3VL4

3-isopropylmalate dehydrogenase from Shewanella oneidensis MR-1 at 410 MPa

Summary for 3VL4

• Entry DOI: 10.2210/pdb3vl4/pdb
• Related: 3VL2 3VL3 3VL6 3VL7 3VLZ
• Descriptor: 3-isopropylmalate dehydrogenase, 3-ISOPROPYLMALIC ACID, CALCIUM ION, ... (5 entities in total)
• Functional Keywords: 3-isopropylmalate dehydrogenase, ipmdh, high-pressure, diamond-anvil cell, dac, oxidoreductase
• Biological source: Shewanella oneidensis
• Cellular location: Cytoplasm : Q8E9N3
• Total number of polymer chains: 1
• Total formula weight: 40941.00

Authors

Nagae, T.,Watanabe, N. (deposition date: 2011-11-29, release date: 2012-02-29, Last modification date: 2023-11-08)

Primary citation

Nagae, T.,Kawamura, T.,Chavas, L.M.G.,Niwa, K.,Hasegawa, M.,Kato, C.,Watanabe, N.
High-pressure-induced water penetration into 3-isopropylmalate dehydrogenase
Acta Crystallogr.,Sect.D, 68:300-309, 2012

PubMed 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.

PubMed: 22349232
DOI: 10.1107/S0907444912001862

Experimental method

X-RAY DIFFRACTION (1.88 Å)