PDBsum entry 3faq

Oxidoreductase

PDB id: 3faq

Contents

Protein chain

595 a.a. *

Ligands

NAG-NAG ×2

NAG-NAG-MAN

NAG-NAG-BMA-MAN

HEM

SCN ×2

CYN

Metals

IOD ×7

_CA

Waters ×274

* Residue conservation analysis

PDB id:

3faq

Name:

Oxidoreductase

Title:

Crystal structure of lactoperoxidase complex with cyanide

Structure:

Lactoperoxidase. Chain: a. Fragment: unp residues 118-712. Synonym: lpo,wblp. Ec: 1.11.1.7

Source:

Bubalus bubalis. Water buffalo. Organism_taxid: 89462. Strain: mammary gland secretion

Resolution:

2.70Å R-factor: 0.208 R-free: 0.235

Authors:

I.A.Sheikh,N.Singh,S.Sharma,P.Kaur,A.Srinivasan,T.P.Singh

Key ref:

I.A.Sheikh et al. (2009). Structural evidence of substrate specificity in mammalian peroxidases: Structure of the thiocyanate complex with lactoperoxidase and its interactions at 2.4 angstrom resolution. J Biol Chem, 284, 14849-14856. PubMed id: 19339248 DOI: 10.1074/jbc.M807644200

Date:

18-Nov-08 Release date: 31-Mar-09

Protein chain

A5JUY8  (PERL_BUBBU) -  Lactoperoxidase from Bubalus bubalis

Seq: 712 a.a.

Struc: 595 a.a.

Enzyme reactions

• Enzyme class: E.C.1.11.1.7 - peroxidase.
• Reaction: 2 a phenolic donor + H2O2 = 2 a phenolic radical donor + 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

Added reference

DOI no: 10.1074/jbc.M807644200

J Biol Chem 284:14849-14856 (2009)

PubMed id: 19339248

Structural evidence of substrate specificity in mammalian peroxidases: Structure of the thiocyanate complex with lactoperoxidase and its interactions at 2.4 angstrom resolution.

I.A.Sheikh, A.K.Singh, N.Singh, M.Sinha, S.B.Singh, A.Bhushan, P.Kaur, A.Srinivasan, S.Sharma, T.P.Singh.

ABSTRACT

The crystal structure of the complex of lactoperoxidase (LPO) with its physiological substrate thiocyanate (SCN-) has been determined at 2.4A resolution. It revealed that the SCN- ion is bound to LPO in the distal heme cavity. The observed orientation of SCN- ion shows that the sulfur atom is closer to the heme iron than the nitrogen atom. The nitrogen atom of SCN- forms a hydrogen bond with water molecule W6'. This water molecule is stabilized by two hydrogen bonds with Gln423 NE2 and Phe422 O. In contrast, the placement of SCN- ion in the structure of myeloperoxidase (MPO) occurs with an opposite orientation in which the nitrogen atom is closer to the heme iron than the sulfur atom. The site corresponding to the positions of Gln423, Phe422 O and W6' in LPO is occupied primarily by the side chain of Phe407 in MPO due to an entirely different conformation of the loop corresponding to the segment, Arg418-Phe431 of LPO. This arrangement in MPO does not favour a similar orientation of SCN- ion. The orientation of the catalytic product OSCN- ion as reported in the structure of LPO-OSCN- is similar to the orientation of SCN- in the structure of LPO-SCN-. Similarly, in the structure of LPO-SCN--CN- in which CN- binds at the position of W1, the position and orientation of SCN- ion are also identical to that observed in the structure of LPO-SCN-.

Selected figure(s)

Figure 1.
Difference Fourier |F[o] – F[c]| map indicating the presence of SCN^– ions in the complex of LPO·SCN^–. The cutoff on the left of the pearshaped electron density corresponds to 2σ (blue), and on the right, it is at 9σ (red).

Figure 2.
Difference Fourier map calculated in the structures of LPO·SCN^–·CN^– for SCN^– and CN^– ions. The electron density from the difference Fourier map with 2σ cutoff on the left and 9σ cutoff on the right. The rod-like density for the CN^– ion is also observed at the distal heme side.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2009, 284, 14849-14856) copyright 2009.

Figures were selected by an automated process.