3QZX

3D Structure of ferric methanosarcina acetivorans protoglobin Y61A mutant with unknown ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.134 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural heterogeneity and ligand gating in ferric methanosarcina acetivorans protoglobin mutants.

Pesce, A.Tilleman, L.Dewilde, S.Ascenzi, P.Coletta, M.Ciaccio, C.Bruno, S.Moens, L.Bolognesi, M.Nardini, M.

(2011) IUBMB Life 63: 287-294

  • DOI: 10.1002/iub.484
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Protoglobin from Methanosarcina acetivorans C2A (MaPgb), a strictly anaerobic methanogenic Archaea, displays peculiar structural and functional properties within members of the hemoglobin superfamily. In fact, MaPgb-specific loops and a N-terminal ex ...

    Protoglobin from Methanosarcina acetivorans C2A (MaPgb), a strictly anaerobic methanogenic Archaea, displays peculiar structural and functional properties within members of the hemoglobin superfamily. In fact, MaPgb-specific loops and a N-terminal extension (20 amino acid residues) completely bury the heme within the protein matrix. Therefore, the access of diatomic gaseous molecules to the heme is granted by two apolar tunnels reaching the heme distal site from locations at the B/G and B/E helix interfaces. The presence of two tunnels within the protein matrix could be partly responsible for the slightly biphasic ligand binding behavior. Unusually, MaPgb oxygenation is favored with respect to carbonylation. Here, the crucial role of Tyr(B10)61 and Ile(G11)149 residues, located in the heme distal site and lining the protein matrix tunnels 1 and 2, respectively, on ligand binding to the heme-Fe-atom and on distal site structural organization is reported. In particular, tunnel 1 accessibility is modulated by a complex reorganization of the Trp(B9)60 and Phe(E11)93 side-chains, triggered by mutations of the Tyr(B10)61 and Ile(G11)149 residues, and affected by the presence and type of the distal heme-bound ligand.


    Related Citations: 
    • Archaeal protoglobin structure indicates new ligand diffusion paths and modulation of haem-reactivity
      Nardini, M., Pesce, A., Thijs, L., Saito, J.A., Dewilde, S., Alam, M., Ascenzi, P., Coletta, M., Ciaccio, C., Moens, L., Bolognesi, M.
      (2008) EMBO Rep 9: 157

    Organizational Affiliation

    Department of Physics, University of Genova, Genova, Italy.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methanosarcina acetivorans protoglobinA195Methanosarcina acetivoransMutation(s): 2 
Gene Names: MA_2883
Find proteins for Q8TLY9 (Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A))
Explore Q8TLY9 
Go to UniProtKB:  Q8TLY9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.134 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.089α = 90
b = 49.239β = 92.57
c = 51.514γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-06-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Database references