7V5Q

The dimeric structure of G80A/H81A/L137E myoglobin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

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Literature

Experimental and theoretical study on converting myoglobin into a stable domain-swapped dimer by utilizing a tight hydrogen bond network at the hinge region.

Xie, C.Shimoyama, H.Yamanaka, M.Nagao, S.Komori, H.Shibata, N.Higuchi, Y.Shigeta, Y.Hirota, S.

(2021) RSC Adv 11: 37604-37611

  • DOI: 10.1039/d1ra06888a
  • Primary Citation of Related Structures:  
    7V5P, 7V5Q, 7V5R

  • PubMed Abstract: 
  • Various factors, such as helical propensity and hydrogen bonds, control protein structures. A frequently used model protein, myoglobin (Mb), can perform 3D domain swapping, in which the loop at the hinge region is converted to a helical structure in the dimer ...

    Various factors, such as helical propensity and hydrogen bonds, control protein structures. A frequently used model protein, myoglobin (Mb), can perform 3D domain swapping, in which the loop at the hinge region is converted to a helical structure in the dimer. We have previously succeeded in obtaining monomer-dimer equilibrium in the native state by introducing a high α-helical propensity residue, Ala, to the hinge region. In this study, we focused on another factor that governs the protein structure, hydrogen bonding. X-ray crystal structures and thermodynamic studies showed that the myoglobin dimer was stabilized over the monomer when keeping His82 to interact with Lys79 and Asp141 through water moleclues and mutating Leu137, which was located close to the H-bond network at the dimer hinge region, to a hydrophilic amino acid (Glu or Asp). Molecular dynamics simulation studies confirmed that the number of H-bonds increased and the α-helices at the hinge region became more rigid for mutants with a tighter H-bond network, supporting the hypothesis that the myoglobin dimer is stabilized when the H-bond network at the hinge region is enhanced. This demonstrates the importance and utility of hydrogen bonds for designing a protein dimer from its monomer with 3D domain swapping.


    Organizational Affiliation

    Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology 8916-5 Takayama, Ikoma Nara 630-0192 Japan hirota@ms.naist.jp.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MyoglobinA, B153Equus caballusMutation(s): 3 
Gene Names: MB
UniProt
Find proteins for P68082 (Equus caballus)
Explore P68082 
Go to UniProtKB:  P68082
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68082
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.46α = 90
b = 63.03β = 90
c = 83.43γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
pointlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP21H02060
Japan Society for the Promotion of Science (JSPS)JapanJP19K05695
Japan Science and TechnologyJapanJP20338388

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-29
    Type: Initial release