PDBsum entry 1dwt

Oxygen transport

PDB id: 1dwt

Contents

Protein chain

152 a.a. *

Ligands

HEM

CMO

SO4 ×2

Waters ×163

* Residue conservation analysis

PDB id:

1dwt

Name:

Oxygen transport

Title:

Photorelaxed horse heart myoglobin co complex

Structure:

Myoglobin. Chain: a

Source:

Equus caballus. Horse. Organism_taxid: 9796. Organ: heart

Resolution:

1.40Å R-factor: 0.197 R-free: 0.243

Authors:

K.Chu,J.Vojtechovsky,B.H.Mcmahon,R.M.Sweet,J.Berendzen,I.Schlichting

Key ref:

K.Chu et al. (2000). Structure of a ligand-binding intermediate in wild-type carbonmonoxy myoglobin. Nature, 403, 921-923. PubMed id: 10706294 DOI: 10.1038/35002641

Date:

12-Dec-99 Release date: 03-Mar-00

Protein chain

P68082  (MYG_HORSE) -  Myoglobin from Equus caballus

Seq: 154 a.a.

Struc: 152 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: 10.1038/35002641

Nature 403:921-923 (2000)

PubMed id: 10706294

Structure of a ligand-binding intermediate in wild-type carbonmonoxy myoglobin.

K.Chu, J.Vojtchovský, B.H.McMahon, R.M.Sweet, J.Berendzen, I.Schlichting.

ABSTRACT

Small molecules such as NO, O2, CO or H2 are important biological ligands that bind to metalloproteins to function crucially in processes such as signal transduction, respiration and catalysis. A key issue for understanding the regulation of reaction mechanisms in these systems is whether ligands gain access to the binding sites through specific channels and docking sites, or by random diffusion through the protein matrix. A model system for studying this issue is myoglobin, a simple haem protein. Myoglobin has been studied extensively by spectroscopy, crystallography, computation and theory. It serves as an aid to oxygen diffusion but also binds carbon monoxide, a byproduct of endogenous haem catabolism. Molecular dynamics simulations, random mutagenesis and flash photolysis studies indicate that ligand migration occurs through a limited number of pathways involving docking sites. Here we report the 1.4 A resolution crystal structure of a ligand-binding intermediate in carbonmonoxy myoglobin that may have far-reaching implications for understanding the dynamics of ligand binding and catalysis.

Selected figure(s)

Figure 1.
Figure 1: Position of the CO molecule in states A and B. a, Electron-density map of F[obs](MbCO*) - F[obs](CO bound) shows positive (black, 10 ) and negative (grey, 7 ) electron density at the position of CO* (B) and bound CO (A), respectively. b, Electron density map of 2F[obs ]- F[calc] (1.0 ) of state B generated by photolysis. The iron is located below the haem plane; the CO molecule is shown almost along its axis. c, Electron density map of 2F[obs ]- F[calc] (1.0 ) of state A. The iron is in the haem plane; CO is bound almost perpendicular to the haem plane.

Figure 2.
Figure 2: Position of the CO molecule in state D. a, Electron density map of F[obs](Mb**CO) - F[obs ](CO rebound) shows positive (black, 4.2 ) and negative (grey, 5.2 ) electron density below the haem and at the position of bound CO, respectively. b, Electron density maps of 2F[obs ]-[]F[calc] (1.0 ). The iron is below the haem plane; no electron density associated with CO is seen at the distal side of the haem, but a new peak interpreted as CO* appears below the haem. c, The CO-bound complex obtained after briefly thawing the photorelaxed complex shown in a, b.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2000, 403, 921-923) copyright 2000.