1MYJ

DISTAL POLARITY IN LIGAND BINDING TO MYOGLOBIN: STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF A THREONINE68(E11) MUTANT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Distal pocket polarity in ligand binding to myoglobin: structural and functional characterization of a threonine68(E11) mutant.

Smerdon, S.J.Dodson, G.G.Wilkinson, A.J.Gibson, Q.H.Blackmore, R.S.Carver, T.E.Olson, J.S.

(1991) Biochemistry 30: 6252-6260


  • PubMed Abstract: 
  • Site-directed mutagenesis studies have confirmed that the distal histidine in myoglobin stabilizes bound O2 by hydrogen bonding and have suggested that it is the polar character of the imidazole side chain rather than its size that limits the rate of ...

    Site-directed mutagenesis studies have confirmed that the distal histidine in myoglobin stabilizes bound O2 by hydrogen bonding and have suggested that it is the polar character of the imidazole side chain rather than its size that limits the rate of ligand entry into the protein. We constructed an isosteric Val68 to Thr replacement in pig myoglobin (i) to investigate whether the O2 affinity could be increased by the introduction of a second hydrogen-bonding group into the distal heme pocket and (ii) to examine the influence of polarity on the ligand binding rates more rigorously. The 1.9-A crystal structure of Thr68 aquometmyoglobin confirms that the mutant and wild-type proteins are essentially isostructural and reveals that the beta-OH group of Thr68 is in a position to form hydrogen-bonding interactions both with the coordinated water molecule and with the main chain greater than C=O of residue 64. The rate of azide binding to the ferric form of the Thr68 mutant was 60-fold lower than that for the wild-type protein, consistent with the proposed stabilization of the coordinated water molecule. However, bound O2 is destabilized in the ferrous form of the mutant protein. The observed 17-fold lowering of the O2 affinity may be a consequence of the hydrogen-bonding interaction made between the Thr68 beta-OH group and the carbonyl oxygen of residue 64. Overall association rate constants for O2, NO, and alkyl isocyanide binding to ferrous pig myoglobin were 3-10-fold lower for the mutant compared to the wild-type protein, whereas that for CO binding was little affected.(ABSTRACT TRUNCATED AT 250 WORDS)


    Related Citations: 
    • Apomyoglobin as a Molecular Recognition Surface: Expression, Reconstitution and Crystallisation of Recombinant Porcine Myoglobin in Escherichia Coli
      Dodson, G.G.,Hubbard, R.E.,Oldfield, T.J.,Smerdon, S.J.,Wilkinson, A.J.
      (1988) Protein Eng. 2: 233
    • Determination of the Crystal Structure of Recombinant Pig Myoglobin by Molecular Replacement and its Refinement
      Smerdon, S.J.,Oldfield, T.J.,Dodson, E.J.,Dodson, G.G.,Hubbard, R.E.,Wilkinson, A.J.
      (1990) Acta Crystallogr.,Sect.B 46: 370


    Organizational Affiliation

    Department of Chemistry, University of York, Heslington, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MYOGLOBIN
A, B
153Sus scrofaGene Names: MB
Find proteins for P02189 (Sus scrofa)
Go to Gene View: MB
Go to UniProtKB:  P02189
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • Space Group: I 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 123.750α = 90.00
b = 42.480β = 92.05
c = 92.050γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance