PDBsum entry 3ogb

Oxygen transport

PDB id: 3ogb

Contents

Protein chain

154 a.a. *

Ligands

HEM

SO4 ×9

Waters ×249

* Residue conservation analysis

PDB id:

3ogb

Name:

Oxygen transport

Title:

Sperm whale myoglobin mutant h64w deoxy-form

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:

1.60Å R-factor: 0.181 R-free: 0.203

Authors:

I.Birukou,J.Soman,J.S.Olson

Key ref:

I.Birukou et al. (2011). Blocking the gate to ligand entry in human hemoglobin. J Biol Chem, 286, 10515-10529. PubMed id: 21193395 DOI: 10.1074/jbc.M110.176271

Date:

16-Aug-10 Release date: 08-Sep-10

Protein chain

P02185  (MYG_PHYMC) -  Myoglobin from Physeter macrocephalus

Seq: 154 a.a.

Struc: 154 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DOI no: 10.1074/jbc.M110.176271

J Biol Chem 286:10515-10529 (2011)

PubMed id: 21193395

Blocking the gate to ligand entry in human hemoglobin.

I.Birukou, J.Soman, J.S.Olson.

ABSTRACT

His(E7) to Trp replacements in HbA lead to markedly biphasic bimolecular CO rebinding after laser photolysis. For isolated mutant subunits, the fraction of fast phase increases with increasing [CO], suggesting a competition between binding to an open conformation with an empty E7 channel and relaxation to blocked or closed, slowly reacting states. The rate of conformational relaxation of the open state is ∼18,000 s(-1) in α subunits and ∼10-fold faster in β subunits, ∼175,000 s(-1). Crystal structures were determined for tetrameric α(WT)β(Trp-63) HbCO, α(Trp-58)β(WT) deoxyHb, and Trp-64 deoxy- and CO-Mb as controls. In Trp-63(E7) βCO, the indole side chain is located in the solvent interface, blocking entry into the E7 channel. Similar blocked Trp-64(E7) conformations are observed in the mutant Mb crystal structures. In Trp-58(E7) deoxy-α subunits, the indole side chain fills both the channel and the distal pocket, forming a completely closed state. The bimolecular rate constant for CO binding, k'(CO), to the open conformations of both mutant Hb subunits is ∼80-90 μm(-1) s(-1), whereas k'(CO) for the completely closed states is 1000-fold slower, ∼0.08 μm(-1) s(-1). A transient intermediate with k'(CO) ≈ 0.7 μm(-1) s(-1) is observed after photolysis of Trp-63(E7) βCO subunits and indicates that the indole ring blocks the entrance to the E7 channel, as observed in the crystal structures of Trp(E7) deoxyMb and βCO subunits. Thus, either blocking or completely filling the E7 channel dramatically slows bimolecular binding, providing strong evidence that the E7 channel is the major pathway (≥90%) for ligand entry in human hemoglobin.