8OH5

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

• PDB DOI:  https://doi.org/10.2210/pdb8OH5/pdb
• EM Map EMD-16878: EMDB EMDataResource

• Classification: ELECTRON TRANSPORT
• Organism(s): Sporomusa ovata DSM 2662
• Mutation(s): No 


• Deposited: 2023-03-20 Released: 2023-09-13 
• Deposition Author(s): Kumar, A., Kremp, F., Mueller, V., Schuller, J.M.
• Funding Organization(s): European Research Council (ERC), German Research Foundation (DFG)

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Experimental Data Snapshot

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

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

• PubMed: 37673911 
• 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.

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Organizational Affiliation: 

SYNMIKRO Research Center and Department of Chemistry, Philipps-University of Marburg, Marburg, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Hetero 12-mer - A4B4C4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 861.76 kDa 
• Atom Count: 58,624 
• Modelled Residue Count: 7,624 
• Deposited Residue Count: 7,736 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent formate dehydrogenase gamma subunit	A, D, G, J	178	Sporomusa ovata DSM 2662	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-reducing hydrogenase subunit HoxF	B, E, H, K	584	Sporomusa ovata DSM 2662	Mutation(s): 0  EC: 1.12.1.2

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Formate dehydrogenase-O, major subunit	C, F, I, L	1,172	Sporomusa ovata DSM 2662	Mutation(s): 0  EC: 1.2.1.2

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD (Subject of Investigation/LOI)	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)	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)	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)	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)	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-VKOJMFJBAC
FES (Subject of Investigation/LOI)	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)	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

Entry History & Funding Information

Deposition Data

• Released Date: 2023-09-13 
Deposition Author(s): Kumar, A., Kremp, F., Mueller, V., Schuller, J.M.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	101075992
German Research Foundation (DFG)	Germany	SCHU 3364/1-1

Revision History  

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