PDBsum entry 1cik

Oxygen storage/transport

PDB id: 1cik

Contents

Protein chain

154 a.a. *

Ligands

SO4

HEM

Waters ×171

* Residue conservation analysis

PDB id:

1cik

Name:

Oxygen storage/transport

Title:

Recombinant sperm whale myoglobin i99a mutant (met)

Structure:

Protein (myoglobin). Chain: a. Engineered: yes. Mutation: yes

Source:

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

Biol. unit:

Hexamer (from PQS)

Resolution:

1.70Å R-factor: 0.151 R-free: 0.193

Authors:

E.C.Liong,G.N.Phillips Jr.

Key ref:

E.C.Liong et al. (2001). Waterproofing the heme pocket. Role of proximal amino acid side chains in preventing hemin loss from myoglobin. J Biol Chem, 276, 9093-9100. PubMed id: 11084036 DOI: 10.1074/jbc.M008593200

Date:

01-Apr-99 Release date: 09-Apr-99

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.M008593200

J Biol Chem 276:9093-9100 (2001)

PubMed id: 11084036

Waterproofing the heme pocket. Role of proximal amino acid side chains in preventing hemin loss from myoglobin.

E.C.Liong, Y.Dou, E.E.Scott, J.S.Olson, G.N.Phillips.

ABSTRACT

The ability of myoglobin to bind oxygen reversibly depends critically on retention of the heme prosthetic group. Globin side chains at the Leu(89)(F4), His(97)(FG3), Ile(99)(FG5), and Leu(104)(G5) positions on the proximal side of the heme pocket strongly influence heme affinity. The roles of these amino acids in preventing heme loss have been examined by determining high resolution structures of 14 different mutants at these positions using x-ray crystallography. Leu(89) and His(97) are important surface amino acids that interact either sterically or electrostatically with the edges of the porphyrin ring. Ile(99) and Leu(104) are located in the interior region of the proximal pocket beneath ring C of the heme prosthetic group. The apolar amino acids Leu(89), Ile(99), and Leu(104) "waterproof" the heme pocket by forming a barrier to solvent penetration, minimizing the size of the proximal cavity, and maintaining a hydrophobic environment. Substitutions with smaller or polar side chains at these positions result in exposure of the heme to solvent, the appearance of crystallographically defined water molecules in or near the proximal pocket, and large increases in the rate of hemin loss. Thus, the naturally occurring amino acid side chains at these positions serve to prevent hydration of the His(93)-Fe(III) bond and are highly conserved in all known myoglobins and hemoglobins.

Selected figure(s)

Figure 1.
Fig. 1. Space-filling representation of the proximal heme pocket of sperm whale myoglobin showing the position of the Leu89(F4) side chain (dark, space-filling) relative to the heme (shown in stick representation).

Figure 5.
Fig. 5. Stereo view of superposed stick representations of the heme pocket of sperm whale myoglobin showing tilting of the heme because of substitutions at position 99(FG5). Wild-type protein (Ile^99) is shown in yellow, I99V is in blue, and I99A is in red.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2001, 276, 9093-9100) copyright 2001.

Figures were selected by an automated process.