PDBsum entry: 1bdm

Oxidoreductase(NAD(a)-choh(d))

PDB id: 1bdm

Contents

Protein chains

318 a.a. *

Ligands

NAX ×2

Waters ×202

* Residue conservation analysis

PDB id:

1bdm

Name:

Oxidoreductase(NAD(a)-choh(d))

Title:

The structure at 1.8 angstroms resolution of a single site mutant (t189i) of malate dehydrogenase from thermus flavus with increased enzymatic activity

Structure:

Malate dehydrogenase. Chain: a, b. Engineered: yes

Source:

Thermus thermophilus. Organism_taxid: 274.

Biol. unit:

Dimer (from PQS)

Resolution:

1.80Å R-factor: 0.169

Authors:

C.A.Kelly,J.J.Birktoft

Key ref:

C.A.Kelly et al. (1993). Determinants of protein thermostability observed in the 1.9-A crystal structure of malate dehydrogenase from the thermophilic bacterium Thermus flavus. Biochemistry, 32, 3913-3922. PubMed id: 8471603 DOI: 10.1021/bi00066a010

Date:

16-Feb-93 Release date: 20-Dec-94

Protein chains

P10584  (MDH_THETH) -  Malate dehydrogenase

Seq: 327 a.a.

Struc: 318 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.1.1.1.37 - Malate dehydrogenase.
• Pathway: Citric acid cycle
• Reaction: (S)-malate + NAD⁺ = oxaloacetate + NADH

(S)-malate + NAD(+) (Bound ligand (Het Group name = NAX) matches with 97.00% similarity) = oxaloacetate + NADH

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

 Gene Ontology (GO) functional annotation 

• Biological process: oxidation-reduction process (5 terms)
• Biochemical function: catalytic activity (6 terms)

reference

DOI no: 10.1021/bi00066a010

Biochemistry 32:3913-3922 (1993)

PubMed id: 8471603

Determinants of protein thermostability observed in the 1.9-A crystal structure of malate dehydrogenase from the thermophilic bacterium Thermus flavus.

C.A.Kelly, M.Nishiyama, Y.Ohnishi, T.Beppu, J.J.Birktoft.

ABSTRACT

A binary complex of malate dehydrogenase from the thermophilic bacterium Thermus flavus (tMDH) with NADH has been crystallized from poly(ethylene glycol) 3500, pH 8.5, yielding diffraction-quality crystals in space group P2(1)2(1)2(1). The structure was solved at 1.9-A resolution using molecular replacement and refined to an R factor of 15.8% with good geometry. The primary sequence of tMDH is 55% identical to that of cytoplasmic malate dehydrogenase (cMDH) [Birktoft, J. J., Rhodes, G., & Banaszak, L. J. (1989) Biochemistry 28, 6065-6081], and overall their three-dimensional structures are very similar. Like cMDH, tMDH crystallized as a dimer with one coenzyme bound per subunit. The coenzyme binds in the extended conformation, and most of the interactions with enzyme are similar to those in cMDH. In tMDH, small local conformational changes are caused by the replacement of a glutamic acid for the aspartic acid involved in hydrogen bonding to the adenine ribose of NADH. Comparison of tMDH with cMDH reveals that both tMDH subunits more closely resemble the B subunit of cMDH which therefore is the more likely representative of the solution conformation. While cMDH is inactivated at temperatures above about 50 degrees C, tMDH is fully active at 90 degrees C. On the basis of the X-ray crystal structure, a number of factors have been identified which are likely to contribute to the relative thermostability of tMDH compared to cMDH. The most striking of the differences involves the introduction of four ion pairs per monomer. All of these ion pairs are solvent-accessible. Three of these ion pairs are located in the dimer interface, Glu27-Lys31, Glu57-Lys168, and Glu57-Arg229, and one ion pair, Glu275-Arg149, is at the domain interface within each subunit. Additionally, we observe incorporation of additional alanines into alpha-helices of tMDH and, in one instance, incorporation of an aspartate that functions as a counterchange to an alpha-helix dipole. The possible contributions of these and other factors to protein thermostability in tMDH are discussed.