PDBsum entry 5mdh

Oxidoreductase

PDB id: 5mdh

Contents

Protein chains

333 a.a. *

Ligands

NAD ×2

MAK ×2

Waters ×354

* Residue conservation analysis

PDB id:

5mdh

Name:

Oxidoreductase

Title:

Crystal structure of ternary complex of porcine cytoplasmic malate dehydrogenase alpha-ketomalonate and tnad at 2.4 angstroms resolution

Structure:

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

Source:

Sus scrofa. Pig. Organism_taxid: 9823. Organ: heart. Tissue: muscle. Cellular_location: cytoplasm. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

2.40Å R-factor: 0.199 R-free: 0.253

Authors:

A.D.M.Chapman,A.Cortes,T.R.Dafforn,A.R.Clarke,R.L.Brady

Key ref:

A.D.Chapman et al. (1999). Structural basis of substrate specificity in malate dehydrogenases: crystal structure of a ternary complex of porcine cytoplasmic malate dehydrogenase, alpha-ketomalonate and tetrahydoNAD. J Mol Biol, 285, 703-712. PubMed id: 10075524 DOI: 10.1006/jmbi.1998.2357

Date:

08-Oct-98 Release date: 18-May-99

Protein chains

P11708  (MDHC_PIG) -  Malate dehydrogenase, cytoplasmic from Sus scrofa

Seq: 334 a.a.

Struc: 333 a.a.

Enzyme reactions

• Enzyme class 1: E.C.1.1.1.37 - malate dehydrogenase.
• Pathway: Citric acid cycle
• Reaction: (S)-malate + NAD⁺ = oxaloacetate + NADH + H⁺

(S)-malate (Bound ligand (Het Group name = MAK) matches with 54.55% similarity) + NAD(+) (Bound ligand (Het Group name = NAD) corresponds exactly) = oxaloacetate + NADH + H(+)

• Enzyme class 2: E.C.1.1.1.96 - diiodophenylpyruvate reductase.
• Reaction: 3-(3,5-diiodo-4-hydroxyphenyl)lactate + NAD⁺ = 3-(3,5-diiodo-4- hydroxyphenyl)pyruvate + NADH + H⁺

3-(3,5-diiodo-4-hydroxyphenyl)lactate + NAD(+) (Bound ligand (Het Group name = NAD) corresponds exactly) = 3-(3,5-diiodo-4- hydroxyphenyl)pyruvate + NADH + H(+)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1006/jmbi.1998.2357

J Mol Biol 285:703-712 (1999)

PubMed id: 10075524

Structural basis of substrate specificity in malate dehydrogenases: crystal structure of a ternary complex of porcine cytoplasmic malate dehydrogenase, alpha-ketomalonate and tetrahydoNAD.

A.D.Chapman, A.Cortés, T.R.Dafforn, A.R.Clarke, R.L.Brady.

ABSTRACT

The structural basis for the extreme discrimination achieved by malate dehydrogenases between a variety of closely related substrates encountered within the cell has been difficult to assess because of the lack of an appropriate catalytically competent structure of the enzyme. Here, we have determined the crystal structure of a ternary complex of porcine cytoplasmic malate dehydrogenase with the alternative substrate alpha-ketomalonate and the coenzyme analogue 1,4,5,6-tetrahydronicotinamide. Both subunits of the dimeric porcine heart, and from the prokaryotes Escherichia coli and Thermus flavus. However, large changes are noted around the active site, where a mobile loop now closes to bring key residues into contact with the substrate. This observation substantiates a postulated mechanism in which the enzyme achieves high levels of substrate discrimination through charge balancing in the active site. As the activated cofactor/substrate complex has a net negative charge, a positive counter-charge is provided by a conserved arginine in the active site loop. The enzyme must, however, also discriminate against smaller substrates, such as pyruvate. The structure shows in the closed (loop down) catalytically competent complex two arginine residues (91 and 97) are driven into close proximity. Without the complimentary, negative charge of the substrate side-chain of oxaloacetate or alpha-ketomalonate, charge repulsion would resist formation production of this catalytically productive conformation, hence minimising the effectiveness of pyruvate as a substrate. By this mechanism, malate dehydrogenase uses charge balancing to achieve fivefold orders of magnitude in discrimination between potential substrates.

Selected figure(s)

Figure 7.
Figure 7. The position of the α-ketomalonate substrate within the active site. The electron density was generated by calculating 2|F[obs]|−|F[calc]| difference maps contoured at 1.3σ.

Figure 8.
Figure 8. The hydrogen-bonding interactions of α-ketomalonate with the key active site residues. This Figure was generated using the program LIGPLOT [Wallace et al 1995].

The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 285, 703-712) copyright 1999.

Figures were selected by the author.