3VM9

Dimeric horse myoglobin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural and oxygen binding properties of dimeric horse myoglobin

Nagao, S.Osuka, H.Yamada, T.Uni, T.Shomura, Y.Imai, K.Higuchi, Y.Hirota, S.

(2012) Dalton Trans 41: 11378-11385

  • DOI: 10.1039/c2dt30893b

  • PubMed Abstract: 
  • Myoglobin (Mb) stores dioxygen in muscles, and is a fundamental model protein widely used in molecular design. The presence of dimeric Mb has been known for more than forty years, but its structural and oxygen binding properties remain unknown. From ...

    Myoglobin (Mb) stores dioxygen in muscles, and is a fundamental model protein widely used in molecular design. The presence of dimeric Mb has been known for more than forty years, but its structural and oxygen binding properties remain unknown. From an X-ray crystallographic analysis at 1.05 Å resolution, we found that dimeric metMb exhibits a domain-swapped structure with two extended α-helices. Each new long α-helix is formed by the E and F helices and the EF-loop of the original monomer, and as a result the proximal and distal histidines of the heme originate from different protomers. The heme orientation in the dimer was in the normal mode as in the monomer, but regulated faster from the reverse to normal orientation. The dimer possessed the oxygen binding property, although it exhibited a slightly higher oxygen binding affinity (∼1.4 fold) compared to the monomer and showed no cooperativity for oxygen binding. The oxygen binding rate constant (k(on)) of the dimer ((14.0 ± 0.7) × 10(6) M(-1) s(-1)) was similar to that of the monomer, whereas the oxygen dissociation rate constant (k(off)) of the dimer (8 ± 1 s(-1)) was smaller than that of the monomer (12 ± 1 s(-1)). We attribute the similar k(on) values to their active site structures being similar, whereas the faster regulation of the heme orientation and the smaller k(off) in the dimer are presumably due to the slight change in the active site structure and/or more rigid structure compared to the monomer. These results show that domain swapping may be a new tool for protein engineering.


    Organizational Affiliation

    Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0192, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Myoglobin
A, B
153Equus caballusMutation(s): 0 
Gene Names: MB
Find proteins for P68082 (Equus caballus)
Go to Gene View: MB
Go to UniProtKB:  P68082
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
O
Query on O

Download SDF File 
Download CCD File 
A, B
OXYGEN ATOM
O
XLYOFNOQVPJJNP-UHFFFAOYSA-N
 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: 1.05 Å
  • R-Value Free: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.340α = 90.00
b = 62.523β = 90.00
c = 83.354γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
SHELXL-97refinement
BSSdata collection
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-09-12
    Type: Initial release