1MNK

INTERACTIONS AMONG RESIDUES CD3, E7, E10 AND E11 IN MYOGLOBINS: ATTEMPTS TO SIMULATE THE O2 AND CO BINDING PROPERTIES OF APLYSIA MYOGLOBIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Interactions among residues CD3, E7, E10, and E11 in myoglobins: attempts to simulate the ligand-binding properties of Aplysia myoglobin.

Smerdon, S.J.Krzywda, S.Brzozowski, A.M.Davies, G.J.Wilkinson, A.J.Brancaccio, A.Cutruzzola, F.Allocatelli, C.T.Brunori, M.Li, T.Brantley Jr., R.E.Carver, T.E.Eich, R.F.Singleton, E.Olson, J.S.

(1995) Biochemistry 34: 8715-8725

  • Primary Citation of Related Structures:  1MNH, 1MNJ

  • PubMed Abstract: 
  • Site-directed mutations have been introduced singly and in combination at residues lysine/arginine45 (CD3), histidine64 (E7), threonine67 (E10), and valine68 (E11) in pig and sperm whale myoglobins. The mutations probe the roles of these key distal p ...

    Site-directed mutations have been introduced singly and in combination at residues lysine/arginine45 (CD3), histidine64 (E7), threonine67 (E10), and valine68 (E11) in pig and sperm whale myoglobins. The mutations probe the roles of these key distal pocket residues and represent attempts to mimic the heme environment of Aplysia limacina myoglobin which achieves moderately high O2 affinity in the absence of a distal histidine. In the mollusc myoglobin, arginine-E10 is believed to swing into the heme pocket and provide a hydrogen bond to the bound O2. The association and dissociation rate constants for oxygen and carbon monoxide binding to H64V, T67A, T67V, T67E, T67R, V68I, V68T, H64V-T67R, H64V-V68T, H64V-V68I, and H64V-T67R-V68I pig myoglobin mutants and T67R, H64V-T67R, and R45D-H64V-T67R mutants of sperm whale myoglobin have been measured using stopped-flow rapid mixing and flash photolysis techniques. Replacement of histidine-E7 with valine in either pig or sperm whale myoglobin drastically lowers O2 affinity while increasing CO affinity. Two second-site mutations, T67R and V68T, increase O2 affinity in the H64V mutant, even though when introduced singly these mutations have no effect or lower KO2, respectively. However, the oxygen affinities of the H64V-T67R mutants are 5-10-fold lower than that of A. limacina myoglobin. The crystal structure of the pig H64V-T67R double mutant reveals that the valine-E7 side chain is approximately 1 A closer to the heme plane than in the mollusc protein which may restrict access of the arginine-E10 side chain into the heme pocket. The O2 affinity of the H64V-T67R double mutant is not altered by the R45D replacement but is reduced 10-fold by the V68I mutation. The interactive effects of the T67R, V68I, and V68T mutations with the H64V substitution are discussed in terms of O2, CO, and N3-binding and the crystal structures of the H64V-T67R, H64V-V68I, and H64V-V68T double-mutant proteins. In many instances, the effects of second-site mutations in the valine64 background are the opposite of those observed for the corresponding single mutations in the wild type background. These results can be understood in terms of the changes in the rate-determining steps for ligand association and dissociation and the loss of distal pocket water molecules which follow replacement of histidine64 by valine.


    Related Citations: 
    • High Resolution X-Ray Structures of Pig Metmyoglobin and Two Cd3 Mutants Mb(Lys45-->Arg) and Mb(Lys45-->Ser)
      Oldfield, T.J.,Smerdon, S.J.,Dauter, Z.,Petratos, K.,Wilson, K.S.,Wilkinson, A.J.
      (1992) Biochemistry 31: 8732
    • Distal Pocket Polarity in Ligand Binding to Myoglobin: Deoxy and Carbonmonoxy Forms of Threonine68(E11) Mutant Investigated by X-Ray Crystallography and Infrared Spectroscopy
      Cameron, A.D.,Smerdon, S.J.,Wilkinson, A.J.,Habash, J.,Helliwell, J.R.,Li, T.,Olson, J.S.
      (1993) Biochemistry 32: 13061
    • 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, 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • Space Group: I 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 125.260α = 90.00
b = 42.490β = 92.29
c = 92.370γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement
ARP/wARPmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-04-20
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2012-02-22
    Type: Database references