5JLI

Nitric oxide complex of the L16A mutant of cytochrome c prime from Alcaligenes xylosoxidans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Engineering proximal vs. distal heme-NO coordination via dinitrosyl dynamics: implications for NO sensor design.

Kekilli, D.Petersen, C.A.Pixton, D.A.Ghafoor, D.D.Abdullah, G.H.Dworkowski, F.S.N.Wilson, M.T.Heyes, D.J.Hardman, S.J.O.Murphy, L.M.Strange, R.W.Scrutton, N.S.Andrew, C.R.Hough, M.A.

(2017) Chem Sci 8: 1986-1994

  • DOI: 10.1039/c6sc04190f
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Proximal <i>vs. </i> distal heme-NO coordination is a novel strategy for selective gas response in heme-based NO-sensors. In the case of <i>Alcaligenes xylosoxidans </i> cytochrome c' (AXCP), formation of a transient distal 6cNO complex is followed ...

    Proximal vs. distal heme-NO coordination is a novel strategy for selective gas response in heme-based NO-sensors. In the case of Alcaligenes xylosoxidans cytochrome c' (AXCP), formation of a transient distal 6cNO complex is followed by scission of the trans Fe-His bond and conversion to a proximal 5cNO product via a putative dinitrosyl species. Here we show that replacement of the AXCP distal Leu16 residue with smaller or similar sized residues (Ala, Val or Ile) traps the distal 6cNO complex, whereas Leu or Phe residues lead to a proximal 5cNO product with a transient or non-detectable distal 6cNO precursor. Crystallographic, spectroscopic, and kinetic measurements of 6cNO AXCP complexes show that increased distal steric hindrance leads to distortion of the Fe-N-O angle and flipping of the heme 7-propionate. However, it is the kinetic parameters of the distal NO ligand that determine whether 6cNO or proximal 5cNO end products are formed. Our data support a 'balance of affinities' mechanism in which proximal 5cNO coordination depends on relatively rapid release of the distal NO from the dinitrosyl precursor. This mechanism, which is applicable to other proteins that form transient dinitrosyls, represents a novel strategy for 5cNO formation that does not rely on an inherently weak Fe-His bond. Our data suggest a general means of engineering selective gas response into biologically-derived gas sensors in synthetic biology.


    Organizational Affiliation

    School of Biological Sciences , University of Essex , Wivenhoe Park , Colchester , Essex CO4 3SQ , UK . Email: mahough@essex.ac.uk.,Faculty of Science and Education Science , University of Sulaimani , Sulaymaniyah , Iraq.,Medical Research Center , Hawler Medical University , Erbil , Iraq.,Molecular Biophysics Group , Institute of Integrative Biology , Faculty of Health and Life Sciences , University of Liverpool , Liverpool , L69 7ZB , UK.,Department of Chemistry and Biochemistry , Eastern Oregon University , La Grande , Oregon 97850 , USA . Email: candrew@eou.edu.,School of Chemistry , Bangor University , Bangor , Gwynedd , Wales LL57 2UW , UK.,Manchester Institute of Biotechnology , 131 Princess Street , Manchester M1 7DN , UK.,Swiss Light Source , Paul Scherrer Institute , Villigen PSI , CH-5232 , Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c'
A
127Alcaligenes xylosoxydans xylosoxydansMutation(s): 1 
Find proteins for P00138 (Alcaligenes xylosoxydans xylosoxydans)
Go to UniProtKB:  P00138
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ASC
Query on ASC

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Download CCD File 
A
ASCORBIC ACID
C6 H8 O6
CIWBSHSKHKDKBQ-JLAZNSOCSA-N
 Ligand Interaction
HEC
Query on HEC

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Download CCD File 
A
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
NO
Query on NO

Download SDF File 
Download CCD File 
A
NITRIC OXIDE
Nitrogen monoxide
N O
ODUCDPQEXGNKDN-UHFFFAOYAM
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.171 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 53.629α = 90.00
b = 53.629β = 90.00
c = 180.523γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-03-08
    Type: Initial release
  • Version 1.1: 2017-12-06
    Type: Database references