PDBsum entry 1lyc

Oxidoreductase

PDB id: 1lyc

Contents

Protein chains

336 a.a. *

Ligands

HEM ×2

Metals

_CA ×4

Waters ×337

* Residue conservation analysis

PDB id:

1lyc

Name:

Oxidoreductase

Title:

The impact of the physical and chemical enviroment on the molecular structure of coprinus cinereus peroxidase

Structure:

Peroxidase. Chain: a, b. Engineered: yes

Source:

Coprinopsis cinerea. Organism_taxid: 5346. Gene: cip1. Expressed in: aspergillus oryzae. Expression_system_taxid: 5062

Resolution:

1.57Å R-factor: 0.223 R-free: 0.265

Authors:

K.Houborg,P.Harris,J.F.W.Petersen,P.Rowland,J.-C.N.Poulsen, P.Schneider,J.Vind,S.Larsen

Key ref:

K.Houborg et al. (2003). Impact of the physical and chemical environment on the molecular structure of Coprinus cinereus peroxidase. Acta Crystallogr D Biol Crystallogr, 59, 989-996. PubMed id: 12777760 DOI: 10.1107/S0907444903006772

Date:

07-Jun-02 Release date: 14-Jun-02

Protein chains

P28314  (PER_COPCI) -  Peroxidase from Coprinopsis cinerea

Seq: 363 a.a.

Struc: 336 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

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: 10.1107/S0907444903006772

Acta Crystallogr D Biol Crystallogr 59:989-996 (2003)

PubMed id: 12777760

Impact of the physical and chemical environment on the molecular structure of Coprinus cinereus peroxidase.

K.Houborg, P.Harris, J.Petersen, P.Rowland, J.C.Poulsen, P.Schneider, J.Vind, S.Larsen.

ABSTRACT

The structure of the peroxidase from Coprinus cinereus (CiP) has been determined in three different space groups and crystalline environments. Two of these are of the recombinant glycosylated form (rCiP), which crystallized in space groups P2(1)2(1)2(1) and C2. The third crystal form was obtained from a variant of CiP in which the glycosylation sites have been removed (rCiPON). It crystallizes in space group P2(1) with beta approximately 90 degrees; the structure was determined from room-temperature data and low-temperature data obtained from twinned crystals. Two independent molecules of CiP related by non-crystallographic symmetry are contained in the three crystal forms. The packing in the two structures of the glycosylated form of rCiP is closely related, but differs from the packing in the unglycosylated rCiPON. A database search based on small-molecule porphinato iron (III) complexes has been performed and related to observations of the spin states and coordination numbers of the iron ion. The room-temperature structures of CiP and one structure of the almost identical peroxidase from Arthromyces ramosus (ARP) have been used to identify 66 conserved water molecules and to assign a structural role to most of them.

Selected figure(s)

Figure 5.
Figure 5 A structural representation of CiPON-RT with the conserved water molecules in red (1028, 1027, 1009, 1023, 1034), pink (1001, 1006, 1025, 1017), orange (1011, 1029, 1066, 1056) and blue, the two calcium ions in green and the haem group in black. The figure was prepared using the program MOLSCRIPT (Kraulis, 1991[Kraulis, P. J. (1991). J. Appl. Cryst. 24, 946-950.]).

Figure 6.
Figure 6 The water molecules found in the region around the haem group in the CiP and ARP structures. The figure was prepared using the program MOLSCRIPT (Kraulis, 1991[Kraulis, P. J. (1991). J. Appl. Cryst. 24, 946-950.]).

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2003, 59, 989-996) copyright 2003.

Figures were selected by an automated process.