PDBsum entry 1vxb

Oxygen storage

PDB id: 1vxb

Contents

Protein chain

153 a.a. *

Ligands

SO4 ×2

HEM

Waters ×148

* Residue conservation analysis

PDB id:

1vxb

Name:

Oxygen storage

Title:

Native sperm whale myoglobin

Structure:

Myoglobin. Chain: a. Other_details: ph 4.0, 4 degrees celsius

Source:

Physeter catodon. Sperm whale. Organism_taxid: 9755. Organ: skeletal. Tissue: skeletal muscle

Resolution:

2.00Å R-factor: 0.200

Authors:

F.Yang,G.N.Phillips Jr.

Key ref:

F.Yang and G.N.Phillips (1996). Crystal structures of CO-, deoxy- and met-myoglobins at various pH values. J Mol Biol, 256, 762-774. PubMed id: 8642596 DOI: 10.1006/jmbi.1996.0123

Date:

09-Jan-96 Release date: 01-Aug-96

Protein chain

P02185  (MYG_PHYMC) -  Myoglobin from Physeter macrocephalus

Seq: 154 a.a.

Struc: 153 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1006/jmbi.1996.0123

J Mol Biol 256:762-774 (1996)

PubMed id: 8642596

Crystal structures of CO-, deoxy- and met-myoglobins at various pH values.

F.Yang, G.N.Phillips.

ABSTRACT

The distal histidine residue, His64(E7), and the proximal histidine residue, His93(F8), in myoglobin (Mb) are important for the function of the protein. For example, the increase in the association rate constant for CO binding at low pH has been suggested to be caused by the protonation of these histidine residues. In order to investigate the influence of protonation on the structure of myoglobin, we determined the crystal structures of sperm whale myoglobin to 2.0 A or better in different states of ligation (MbCO, deoxyMb and metMb) at pH values of 4, 5 and 6. The most dramatic change found at low pH is that His64 swings out of the distal pocket in the MbCO structure at pH 4, opening a direct channel from the solvent to the iron atom. This rotation seems to be facilitated by conformational changes in the CD corner. The benzyl side-chain of Phe46(CD4), which has been suggested to be a critical residue in controlling the rotation of His64, moves away from His64 at pH 4 in the deoxyMb structure, allowing more free rotation of His64. Arg45(CD3) is also important for the dynamics of myoglobin, since it influences the pK(a) of His64 and forms a hydrogen bond lattice that hinders the rotation of His64 at neutral pH. This hydrogen-bond lattice disappears at low pH. Although His64 rotates out of the distal pocket in the MbCO structure at pH 4, leaving more space for the CO ligand, the Fe-C-O angle refines to about 130 degrees, the same as those at pH 5 and 6. In the MbCO structure at pH 4, significant conformational changes appear in the EF corner. The peptide plane between Lys79(EF2) and Gly80(EF3) flips about 150 degrees. The occupancy of this conformation in the MbCO structures increases with decreases in pH. On the proximal side of the heme, the bond between the heme iron atom and N(epsilon) of His93 remains intact under the experimental conditions in the MbCO and deoxyMb structures, but appears elongated in the metMb structure at pH 4, representing either a weakened bond or the breakage of the bond in some fraction of the molecules in the crystal.

Selected figure(s)

Figure 4.
Figure 4. The heme pocket of metMb at pH 4 (white), 5 (yellow) and 6 (red). On the distal side at pH 4, the movement of the water molecule ligand and His64 is similar to that in the deoxyMb structure at pH 4 due to the protonation of the group (Figure 1(b)). On the proximal side, His93 undergoes significant conformational changes and the distance from the iron atom to N e of His93 is 2.5 Å , representing either a weakened bond or the breakage of the bond in some molecules in the crystal. The =2Fo - Fc= electron density map is contoured at 1.5 standard deviations above the average density of the map for metMb at pH 4.

Figure 6.
Figure 6. The CD corner in deoxyMb at pH 4 (white), pH 5 (yellow) and pH 6 (red). Phe46 moves to the left in the Figure at pH 4, increasing its distance to His64. N d of His48 hydrogen bonds to the carbonyl oxygen atom of Arg45 at pH 4, which may be the cause of the large displacement of these two residues. The rotation of the terminal atoms of the side-chain of Arg45 at pH 4 disrupts the hydrogen-bond lattice. The heme-6-propionate group is in a new conformation at pH 4, probably due to the loss of its hydrogen bond with Arg45. The =2Fo - Fc = electron density map is contoured at 1.5 standard deviations above the average density of the map for deoxyMb at pH 4.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1996, 256, 762-774) copyright 1996.

Figures were selected by an automated process.