PDBsum entry: 1guy

Oxidoreductase

PDB id: 1guy

Contents

Protein chains

296 a.a. *

Ligands

NAD ×2

Metals

_CD ×5

Waters ×315

* Residue conservation analysis

PDB id:

1guy

Name:

Oxidoreductase

Title:

Structural basis for thermophilic protein stability: structures of thermophilic and mesophilic malate dehydrogenases

Structure:

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

Source:

Chloroflexus aurantiacus. Organism_taxid: 1108. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Tetramer (from PDB file)

Resolution:

2.2Å R-factor: 0.174 R-free: 0.197

Authors:

B.Dalhus,M.Sarinen,U.H.Sauer,P.Eklund,K.Johansson, A.Karlsson,S.Ramaswamy,A.Bjork,B.Synstad,K.Naterstad, R.Sirevag,H.Eklund

Key ref:

B.Dalhus et al. (2002). Structural basis for thermophilic protein stability: structures of thermophilic and mesophilic malate dehydrogenases. J Mol Biol, 318, 707-721. PubMed id: 12054817 DOI: 10.1016/S0022-2836(02)00050-5

Date:

04-Feb-02 Release date: 15-Feb-02

Protein chains

P80040  (MDH_CHLAA) -  Malate dehydrogenase

Seq: 309 a.a.

Struc: 296 a.a.*

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

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 = NAD) corresponds exactly) = 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 (5 terms)

reference

DOI no: 10.1016/S0022-2836(02)00050-5

J Mol Biol 318:707-721 (2002)

PubMed id: 12054817

Structural basis for thermophilic protein stability: structures of thermophilic and mesophilic malate dehydrogenases.

B.Dalhus, M.Saarinen, U.H.Sauer, P.Eklund, K.Johansson, A.Karlsson, S.Ramaswamy, A.Bjørk, B.Synstad, K.Naterstad, R.Sirevåg, H.Eklund.

ABSTRACT

The three-dimensional structure of four malate dehydrogenases (MDH) from thermophilic and mesophilic phototropic bacteria have been determined by X-ray crystallography and the corresponding structures compared. In contrast to the dimeric quaternary structure of most MDHs, these MDHs are tetramers and are structurally related to tetrameric malate dehydrogenases from Archaea and to lactate dehydrogenases. The tetramers are dimers of dimers, where the structures of each subunit and the dimers are similar to the dimeric malate dehydrogenases. The difference in optimal growth temperature of the corresponding organisms is relatively small, ranging from 32 to 55 degrees C. Nevertheless, on the basis of the four crystal structures, a number of factors that are likely to contribute to the relative thermostability in the present series have been identified. It appears from the results obtained, that the difference in thermostability between MDH from the mesophilic Chlorobium vibrioforme on one hand and from the moderate thermophile Chlorobium tepidum on the other hand is mainly due to the presence of polar residues that form additional hydrogen bonds within each subunit. Furthermore, for the even more thermostable Chloroflexus aurantiacus MDH, the use of charged residues to form additional ionic interactions across the dimer-dimer interface is favored. This enzyme has a favorable intercalation of His-Trp as well as additional aromatic contacts at the monomer-monomer interface in each dimer. A structural alignment of tetrameric and dimeric prokaryotic MDHs reveal that structural elements that differ among dimeric and tetrameric MDHs are located in a few loop regions.

Selected figure(s)

Figure 3.
Figure 3. Ribbon diagram of the full MDH tetramer with close-up views of two regions in ca-MDH and cv-MDH containing residues that interact across the dimer-dimer interface. The upper panel shows polar interactions across the 2-fold P-axis (A-C) while the lower panel illustrates differences in ionic interactions. The Glu23 (in ca-MDH only) and Asp55 form contacts to residues 241 and 243 between monomers related by the 2-fold R-axis (A-D). Glu164 (in ca-MDH only) and Asp165 interact with residues across the P-axis (B-D). All these interactions occur also on symmetry-related interfaces.

Figure 6.
Figure 6. Arg18-Glu/Asp21 interactions. Ball-and-stick representation of the hydrogen bond interactions between Arg18 and Glu/Asp21 in ct-MDH, hybrid-MDH and cv-MDH, which is probably the major interaction that governs differences in thermostability between the closely related hybrid and cv-MDH. The hydrogen bond distances are mean distances for each interaction.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 318, 707-721) copyright 2002.

Figures were selected by an automated process.