PDBsum entry 2evk

Oxygen storage/transport

PDB id: 2evk

Contents

Protein chain

153 a.a. *

Ligands

HEM-ACY

Waters ×313

* Residue conservation analysis

PDB id:

2evk

Name:

Oxygen storage/transport

Title:

The structures of thiolate- and carboxylate-ligated ferric h93g myoglobin: models for cytochrome p450 and for oxyanion-bound heme proteins

Structure:

Myoglobin. Chain: a. Engineered: yes. Mutation: yes

Source:

Physeter catodon. Sperm whale. Organism_taxid: 9755. Gene: mb. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.40Å R-factor: 0.207 R-free: 0.264

Authors:

J.Qin,R.Perera,L.L.Lovelace,J.H.Dawson,L.Lebioda

Key ref:

J.Qin et al. (2006). Structures of thiolate- and carboxylate-ligated ferric H93G myoglobin: models for cytochrome P450 and for oxyanion-bound heme proteins. Biochemistry, 45, 3170-3177. PubMed id: 16519512 DOI: 10.1021/bi052171s

Date:

31-Oct-05 Release date: 18-Apr-06

Protein chain

P02185  (MYG_PHYMC) -  Myoglobin from Physeter macrocephalus

Seq: 154 a.a.

Struc: 153 a.a.*

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

DOI no: 10.1021/bi052171s

Biochemistry 45:3170-3177 (2006)

PubMed id: 16519512

Structures of thiolate- and carboxylate-ligated ferric H93G myoglobin: models for cytochrome P450 and for oxyanion-bound heme proteins.

J.Qin, R.Perera, L.L.Lovelace, J.H.Dawson, L.Lebioda.

ABSTRACT

Crystal structures of the ferric H93G myoglobin (Mb) cavity mutant containing either an anionic proximal thiolate sulfur donor or a carboxylate oxygen donor ligand are reported at 1.7 and 1.4 A resolution, respectively. The crystal structure and magnetic circular dichroism spectra of the H93G Mb beta-mercaptoethanol (BME) thiolate adduct reveal a high-spin, five-coordinate complex. Furthermore, the bound BME appears to have an intramolecular hydrogen bond involving the alcohol proton and the ligated thiolate sulfur, mimicking one of the three proximal N-H...S hydrogen bonds in cytochrome P450. The Fe is displaced from the porphyrin plane by 0.5 A and forms a 2.41 A Fe-S bond. The Fe(3+)-S-C angle is 111 degrees , indicative of a covalent Fe-S bond with sp(3)-hybridized sulfur. Therefore, the H93G Mb.BME complex provides an excellent protein-derived structural model for high-spin ferric P450. In particular, the Fe-S bond in high-spin ferric P450-CAM has essentially the same geometry despite the constraints imposed by covalent linkage of the cysteine to the protein backbone. This suggests that evolution led to the geometric optimization of the proximal Fe-S(cysteinate) bond in P450. The crystal structure and spectral properties of the H93G Mb acetate adduct reveal a high-spin, six-coordinate complex with proximal acetate and distal water axial ligands. The distal His-64 forms a hydrogen bond with the bound water. The Fe-acetate bonding geometry is inconsistent with an electron pair along the Fe-O bond as the Fe-O-C angle is 152 degrees and the Fe is far from the plane of the acetate. Thus, the Fe-O bonding is ionic. The H93G Mb cavity mutant has already been shown to be a versatile model system for the study of ligand binding to heme proteins; this investigation affords the first structural evidence that nonimidazole exogenous ligands bind in the proximal ligation site.