1E8E

Solution Structure of Methylophilus methylotrophus Cytochrome c''. Insights into the Structural Basis of Haem-Ligand Detachment


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 400 
  • Conformers Submitted: 20 
  • Selection Criteria: LEAST RESTRAINT VIOLATION 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Solution Structure of Methylophilus Methylotrophus Cytochrome C": Insights Into the Structural Basis of Haem-Ligand Detachment

Brennan, L.Turner, D.L.Fareleira, P.Santos, H.

(2001) J Mol Biol 308: 353

  • DOI: https://doi.org/10.1006/jmbi.2001.4600
  • Primary Citation of Related Structures:  
    1E8E

  • PubMed Abstract: 

    Cytochrome c" from Methylophilus methylotrophus is a monohaem protein with 124 amino acid residues. The iron has two histidine ligands in the oxidised form, one of which detaches and picks up a proton when the protein is reduced. Thus, both forms are paramagnetic. The structure of the oxidised form in solution, determined from NMR data is presented. The family of structures has an average backbone rmsd value of 0.53 A, and a heavy atom rmsd value of 0.95 A, within a target function range of 32 %. This structure is related to class I cytochromes with an additional helix at the N terminus. The haem-binding site occurs in a domain essentially lacking secondary structure motifs and the axial histidinyl residues were found in an unusual near perpendicular orientation. Moreover, a disulfide bridge is present, an uncommon structural feature among c-type cytochromes. The disulfide bridge, linking cysteine residues 96 and 104, forms a loop that confers rigidity and is essential to the detachment of the axial histidine (His95) as demonstrated by chemical disruption of the S-S bond. A route for protonation of the distal histidine involving haem propionate 17 is proposed and discussed in the light of available models for complex membrane proton pumps.


  • Organizational Affiliation

    Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Rua da Quinta Grande, 6 Apt. 127, Oeiras, Portugal.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME C''124Methylophilus methylotrophusMutation(s): 0 
UniProt
Find proteins for Q9RQB9 (Methylophilus methylotrophus)
Explore Q9RQB9 
Go to UniProtKB:  Q9RQB9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RQB9
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download Ideal Coordinates CCD File 
B [auth A]HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 400 
  • Conformers Submitted: 20 
  • Selection Criteria: LEAST RESTRAINT VIOLATION 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-09-20
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-01-15
    Changes: Derived calculations, Other