PDBsum entry 1oaf

Oxidoreductase

PDB id: 1oaf

Contents

Protein chain

250 a.a. *

Ligands

HEM

ASC

Metals

_NA

Waters ×505

* Residue conservation analysis

PDB id:

1oaf

Name:

Oxidoreductase

Title:

Ascobate peroxidase from soybean cytosol in complex with ascorbate

Structure:

Ascorbate peroxidase. Chain: a. Engineered: yes

Source:

Glycine max. Soybean. Organism_taxid: 3847. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: n-terminal 6-his tag

Resolution:

1.40Å R-factor: 0.163 R-free: 0.196

Authors:

K.H.Sharp,E.L.Raven,P.C.E.Moody

Key ref:

K.H.Sharp et al. (2003). Crystal structure of the ascorbate peroxidase-ascorbate complex. Nat Struct Biol, 10, 303-307. PubMed id: 12640445 DOI: 10.1038/nsb913

Date:

13-Jan-03 Release date: 20-Mar-03

Protein chain

Q43758  (Q43758_SOYBN) -  L-ascorbate peroxidase from Glycine max

Seq: 250 a.a.

Struc: 250 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.1.11.1.11 - L-ascorbate peroxidase.
• Reaction: L-ascorbate + H2O2 = L-dehydroascorbate + 2 H2O

L-ascorbate + H2O2 (Bound ligand (Het Group name = ASC) corresponds exactly) = L-dehydroascorbate + 2 × H2O

• Cofactor: Heme

Heme (Bound ligand (Het Group name = HEM) matches with 95.45% similarity)

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

reference

DOI no: 10.1038/nsb913

Nat Struct Biol 10:303-307 (2003)

PubMed id: 12640445

Crystal structure of the ascorbate peroxidase-ascorbate complex.

K.H.Sharp, M.Mewies, P.C.Moody, E.L.Raven.

ABSTRACT

Heme peroxidases catalyze the H2O2-dependent oxidation of a variety of substrates, most of which are organic. Mechanistically, these enzymes are well characterized: they share a common catalytic cycle that involves formation of a two-electron, oxidized Compound I intermediate followed by two single-electron reduction steps by substrate. The substrate specificity is more diverse--most peroxidases oxidize small organic substrates, but there are prominent exceptions--and there is a notable absence of structural information for a representative peroxidase-substrate complex. Thus, the features that control substrate specificity remain undefined. We present the structure of the complex of ascorbate peroxidase-ascorbate. The structure defines the ascorbate-binding interaction for the first time and provides new rationalization of the unusual functional features of the related cytochrome c peroxidase enzyme, which has been a benchmark for peroxidase catalysis for more than 20 years. A new mechanism for electron transfer is proposed that challenges existing views of substrate oxidation in other peroxidases.

Selected figure(s)

Figure 1.
Figure 1. The active site of rsAPX32, 33. The key residues are labeled, and water molecules are shown as red spheres. Hydrogen bonds are indicated by green dotted lines.

Figure 2.
Figure 2. The ascorbate-binding site. a, Stereo representation of the overall structure of the rsAPX -ascorbate complex34, showing the heme, the proximal and distal histidine residues, the coordinated water molecule and the bound ascorbate. The regions 20 -35 and 179 -181 (shown in Fig. 3) are highlighted in magenta. b, The structure of L-ascorbic acid, showing the L configuration at C^5. The pK[a]s of the 2-OH and 3-OH groups are 11.3 and 4.0, respectively35. c, The structure of rsAPX showing the -meso and -meso positions of the heme and bound solvent in the ascorbate-binding site. d, Stereo view of the rsAPX -ascorbate complex, showing refined electron density (green) and the binding of the ascorbate. Hydrogen bonds are indicated (dotted lines)32, 33.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2003, 10, 303-307) copyright 2003.

Figures were selected by an automated process.