8OH5

Cryo-EM structure of the electron bifurcating transhydrogenase StnABC complex from Sporomusa Ovata (state 2)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular architecture and electron transfer pathway of the Stn family transhydrogenase.

Kumar, A.Kremp, F.Roth, J.Freibert, S.A.Muller, V.Schuller, J.M.

(2023) Nat Commun 14: 5484-5484

  • DOI: https://doi.org/10.1038/s41467-023-41212-x
  • Primary Citation of Related Structures:  
    8OH5, 8OH9

  • PubMed Abstract: 

    The challenge of endergonic reduction of NADP + using NADH is overcome by ferredoxin-dependent transhydrogenases that employ electron bifurcation for electron carrier adjustments in the ancient Wood-Ljungdahl pathway. Recently, an electron-bifurcating transhydrogenase with subunit compositions distinct from the well-characterized Nfn-type transhydrogenase was described: the Stn complex. Here, we present the single-particle cryo-EM structure of the Stn family transhydrogenase from the acetogenic bacterium Sporomusa ovata and functionally dissect its electron transfer pathway. Stn forms a tetramer consisting of functional heterotrimeric StnABC complexes. Our findings demonstrate that the StnAB subunits assume the structural and functional role of a bifurcating module, homologous to the HydBC core of the electron-bifurcating HydABC complex. Moreover, StnC contains a NuoG-like domain and a GltD-like NADPH binding domain that resembles the NfnB subunit of the NfnAB complex. However, in contrast to NfnB, StnC lost the ability to bifurcate electrons. Structural comparison allows us to describe how the same fold on one hand evolved bifurcation activity on its own while on the other hand combined with an associated bifurcating module, exemplifying modular evolution in anaerobic metabolism to produce activities critical for survival at the thermodynamic limit of life.


  • Organizational Affiliation

    SYNMIKRO Research Center and Department of Chemistry, Philipps-University of Marburg, Marburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD-dependent formate dehydrogenase gamma subunit
A, D, G, J
178Sporomusa ovata DSM 2662Mutation(s): 0 
UniProt
Find proteins for A0A0U1KYW8 (Sporomusa ovata)
Explore A0A0U1KYW8 
Go to UniProtKB:  A0A0U1KYW8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0U1KYW8
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NAD-reducing hydrogenase subunit HoxF
B, E, H, K
584Sporomusa ovata DSM 2662Mutation(s): 0 
UniProt
Find proteins for A0A0U1KYM9 (Sporomusa ovata)
Explore A0A0U1KYM9 
Go to UniProtKB:  A0A0U1KYM9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0U1KYM9
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Formate dehydrogenase-O, major subunit
C, F, I, L
1,172Sporomusa ovata DSM 2662Mutation(s): 0 
UniProt
Find proteins for A0A0U1KYI6 (Sporomusa ovata)
Explore A0A0U1KYI6 
Go to UniProtKB:  A0A0U1KYI6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0U1KYI6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
CB [auth I],
LA [auth F],
TB [auth L],
U [auth C]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
NDP (Subject of Investigation/LOI)
Query on NDP

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EB [auth I],
NA [auth F],
VB [auth L],
W [auth C]
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
NAD (Subject of Investigation/LOI)
Query on NAD

Download Ideal Coordinates CCD File 
AB [auth H],
JA [auth E],
RB [auth K],
S [auth B]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
FMN (Subject of Investigation/LOI)
Query on FMN

Download Ideal Coordinates CCD File 
GA [auth E],
OB [auth K],
P [auth B],
XA [auth H]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
AA [auth C]
AC [auth L]
BA [auth C]
BB [auth H]
DB [auth I]
AA [auth C],
AC [auth L],
BA [auth C],
BB [auth H],
DB [auth I],
FB [auth I],
GB [auth I],
HA [auth E],
HB [auth I],
IA [auth E],
IB [auth I],
JB [auth I],
KA [auth E],
MA [auth F],
OA [auth F],
PA [auth F],
PB [auth K],
Q [auth B],
QA [auth F],
QB [auth K],
R [auth B],
RA [auth F],
SA [auth F],
SB [auth K],
T [auth B],
UB [auth L],
V [auth C],
WB [auth L],
X [auth C],
XB [auth L],
Y [auth C],
YA [auth H],
YB [auth L],
Z [auth C],
ZA [auth H],
ZB [auth L]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES (Subject of Investigation/LOI)
Query on FES

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BC [auth L]
CA [auth C]
DA [auth D]
FA [auth E]
KB [auth I]
BC [auth L],
CA [auth C],
DA [auth D],
FA [auth E],
KB [auth I],
LB [auth J],
M [auth A],
NB [auth K],
O [auth B],
TA [auth F],
UA [auth G],
WA [auth H]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
EA [auth E],
MB [auth K],
N [auth B],
VA [auth H]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union101075992
German Research Foundation (DFG)GermanySCHU 3364/1-1

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-13
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Database references