PDBsum entry 2ghh

Oxidoreductase

PDB id: 2ghh

Contents

Protein chain

250 a.a. *

Ligands

HEM-_NO

Metals

__K

Waters ×317

* Residue conservation analysis

PDB id:

2ghh

Name:

Oxidoreductase

Title:

Conformational mobility in the active site of a heme peroxidase

Structure:

Cytosolic ascorbate peroxidase 1. Chain: x. Engineered: yes

Source:

Glycine max. Soybean. Organism_taxid: 3847. Gene: ascorbate peroxidase. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.01Å R-factor: 0.187 R-free: 0.258

Authors:

S.K.Badyal,M.G.Joyce,K.H.Sharp,E.L.Raven,P.C.E.Moody

Key ref:

S.K.Badyal et al. (2006). Conformational mobility in the active site of a heme peroxidase. J Biol Chem, 281, 24512-24520. PubMed id: 16762924 DOI: 10.1074/jbc.M602602200

Date:

27-Mar-06 Release date: 13-Jun-06

Protein chain

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

Seq: 250 a.a.

Struc: 251 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
• 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: 10.1074/jbc.M602602200

J Biol Chem 281:24512-24520 (2006)

PubMed id: 16762924

Conformational mobility in the active site of a heme peroxidase.

S.K.Badyal, M.G.Joyce, K.H.Sharp, H.E.Seward, M.Mewies, J.Basran, I.K.Macdonald, P.C.Moody, E.L.Raven.

ABSTRACT

Conformational mobility of the distal histidine residue has been implicated for several different heme peroxidase enzymes, but unambiguous structural evidence is not available. In this work, we present mechanistic, spectroscopic, and structural evidence for peroxide- and ligand-induced conformational mobility of the distal histidine residue (His-42) in a site-directed variant of ascorbate peroxidase (W41A). In this variant, His-42 binds "on" to the heme in the oxidized form, duplicating the active site structure of the cytochromes b but, in contrast to the cytochromes b, is able to swing "off" the iron during catalysis. This conformational flexibility between the on and off forms is fully reversible and is used as a means to overcome the inherently unreactive nature of the on form toward peroxide, so that essentially complete catalytic activity is maintained. Contrary to the widely adopted view of heme enzyme catalysis, these data indicate that strong coordination of the distal histidine to the heme iron does not automatically undermine catalytic activity. The data add a new dimension to our wider appreciation of structure/activity correlations in other heme enzymes.

Selected figure(s)

Figure 4.
FIGURE 4. A, the active site of ferric W41A, showing the coordination of His-42 to the iron. SigmaA-weighted 2F[o] - F[c] electron density at 1 is shown in blue, and sigmaA-weighted F[o] - F[c] electron density at 3 is shown in green. The positive F[o] - F[c] electron density in green overlays with the position of His-42 in the structure of rsAPX. Water molecules are shown as red spheres. B, stereo view of a structural alignment of the orientation of His-42 in rsAPX (in blue, Protein Data Bank code 1OAG) with the active site in W41A (in green). Water molecules are shown as red spheres for W41A. This figure was created using PyMOL (40).

Figure 7.
FIGURE 7. Overlay of the structures of ferric W41A (green) and ferric W41A after reaction with H[2]O[2] (yellow). Water molecules in the two structures are shown in green and yellow, respectively. The orientation of His-42 after reaction with H[2]O[2] (yellow) overlays with that of rsAPX (see Fig. 4B). This figure was created using PyMOL (40).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 24512-24520) copyright 2006.

Figures were selected by an automated process.