3VMK

3-isopropylmalate dehydrogenase from Shewanella benthica DB21 MT-2

Summary for 3VMK

• Entry DOI: 10.2210/pdb3vmk/pdb
• Related: 3VMJ 3VML
• Descriptor: 3-isopropylmalate dehydrogenase, 3-ISOPROPYLMALIC ACID, MAGNESIUM ION, ... (5 entities in total)
• Functional Keywords: oxidoreductase, decarboxylating dehydrogenase
• Biological source: Shewanella benthica
• Cellular location: Cytoplasm : D2YZL2
• Total number of polymer chains: 2
• Total formula weight: 81830.19

Authors

Nagae, T.,Watanabe, N. (deposition date: 2011-12-13, release date: 2012-02-29, Last modification date: 2023-11-08)

Primary citation

Nagae, T.,Kato, C.,Watanabe, N.
Structural analysis of 3-isopropylmalate dehydrogenase from the obligate piezophile Shewanella benthica DB21MT-2 and the nonpiezophile Shewanella oneidensis MR-1
Acta Crystallogr.,Sect.F, 68:265-268, 2012

PubMed Abstract: Organisms living in deep seas such as the Mariana Trench must be adapted to the extremely high pressure environment. For example, the 3-isopropylmalate dehydrogenase from the obligate piezophile Shewanella benthica DB21MT-2 (SbIPMDH) remains active in extreme conditions under which that from the land bacterium S. oneidensis MR-1 (SoIPMDH) becomes inactivated. In order to unravel the differences between these two IPMDHs, their structures were determined at ~1.5 Å resolution. Comparison of the structures of the two enzymes shows that SbIPMDH is in a more open form and has a larger internal cavity volume than SoIPMDH at atmospheric pressure. This loosely packed structure of SbIPMDH could help it to avoid pressure-induced distortion of the native structure and to remain active at higher pressures than SoIPMDH.

PubMed: 22442218
DOI: 10.1107/S1744309112001443

Experimental method

X-RAY DIFFRACTION (1.48 Å)