PDBsum entry 1f0x

Oxidoreductase

PDB id: 1f0x

Contents

Protein chains

502 a.a. *

Ligands

FAD ×2

Waters ×321

* Residue conservation analysis

PDB id:

1f0x

Name:

Oxidoreductase

Title:

Crystal structure of d-lactate dehydrogenase, a peripheral membrane respiratory enzyme.

Structure:

D-lactate dehydrogenase. Chain: a, b. Synonym: dldh. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.90Å R-factor: 0.209 R-free: 0.248

Authors:

O.Dym,E.A.Pratt,C.Ho,D.Eisenberg

Key ref:

O.Dym et al. (2000). The crystal structure of D-lactate dehydrogenase, a peripheral membrane respiratory enzyme. Proc Natl Acad Sci U S A, 97, 9413-9418. PubMed id: 10944213 DOI: 10.1073/pnas.97.17.9413

Date:

17-May-00 Release date: 23-Aug-00

Protein chains

P06149  (DLD_ECOLI) -  Quinone-dependent D-lactate dehydrogenase from Escherichia coli (strain K12)

Seq: 571 a.a.

Struc: 502 a.a.

Enzyme reactions

• Enzyme class: E.C.1.1.5.12 - D-lactate dehydrogenase (quinone).
• Reaction: (R)-lactate + a quinone = a quinol + pyruvate
• Cofactor: FAD

FAD (Bound ligand (Het Group name = FAD) corresponds exactly)

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

reference

DOI no: 10.1073/pnas.97.17.9413

Proc Natl Acad Sci U S A 97:9413-9418 (2000)

PubMed id: 10944213

The crystal structure of D-lactate dehydrogenase, a peripheral membrane respiratory enzyme.

O.Dym, E.A.Pratt, C.Ho, D.Eisenberg.

ABSTRACT

d-Lactate dehydrogenase (d-LDH) of Escherichia coli is a peripheral membrane respiratory enzyme involved in electron transfer, located on the cytoplasmic side of the inner membrane. d-LDH catalyzes the oxidation of d-lactate to pyruvate, which is coupled to transmembrane transport of amino acids and sugars. Here we describe the crystal structure at 1.9 A resolution of the three domains of d-LDH: the flavin adenine dinucleotide (FAD)-binding domain, the cap domain, and the membrane-binding domain. The FAD-binding domain contains the site of d-lactate reduction by a noncovalently bound FAD cofactor and has an overall fold similar to other members of a recently discovered FAD-containing family of proteins. This structural similarity extends to the cap domain as well. The most prominent difference between d-LDH and the other members of the FAD-containing family is the membrane-binding domain, which is either absent in some of these proteins or differs significantly. The d-LDH membrane-binding domain presents an electropositive surface with six Arg and five Lys residues, which presumably interacts with the negatively charged phospholipid head groups of the membrane. Thus, d-LDH appears to bind the membrane through electrostatic rather than hydrophobic forces.

Selected figure(s)

Figure 3.
Fig. 3. Schematic diagram of D-LDH interactions with the FAD cofactor was created by using the program LIGPLOT (42). All van der Waals interactions and hydrogen bond contacts to the FAD cofactor (Middle) are contributed solely from residues of the FAD-binding domain. The residues that form hydrogen-bonds to the FAD are shown in ball-and-stick representation. Hydrogen bonds are presented as dashed lines and the interatomic distances are shown in angstroms. The residues that form van der Waals contacts with the FAD are depicted as labeled arcs with radial spokes that point toward the ligand atoms with which they interact.

Figure 4.
Fig. 4. Cartoon of D-LDH associating with the membrane. D-LDH is anchored to the membrane by electrostatic interactions between basic residues (blue balls) from the observed membrane-binding domain (blue) and possibly from the modeled missing segment (dashed yellow) comprising nine basic residues (yellow balls) and the negatively charged phospholipid head groups (red balls) of the membrane. The cap domain (pink) and FAD-binding domain (cyan) are also shown. The stick drawing of the FAD cofactor is depicted with gray balls for atoms in the adenine and sugar rings, with red balls for phosphate and oxygen atoms, and with black balls for atoms in the isoalloxazine ring. In this model, the substrate D-lactate can approach the active site (as shown by the black arrow) near the isoalloxazine ring (visible between pink strands) from behind the cap domain.

Figures were selected by an automated process.