Stabilizing bound O2 in myoglobin by valine68 (E11) to asparagine substitution.

Krzywda, S.; Murshudov, G.N.; Brzozowski, A.M.; Jaskolski, M.; Scott, E.E.; Klizas, S.A.; Gibson, Q.H.; Olson, J.S.; Wilkinson, A.J.

doi:10.2210/pdb1mdn/pdb

Macromolecule Content

Total Structure Weight: 35229.80
Atom Count: 2557
Residue Count: 306
Unique protein chains: 1

1MDN

WILD TYPE MYOGLOBIN WITH CO

DOI: 10.2210/pdb1MDN/pdb

Classification: OXYGEN STORAGE/TRANSPORT
Organism(s): Sus scrofa
Expression System: Escherichia coli
Mutation(s): 1

Deposited: 1998-08-12 Released: 1998-09-30
Deposition Author(s): Murshudov, G.N., Krzywda, S., Brzozowski, A.M., Jaskolski, M., Scott, E.E., Klizas, S.A., Gibson, Q.H., Olson, J.S., Wilkinson, A.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free: 0.262
R-Value Work: 0.198

wwPDB Validation3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Stabilizing bound O2 in myoglobin by valine68 (E11) to asparagine substitution.

Krzywda, S., Murshudov, G.N., Brzozowski, A.M., Jaskolski, M., Scott, E.E., Klizas, S.A., Gibson, Q.H., Olson, J.S., Wilkinson, A.J.

(1998) Biochemistry 37: 15896-15907

PubMed: 9843395 Search on PubMed
DOI: 10.1021/bi9812470
Primary Citation of Related Structures:
1MWD, 1MWC, 1MNO, 1M6M, 1M6C

PubMed Abstract:

The isopropyl side chain of valine68 in myoglobin has been replaced by the acetamide side chain of asparagine in an attempt to engineer higher oxygen affinity. The asparagine replacement introduces a second hydrogen bond donor group into the distal heme pocket which could further stabilize bound oxygen. The Val68 to Asn substitution leads to approximately 3-fold increases in oxygen affinity and 4-6-fold decreases in CO affinity. As a result, the M-value (KCO/KO2) is lowered 15-20-fold to a value close to unity. An even larger enhancement of O2 affinity is seen when asparagine68 is inserted into H64L sperm whale myoglobin which lacks a distal histidine. The overall rate constants for oxygen and carbon monoxide binding to the single V68N myoglobin mutants are uniformly lower than those for the wild-type protein. In contrast, the overall rate constant for NO association is unchanged. Analyses of time courses monitoring the geminate recombination of ligands following nanosecond and picosecond flash photolysis of MbNO and MbO2 indicate that the barrier to ligand binding from within the heme pocket has been raised with little effect on the barrier to diffusion of the ligand into the pocket from the solvent. The crystal structures of the aquomet, deoxy, oxy, and carbon monoxy forms of the V68N mutant have been determined to resolutions ranging from 1.75 to 2.2 A at 150 K. The overall structures are very similar to those of the wild-type protein with the principal alterations taking place within and around the distal heme pocket. In all four structures the asparagine68 side chain lies almost parallel to the plane of the heme with its amide group directed toward the back of the distal heme pocket. The coordinated water molecule in the aquomet form and the bound oxygen in the oxy form can form hydrogen-bonding interactions with both the Asn68 amide group and the imidazole side chain of His64. Surprisingly, in the carbon monoxy form of the V68N mutant, the histidine64 side chain has swung completely out the distal pocket, its place being taken by two ordered water molecules. Overall, these functional and structural results show that the asparagine68 side chain (i) forms a strong hydrogen bond with bound oxygen through its -NH2 group but (ii) sterically hinders the approach of ligands to the iron from within the distal heme pocket.

Organizational Affiliation:

Department of Chemistry, University of York, UK.

Macromolecules

Find similar proteins by: Sequence | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN (MYOGLOBIN)	A, B	153	Sus scrofa	Mutation(s): 1 Gene Names: MB
Find proteins for P02189 (Sus scrofa) Go to Gene View: MB Go to UniProtKB: P02189
Protein Feature View Full Protein Feature View for P02189

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
HEM Query on HEM Download SDF File Download CCD File	A, B	PROTOPORPHYRIN IX CONTAINING FE HEME C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Ligand Interaction