4RKM

Wolinella succinogenes octaheme sulfite reductase MccA, form I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/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 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

    Lehrstuhl Biochemie, Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MccA732Wolinella succinogenes DSM 1740Mutation(s): 0 
Gene Names: mccAWS0379
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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
AB [auth C]
AC [auth E]
AD [auth H]
AE [auth J]
AF [auth L]
AB [auth C],
AC [auth E],
AD [auth H],
AE [auth J],
AF [auth L],
BD [auth H],
BE [auth J],
BF [auth L],
CD [auth H],
CE [auth J],
CF [auth L],
GA [auth B],
GB [auth D],
HA [auth B],
HB [auth D],
HC [auth F],
IA [auth B],
IB [auth D],
IC [auth F],
ID [auth I],
IE [auth K],
IF [auth G],
JA [auth B],
JB [auth D],
JC [auth F],
JD [auth I],
JE [auth K],
JF [auth G],
KA [auth B],
KB [auth D],
KC [auth F],
KD [auth I],
KE [auth K],
KF [auth G],
LA [auth B],
LB [auth D],
LC [auth F],
LD [auth I],
LE [auth K],
LF [auth G],
MA [auth B],
MB [auth D],
MC [auth F],
MD [auth I],
ME [auth K],
MF [auth G],
NA [auth B],
NB [auth D],
NC [auth F],
ND [auth I],
NE [auth K],
NF [auth G],
OC [auth F],
OD [auth I],
OE [auth K],
OF [auth G],
PD [auth I],
PE [auth K],
PF [auth G],
R [auth A],
S [auth A],
T [auth A],
TA [auth C],
TB [auth E],
U [auth A],
UA [auth C],
UB [auth E],
V [auth A],
VA [auth C],
VB [auth E],
VC [auth H],
VD [auth J],
VE [auth L],
W [auth A],
WA [auth C],
WB [auth E],
WC [auth H],
WD [auth J],
WE [auth L],
X [auth A],
XA [auth C],
XB [auth E],
XC [auth H],
XD [auth J],
XE [auth L],
Y [auth A],
YA [auth C],
YB [auth E],
YC [auth H],
YD [auth J],
YE [auth L],
ZA [auth C],
ZB [auth E],
ZC [auth H],
ZD [auth J],
ZE [auth L]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BU3
Query on BU3

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CA [auth B]
DA [auth B]
DB [auth D]
DC [auth F]
EA [auth B]
CA [auth B],
DA [auth B],
DB [auth D],
DC [auth F],
EA [auth B],
EB [auth D],
EC [auth F],
FC [auth F],
FD [auth I],
FE [auth K],
FF [auth G],
GD [auth I],
GE [auth K],
GF [auth G],
O [auth A],
P [auth A],
QA [auth C],
QB [auth E],
RA [auth C],
RB [auth E],
RC [auth H],
SC [auth H],
SD [auth J],
SE [auth L],
TC [auth H],
TD [auth J],
TE [auth L]
(R,R)-2,3-BUTANEDIOL
C4 H10 O2
OWBTYPJTUOEWEK-QWWZWVQMSA-N
SO2
Query on SO2

Download Ideal Coordinates CCD File 
CB [auth D],
ED [auth I],
QF [auth G],
Z [auth A]
SULFUR DIOXIDE
O2 S
RAHZWNYVWXNFOC-UHFFFAOYSA-N
CU1
Query on CU1

Download Ideal Coordinates CCD File 
AA [auth B]
BB [auth D]
BC [auth F]
DD [auth I]
DE [auth K]
AA [auth B],
BB [auth D],
BC [auth F],
DD [auth I],
DE [auth K],
DF [auth G],
M [auth A],
OA [auth C],
OB [auth E],
PC [auth H],
QD [auth J],
QE [auth L]
COPPER (I) ION
Cu
VMQMZMRVKUZKQL-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
FA [auth B]
FB [auth D]
GC [auth F]
HD [auth I]
HE [auth K]
FA [auth B],
FB [auth D],
GC [auth F],
HD [auth I],
HE [auth K],
HF [auth G],
Q [auth A],
SA [auth C],
SB [auth E],
UC [auth H],
UD [auth J],
UE [auth L]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
SX
Query on SX

Download Ideal Coordinates CCD File 
BA [auth B]
CC [auth F]
EE [auth K]
EF [auth G]
N [auth A]
BA [auth B],
CC [auth F],
EE [auth K],
EF [auth G],
N [auth A],
PA [auth C],
PB [auth E],
QC [auth H],
RD [auth J],
RE [auth L]
SULFUR OXIDE
O S
XTQHKBHJIVJGKJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 211.121α = 90
b = 103.042β = 98.46
c = 233.07γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
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
  • Version 1.4: 2024-02-28
    Changes: Data collection, Database references, Derived calculations