4PQB

A sperm whale myoglobin double mutant L29E/F43H Mb with a non-native bis-His (His64/His93) coordination


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.942 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Regulating the coordination state of a heme protein by a designed distal hydrogen-bonding network.

Du, J.F.Li, W.Li, L.Wen, G.B.Lin, Y.W.Tan, X.

(2015) ChemistryOpen 4: 97-101

  • DOI: 10.1002/open.201402108
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Heme coordination state determines the functional diversity of heme proteins. Using myoglobin as a model protein, we designed a distal hydrogen-bonding network by introducing both distal glutamic acid (Glu29) and histidine (His43) residues and regula ...

    Heme coordination state determines the functional diversity of heme proteins. Using myoglobin as a model protein, we designed a distal hydrogen-bonding network by introducing both distal glutamic acid (Glu29) and histidine (His43) residues and regulated the heme into a bis-His coordination state with native ligands His64 and His93. This resembles the heme site in natural bis-His coordinated heme proteins such as cytoglobin and neuroglobin. A single mutation of L29E or F43H was found to form a distinct hydrogen-bonding network involving distal water molecules, instead of the bis-His heme coordination, which highlights the importance of the combination of multiple hydrogen-bonding interactions to regulate the heme coordination state. Kinetic studies further revealed that direct coordination of distal His64 to the heme iron negatively regulates fluoride binding and hydrogen peroxide activation by competing with the exogenous ligands. The new approach developed in this study can be generally applicable for fine-tuning the structure and function of heme proteins.


    Organizational Affiliation

    Laboratory of Protein Structure and Function, University of South China Hengyang, 421001, (P. R. China).,School of Chemistry and Chemical Engineering, Liaocheng University Liaocheng, 252059, (P. R. China).,School of Chemistry and Chemical Engineering, University of South China Hengyang, 421001, (P. R. China)).,School of Chemistry and Chemical Engineering, University of South China Hengyang, 421001, (P. R. China)) ; Laboratory of Protein Structure and Function, University of South China Hengyang, 421001, (P. R. China).,Department of Chemistry and Institute of Biomedical Science, Fudan University Shanghai, 200433, (P. R. China).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Myoglobin
A
154Physeter macrocephalusMutation(s): 2 
Gene Names: MB
Find proteins for P02185 (Physeter macrocephalus)
Go to Gene View: MB
Go to UniProtKB:  P02185
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
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: 1.942 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 33.968α = 90.00
b = 60.898β = 90.00
c = 75.356γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data collection
PHASERphasing
HKL-2000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-14
    Type: Initial release
  • Version 1.1: 2015-05-27
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Refinement description