PDBsum entry 1p4c

Oxidoreductase

PDB id: 1p4c

Contents

Protein chain

353 a.a. *

Ligands

SO4

FMN

MES

Waters ×400

* Residue conservation analysis

PDB id:

1p4c

Name:

Oxidoreductase

Title:

High resolution structure of oxidized active mutant of (s)-mandelate dehydrogenase

Structure:

L(+)-mandelate dehydrogenase. Chain: a. Synonym: s-mandelate dehydrogenase, mdh. Engineered: yes. Other_details: 20 residue substitution from glycolate oxidase at residue 177

Source:

Pseudomonas putida, spinacia oleracea. Spinach. Organism_taxid: 303, 3562. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Tetramer (from PDB file)

Resolution:

1.35Å R-factor: 0.184 R-free: 0.194

Authors:

N.Sukumar,B.Mitra,F.S.Mathews

Key ref:

N.Sukumar et al. (2004). High resolution structures of an oxidized and reduced flavoprotein. The water switch in a soluble form of (S)-mandelate dehydrogenase. J Biol Chem, 279, 3749-3757. PubMed id: 14604988 DOI: 10.1074/jbc.M310049200

Date:

22-Apr-03 Release date: 28-Oct-03

Protein chain

P05414  (GOX_SPIOL) -  Glycolate oxidase from Spinacia oleracea

Seq: 369 a.a.

Struc: 353 a.a.*

Protein chain

P20932  (MDLB_PSEPU) -  (S)-mandelate dehydrogenase from Pseudomonas putida

Seq: 393 a.a.

Struc: 353 a.a.*

* PDB and UniProt seqs differ at 219 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: E.C.1.1.3.15 - (S)-2-hydroxy-acid oxidase.
• Reaction: a (2S)-2-hydroxycarboxylate + O2 = a 2-oxocarboxylate + H2O2
• Cofactor: FMN

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

• Enzyme class 2: E.C.1.1.99.31 - (S)-mandelate dehydrogenase.
• Reaction: (S)-mandelate + A = phenylglyoxylate + AH2

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: 10.1074/jbc.M310049200

J Biol Chem 279:3749-3757 (2004)

PubMed id: 14604988

High resolution structures of an oxidized and reduced flavoprotein. The water switch in a soluble form of (S)-mandelate dehydrogenase.

N.Sukumar, A.R.Dewanti, B.Mitra, F.S.Mathews.

ABSTRACT

The crystal structures of a soluble mutant of the flavoenzyme mandelate dehydrogenase (MDH) from Pseudomonas putida and of the substrate-reduced enzyme have been analyzed at 1.35-A resolution. The mutant (MDH-GOX2) is a fully active chimeric enzyme in which residues 177-215 of the membrane-bound MDH are replaced by residues 176-195 of glycolate oxidase from spinach. Both structures permit full tracing of the polypeptide backbone chain from residues 4-356, including a 4-residue segment that was disordered in an earlier study of the oxidized protein at 2.15 A resolution. The structures of MDH-GOX2 in the oxidized and reduced states are virtually identical with only a slight increase in the bending angle of the flavin ring upon reduction. The only other structural changes within the protein interior are a 10 degrees rotation of an active site tyrosine side chain, the loss of an active site water, and a significant movement of six other water molecules in the active site by 0.45 to 0.78 A. Consistent with solution studies, there is no apparent binding of either the substrate, mandelate, or the oxidation product, benzoylformate, to the reduced enzyme. The observed structural changes upon enzyme reduction have been interpreted as a rearrangement of the hydrogen bonding pattern within the active site that results from binding of a proton to the N-5 position of the anionic hydroquinone form of the reduced flavin prosthetic group. Implications for the low oxidase activity of the reduced enzyme are also discussed.

Selected figure(s)

Figure 4.
FIG. 4. Schematic diagram of the protein environment of FMN in the oxidized form of MDH. Hydrogen bond distances are in Å. Residues making hydrophobic contact to FMN are indicated as shown in the lower right. Carbon atoms are black, oxygen atoms red, and nitrogen atoms cyan. This diagram was prepared using the program LIgplot (33)

Figure 6.
FIG. 6. Comparison of the oxidized and reduced forms of MDH-GOX2 at the enzyme active site. The side chains of Tyr26, Tyr131, backbone of Gly81, the flavin ring, the sulfate anion, and 7 waters of the oxidized protein are shown in atom colors (carbon yellow, oxygen red, nitrogen light blue, and sulfur green). Those atoms of Tyr26 and the 6 waters that show significant movement, as well as of the sulfate anion in the reduced enzyme, are shown in dark blue. This diagram was made using TURBO-FRODO (21).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 3749-3757) copyright 2004.

Figures were selected by an automated process.