4RKM | pdb_00004rkm

Wolinella succinogenes octaheme sulfite reductase MccA, form I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.220 (Depositor), 0.191 (DCC) 
  • R-Value Work: 
    0.184 (Depositor) 
  • R-Value Observed: 
    0.185 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4RKM

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 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.

Macromolecule Content 

  • Total Structure Weight: 1,048.88 kDa 
  • Atom Count: 70,014 
  • Modeled Residue Count: 7,909 
  • Deposited Residue Count: 8,784 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MccA732Wolinella succinogenes DSM 1740Mutation(s): 0 
Gene Names: mccAWS0379
EC: 1.8.99
UniProt
Find proteins for Q7MSJ8 (Wolinella succinogenes (strain ATCC 29543 / DSM 1740 / CCUG 13145 / JCM 31913 / 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



Download:Ideal Coordinates CCD File
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 (Depositor), 0.191 (DCC) 
  • R-Value Work:  0.184 (Depositor) 
  • R-Value Observed: 0.185 (Depositor) 
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