PDBsum entry 3u3e

Oxygen transport

PDB id: 3u3e

Contents

Protein chain

153 a.a.

Ligands

HEM

IPH

SO4 ×5

Waters ×247

PDB id:

3u3e

Name:

Oxygen transport

Title:

Complex of wild type myoglobin with phenol in its proximal cavity

Structure:

Myoglobin. Chain: a. Engineered: yes

Source:

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

Resolution:

1.21Å R-factor: 0.145 R-free: 0.170

Authors:

L.R.Celeste,L.Lebioda

Key ref:

X.Huang et al. (2012). Complex of myoglobin with phenol bound in a proximal cavity. Acta Crystallogr Sect F Struct Biol Cryst Commun, 68, 1465-1471. PubMed id: 23192025 DOI: 10.1107/S1744309112045514

Date:

05-Oct-11 Release date: 28-Nov-12

Protein chain

P02185  (MYG_PHYMC) -  Myoglobin from Physeter macrocephalus

Seq: 154 a.a.

Struc: 153 a.a.

Enzyme reactions

• Enzyme class 2: E.C.1.11.1.- - ?????
• Enzyme class 3: E.C.1.7.-.-

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

DOI no: 10.1107/S1744309112045514

Acta Crystallogr Sect F Struct Biol Cryst Commun 68:1465-1471 (2012)

PubMed id: 23192025

Complex of myoglobin with phenol bound in a proximal cavity.

X.Huang, C.Wang, L.R.Celeste, L.L.Lovelace, S.Sun, J.H.Dawson, L.Lebioda.

ABSTRACT

Sperm whale myoglobin (Mb) has weak dehaloperoxidase activity and catalyzes the peroxidative dehalogenation of 2,4,6-trichlorophenol (TCP) to 2,6-dichloroquinone. Crystals of Mb and of its more active G65T variant were used to study the binding of TCP, 4-iodophenol (4-IP) and phenol. The structures of crystals soaked overnight in a 10 mM solution of phenol revealed that a phenol molecule binds in the proximal cavity, forming a hydrogen bond to the hydroxyl of Tyr146 and hydrophobic contacts which include interactions with C(β) and C(γ) of the proximal histidine His93. The phenol position corresponds to the strongest xenon binding site, Xe1. It appears that the ligand enters the proximal cavity through a gate formed by the flexible loops 79-86 and 93-103. TCP and 4-IP do not bind to Mb in this manner under similar conditions; however, it appears to be likely that dimethyl sulfoxide (DMSO), which was used at a concentration of 0.8 M to facilitate 4-IP dissolution, binds in the phenol/Xe1 binding site. In this structure, a water molecule coordinated to the heme iron was replaced by an oxygen molecule, reflecting the reduction of the heme. Crystals of Mb and G65T Mb soaked for 5-10 min did not show bound phenol. Kinetic studies of TCP dechlorination showed that phenol has a dual effect: it acts as a competitive inhibitor that is likely to interfere with TCP binding at the heme edge and as a weak activator, likely through binding in the proximal cavity. The lack of phenol bound at the heme edge in the crystal structures suggests that its inhibitory binding only takes place when the heme is activated by hydrogen peroxide.