4RKN

Wolinella succinogenes octaheme sulfite reductase MccA, form II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.135 
  • R-Value Observed: 0.137 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

The octahaem MccA is a haem c-copper sulfite reductase.

Hermann, B.Kern, M.La Pietra, L.Simon, J.Einsle, O.

(2015) Nature 520: 706-709

  • DOI: 10.1038/nature14109
  • Primary Citation of Related Structures:  
    4RKM, 4RKN

  • PubMed Abstract: 
  • The six-electron reduction of sulfite to sulfide is the pivot point of the biogeochemical cycle of the element sulfur. The octahaem cytochrome c MccA (also known as SirA) catalyses this reaction for dissimilatory sulfite utilization by various bacteria. It is distinct from known sulfite reductases because it has a substantially higher catalytic activity and a relatively low reactivity towards nitrite ...

    The six-electron reduction of sulfite to sulfide is the pivot point of the biogeochemical cycle of the element sulfur. The octahaem cytochrome c MccA (also known as SirA) catalyses this reaction for dissimilatory sulfite utilization by various bacteria. It is distinct from known sulfite reductases because it has a substantially higher catalytic activity and a relatively low reactivity towards nitrite. The mechanistic reasons for the increased efficiency of MccA remain to be elucidated. Here we show that anoxically purified MccA exhibited a 2- to 5.5-fold higher specific sulfite reductase activity than the enzyme isolated under oxic conditions. We determined the three-dimensional structure of MccA to 2.2 Å resolution by single-wavelength anomalous dispersion. We find a homotrimer with an unprecedented fold and haem arrangement, as well as a haem bound to a CX15CH motif. The heterobimetallic active-site haem 2 has a Cu(I) ion juxtaposed to a haem c at a Fe-Cu distance of 4.4 Å. While the combination of metals is reminiscent of respiratory haem-copper oxidases, the oxidation-labile Cu(I) centre of MccA did not seem to undergo a redox transition during catalysis. Intact MccA tightly bound SO2 at haem 2, a dehydration product of the substrate sulfite that was partially turned over due to photoreduction by X-ray irradiation, yielding the reaction intermediate SO. Our data show the biometal copper in a new context and function and provide a chemical rationale for the comparatively high catalytic activity of MccA.


    Organizational Affiliation

    1] Lehrstuhl Biochemie, Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg, Germany [2] BIOSS Centre for Biological Signalling Studies, Schänzlestrasse 1, 79104 Freiburg, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MccAA, B, C, D732Wolinella succinogenes DSM 1740Mutation(s): 0 
Gene Names: mccAWS0379
EC: 1.8.99
UniProt
Find proteins for Q7MSJ8 (Wolinella succinogenes (strain ATCC 29543 / DSM 1740 / LMG 7466 / NCTC 11488 / FDC 602W))
Explore Q7MSJ8 
Go to UniProtKB:  Q7MSJ8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7MSJ8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
CA [auth C],
DA [auth C],
EA [auth C],
F [auth A],
FA [auth C],
CA [auth C],
DA [auth C],
EA [auth C],
F [auth A],
FA [auth C],
G [auth A],
GA [auth C],
H [auth A],
HA [auth C],
I [auth A],
IA [auth C],
J [auth A],
JA [auth C],
K [auth A],
L [auth A],
M [auth A],
NA [auth D],
OA [auth D],
PA [auth D],
QA [auth D],
R [auth B],
RA [auth D],
S [auth B],
SA [auth D],
T [auth B],
TA [auth D],
U [auth B],
UA [auth D],
V [auth B],
W [auth B],
X [auth B],
Y [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
DTN
Query on DTN

Download Ideal Coordinates CCD File 
BA [auth C],
E [auth A],
MA [auth D],
O [auth A],
Q [auth B]
DITHIONITE
O4 S2
GRWZHXKQBITJKP-UHFFFAOYSA-L
 Ligand Interaction
SO3
Query on SO3

Download Ideal Coordinates CCD File 
AA [auth B],
LA [auth C],
P [auth A],
WA [auth D],
XA [auth D]
SULFITE ION
O3 S
LSNNMFCWUKXFEE-UHFFFAOYSA-L
 Ligand Interaction
CU
Query on CU

Download Ideal Coordinates CCD File 
KA [auth C],
N [auth A],
VA [auth D],
Z [auth B]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.135 
  • R-Value Observed: 0.137 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 186.472α = 90
b = 186.472β = 90
c = 232.836γ = 120
Software Package:
Software NamePurpose
SHARPphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-04
    Type: Initial release
  • Version 1.1: 2015-03-04
    Changes: Database references
  • Version 1.2: 2015-06-24
    Changes: Database references
  • Version 1.3: 2017-11-22
    Changes: Refinement description