5XMJ

Crystal structure of quinol:fumarate reductase from Desulfovibrio gigas


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.236 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history


Literature

Structural insights into the electron/proton transfer pathways in the quinol:fumarate reductase from Desulfovibrio gigas.

Guan, H.H.Hsieh, Y.C.Lin, P.J.Huang, Y.C.Yoshimura, M.Chen, L.Y.Chen, S.K.Chuankhayan, P.Lin, C.C.Chen, N.C.Nakagawa, A.Chan, S.I.Chen, C.J.

(2018) Sci Rep 8: 14935-14935

  • DOI: https://doi.org/10.1038/s41598-018-33193-5
  • Primary Citation of Related Structures:  
    5XMJ

  • PubMed Abstract: 

    The membrane-embedded quinol:fumarate reductase (QFR) in anaerobic bacteria catalyzes the reduction of fumarate to succinate by quinol in the anaerobic respiratory chain. The electron/proton-transfer pathways in QFRs remain controversial. Here we report the crystal structure of QFR from the anaerobic sulphate-reducing bacterium Desulfovibrio gigas (D. gigas) at 3.6 Å resolution. The structure of the D. gigas QFR is a homo-dimer, each protomer comprising two hydrophilic subunits, A and B, and one transmembrane subunit C, together with six redox cofactors including two b-hemes. One menaquinone molecule is bound near heme b L in the hydrophobic subunit C. This location of the menaquinone-binding site differs from the menaquinol-binding cavity proposed previously for QFR from Wolinella succinogenes. The observed bound menaquinone might serve as an additional redox cofactor to mediate the proton-coupled electron transport across the membrane. Armed with these structural insights, we propose electron/proton-transfer pathways in the quinol reduction of fumarate to succinate in the D. gigas QFR.


  • Organizational Affiliation

    Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
fumarate reductase flavoprotein subunitA,
D [auth E],
G [auth I],
J [auth M]
627Megalodesulfovibrio gigasMutation(s): 0 
EC: 1.3.5.1
Membrane Entity: Yes 
UniProt
Find proteins for T2GB49 (Megalodesulfovibrio gigas (strain ATCC 19364 / DSM 1382 / NCIMB 9332 / VKM B-1759))
Explore T2GB49 
Go to UniProtKB:  T2GB49
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupT2GB49
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Succinate dehydrogenase iron-sulfur subunitB,
E [auth F],
H [auth J],
K [auth N]
264Megalodesulfovibrio gigas DSM 1382 = ATCC 19364Mutation(s): 0 
EC: 1.3.5.1
UniProt
Find proteins for T2G9X8 (Megalodesulfovibrio gigas (strain ATCC 19364 / DSM 1382 / NCIMB 9332 / VKM B-1759))
Explore T2G9X8 
Go to UniProtKB:  T2G9X8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupT2G9X8
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
fumarate reductase respiratory complexC,
F [auth G],
I [auth K],
L [auth O]
218Megalodesulfovibrio gigasMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for T2GAT5 (Megalodesulfovibrio gigas (strain ATCC 19364 / DSM 1382 / NCIMB 9332 / VKM B-1759))
Explore T2GAT5 
Go to UniProtKB:  T2GAT5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupT2GAT5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
CA [auth I],
JA [auth M],
M [auth A],
V [auth E]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
MQ7
Query on MQ7

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U [auth C]MENAQUINONE-7
C46 H64 O2
RAKQPZMEYJZGPI-LJWNYQGCSA-N
HEM
Query on HEM

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AA [auth G]
BA [auth G]
HA [auth K]
IA [auth K]
PA [auth O]
AA [auth G],
BA [auth G],
HA [auth K],
IA [auth K],
PA [auth O],
QA [auth O],
R [auth C],
S [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
LMT
Query on LMT

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OA [auth O],
T [auth C]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
SF4
Query on SF4

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FA [auth J],
MA [auth N],
P [auth B],
Y [auth F]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S
Query on F3S

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EA [auth J],
LA [auth N],
O [auth B],
X [auth F]
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
FES
Query on FES

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GA [auth J],
NA [auth N],
Q [auth B],
Z [auth F]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
FUM
Query on FUM

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DA [auth I],
KA [auth M],
N [auth A],
W [auth E]
FUMARIC ACID
C4 H4 O4
VZCYOOQTPOCHFL-OWOJBTEDSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.236 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.136α = 90
b = 131.772β = 94.22
c = 195.428γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science CouncilTaiwan105-2311-B-231-001-MY3

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-06
    Type: Initial release
  • Version 1.1: 2018-12-19
    Changes: Data collection, Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description
  • Version 2.1: 2023-11-22
    Changes: Refinement description