In addition, the generation of a new cleft on the molecular surface accompanied by water penetration could also be observed at pressures over 580 MPa. These water-penetration phenomena are considered to be initial steps in the pressure-denaturation process of IPMDH.