PDBsum entry 1xaa

Oxidoreductase

PDB id: 1xaa

Contents

Protein chain

345 a.a. *

Waters ×888

* Residue conservation analysis

PDB id:

1xaa

Name:

Oxidoreductase

Title:

3-isopropylmalate dehydrogenase, low temperature (100k) structure

Structure:

3-isopropylmalate dehydrogenase. Chain: a. Synonym: ipmdh, imdh. Other_details: low temperature (100k) structure

Source:

Thermus thermophilus. Organism_taxid: 300852. Strain: hb8

Biol. unit:

Dimer (from PQS)

Resolution:

2.10Å R-factor: 0.157

Authors:

C.Nagata,H.Moriyama,N.Tanaka

Key ref:

C.Nagata et al. (1996). Cryocrystallography of 3-Isopropylmalate dehydrogenase from Thermus thermophilus and its chimeric enzyme. Acta Crystallogr D Biol Crystallogr, 52, 623-630. PubMed id: 15299625 DOI: 10.1107/S0907444995016623

Date:

09-Nov-95 Release date: 03-Apr-96

Protein chain

Q5SIY4  (LEU3_THET8) -  3-isopropylmalate dehydrogenase from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 345 a.a.

Struc: 345 a.a.

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

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

reference

DOI no: 10.1107/S0907444995016623

Acta Crystallogr D Biol Crystallogr 52:623-630 (1996)

PubMed id: 15299625

Cryocrystallography of 3-Isopropylmalate dehydrogenase from Thermus thermophilus and its chimeric enzyme.

C.Nagata, H.Moriyama, N.Tanaka, M.Nakasako, M.Yamamoto, T.Ueki, T.Oshima.

ABSTRACT

The crystal structures of thermostable enzyme, 3-isopropylmalate dehydrogenase of Thermus thermophilus (10T) and a chimeric enzyme between T. thermophilus and Bacillus subtilus with one point mutation (cS82R), were determined at both 100 and 150 K. At the cryogenic condition, the volume of the unit cell decreased by 5% as a result of a contraction in the solvent region. Although the overall structures of both enzymes at low temperature were the same as that of 10T at room temperature, interactions between two domains and between two subunits in a functional dimer of cS82R were significantly altered. The decrease in the average temperature factor of 10T at low temperature and no significant decrease for cS82R suggested that the structure of the engineered enzyme (cS82R) may have many conformational substates even at low temperature, while the native enzyme (10T) at low temperature has a more definite conformation than that at room temperature. The location of water molecules around the enzyme molecule and the calculation of the radii of gyration suggested that cS82R had a weaker hydration than 10T.

Selected figure(s)

Figure 6.
Fig. 6. The temperature factors of the amino-acid residues. The solid lines indicate those at 100 K and the dotted lines indicate those at 293 K. (a) 10T. (b) cS82R.

Figure 7.
Fig. 7. Histogram of the hydrogen­bond distance beteen acceptor and donor within 2.4 and 3.4 A for 0T (gray bars) and cS82R (white bars). (a) The protein­protein interaction. (b) The protein­water interaction. (c) The water­water interacton.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1996, 52, 623-630) copyright 1996.

Figures were selected by an automated process.