9BOV | pdb_00009bov

Structure of electron bifurcating Nfn-ABC complexed with NAD from Caldicellulosiruptor saccharolyticus

PDB DOI: https://doi.org/10.2210/pdb9BOV/pdb
EM Map EMD-44751: EMDB EMDataResource

Classification: OXIDOREDUCTASE
Organism(s): Caldicellulosiruptor saccharolyticus
Expression System: Caldicellulosiruptor
Mutation(s): No

Deposited: 2024-05-06 Released: 2025-03-05
Deposition Author(s): Li, H., Li, H.
Funding Organization(s): Department of Energy (DOE, United States)

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 1.0 of the entry. See complete history.

Literature

Cryo-EM reveals a composite flavobicluster electron bifurcation site in the Bfu family member NfnABC.

Li, H., Schut, G.J., Feng, X., Adams, M.W.W., Li, H.

(2025) Commun Biol 8: 239-239

PubMed: 39953182 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s42003-025-07706-8
Primary Citation Related Structures:
9BOV, 9BP5

PubMed Abstract:
The BfuABC family is a diverse group of electron bifurcating enzymes that play key roles in anaerobic microbial metabolism. Previous studies have focused almost exclusively on the BfuABC-type hydrogenases but the mechanism and site of electron bifurcation remain unknown. Herein we focus on the Caldicellulosiruptor saccharolyticus (Csac) NfnABC-type Bfu enzyme that catalyzes the oxidation of NADPH and simultaneous reduction of NAD and the redox protein ferredoxin (Fd). Cryo-EM structures determined with and without NAD and Fd reveal seven FeS clusters and one FAD in NfnA, one FeS cluster in NfnC, and three FeS clusters, two Zn ions, and one FMN in NfnB. The Zn ions take the place of FeS clusters previously proposed in other Bfu family members. Csac Nfn for the first time defines the minimum bifurcation site as a flavobicluster consisting of FMN, a [4Fe-4S] (B1) cluster and a [2Fe-2S] (C1) cluster. Binding of NAD to the FMN triggers a series of conformational changes, crucial to the bifurcation of two electron pairs derived from NADPH by the [B1-FMN-C1] flavobicluster into low and high potential electrons that reduce Fd and NAD, respectively. The structures lay the foundation for investigations of the proposed reaction cycle common to all Bfu enzymes.

Organizational Affiliation

Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.

Macromolecule Content

Total Structure Weight: 872.33 kDa
Atom Count: 55,356
Modeled Residue Count: 7,088
Deposited Residue Count: 7,752
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Molybdopterin oxidoreductase	A, D, G [auth J], J [auth G]	1,178	Caldicellulosiruptor saccharolyticus	Mutation(s): 0 Gene Names: Csac_0621
UniProt
Find proteins for A4XH60 (Caldicellulosiruptor saccharolyticus (strain ATCC 43494 / DSM 8903 / Tp8T 6331)) Explore A4XH60 Go to UniProtKB: A4XH60
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A4XH60
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase (Quinone)	B, E, H [auth K], K [auth H]	584	Caldicellulosiruptor saccharolyticus	Mutation(s): 0 Gene Names: Csac_0620 EC: 1.6.99.5
UniProt
Find proteins for A4XH59 (Caldicellulosiruptor saccharolyticus (strain ATCC 43494 / DSM 8903 / Tp8T 6331)) Explore A4XH59 Go to UniProtKB: A4XH59
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A4XH59
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase (Ubiquinone), 24 kDa subunit	C, F, I [auth L], L [auth I]	176	Caldicellulosiruptor saccharolyticus	Mutation(s): 0 Gene Names: Csac_0619
UniProt
Find proteins for A4XH58 (Caldicellulosiruptor saccharolyticus (strain ATCC 43494 / DSM 8903 / Tp8T 6331)) Explore A4XH58 Go to UniProtKB: A4XH58
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A4XH58
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download:Ideal Coordinates CCD File SDF format, chain DB [auth G] SDF format, chain FA [auth D] SDF format, chain RA [auth J] SDF format, chain T [auth A] MOL2 format, chain DB [auth G] MOL2 format, chain FA [auth D] MOL2 format, chain RA [auth J] MOL2 format, chain T [auth A] mmCIF format, chain DB [auth G] mmCIF format, chain FA [auth D] mmCIF format, chain RA [auth J] mmCIF format, chain T [auth A]	DB [auth G], FA [auth D], RA [auth J], T [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain DB [auth G] Focus chain FA [auth D] Focus chain RA [auth J] Focus chain T [auth A] Interactions & Density Focus chain DB [auth G] Focus chain FA [auth D] Focus chain RA [auth J] Focus chain T [auth A]
NAD (Subject of Investigation/LOI) Query on NAD Download:Ideal Coordinates CCD File SDF format, chain HB [auth H] SDF format, chain JA [auth E] SDF format, chain VA [auth K] SDF format, chain X [auth B] MOL2 format, chain HB [auth H] MOL2 format, chain JA [auth E] MOL2 format, chain VA [auth K] MOL2 format, chain X [auth B] mmCIF format, chain HB [auth H] mmCIF format, chain JA [auth E] mmCIF format, chain VA [auth K] mmCIF format, chain X [auth B]	HB [auth H], JA [auth E], VA [auth K], X [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain HB [auth H] Focus chain JA [auth E] Focus chain VA [auth K] Focus chain X [auth B] Interactions & Density Focus chain HB [auth H] Focus chain JA [auth E] Focus chain VA [auth K] Focus chain X [auth B]
FMN (Subject of Investigation/LOI) Query on FMN Download:Ideal Coordinates CCD File SDF format, chain EB [auth H] SDF format, chain GA [auth E] SDF format, chain SA [auth K] SDF format, chain U [auth B] MOL2 format, chain EB [auth H] MOL2 format, chain GA [auth E] MOL2 format, chain SA [auth K] MOL2 format, chain U [auth B] mmCIF format, chain EB [auth H] mmCIF format, chain GA [auth E] mmCIF format, chain SA [auth K] mmCIF format, chain U [auth B]	EB [auth H], GA [auth E], SA [auth K], U [auth B]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain EB [auth H] Focus chain GA [auth E] Focus chain SA [auth K] Focus chain U [auth B] Interactions & Density Focus chain EB [auth H] Focus chain GA [auth E] Focus chain SA [auth K] Focus chain U [auth B]
SF4 (Subject of Investigation/LOI) Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain AB [auth G] SDF format, chain BA [auth D] SDF format, chain BB [auth G] SDF format, chain CA [auth D] SDF format, chain CB [auth G] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain FB [auth H] SDF format, chain HA [auth E] SDF format, chain LA [auth J] SDF format, chain MA [auth J] SDF format, chain N [auth A] SDF format, chain NA [auth J] SDF format, chain O [auth A] SDF format, chain OA [auth J] SDF format, chain P [auth A] SDF format, chain PA [auth J] SDF format, chain QA [auth J] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain TA [auth K] SDF format, chain V [auth B] SDF format, chain XA [auth G] SDF format, chain YA [auth G] SDF format, chain Z [auth D] SDF format, chain ZA [auth G] SDF format, chain Q [auth A] MOL2 format, chain AA [auth D] MOL2 format, chain AB [auth G] MOL2 format, chain BA [auth D] MOL2 format, chain BB [auth G] MOL2 format, chain CA [auth D] MOL2 format, chain CB [auth G] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain FB [auth H] MOL2 format, chain HA [auth E] MOL2 format, chain LA [auth J] MOL2 format, chain MA [auth J] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth J] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth J] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth J] MOL2 format, chain QA [auth J] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain TA [auth K] MOL2 format, chain V [auth B] MOL2 format, chain XA [auth G] MOL2 format, chain YA [auth G] MOL2 format, chain Z [auth D] MOL2 format, chain ZA [auth G] MOL2 format, chain Q [auth A] mmCIF format, chain AA [auth D] mmCIF format, chain AB [auth G] mmCIF format, chain BA [auth D] mmCIF format, chain BB [auth G] mmCIF format, chain CA [auth D] mmCIF format, chain CB [auth G] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain FB [auth H] mmCIF format, chain HA [auth E] mmCIF format, chain LA [auth J] mmCIF format, chain MA [auth J] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth J] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth J] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth J] mmCIF format, chain QA [auth J] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain TA [auth K] mmCIF format, chain V [auth B] mmCIF format, chain XA [auth G] mmCIF format, chain YA [auth G] mmCIF format, chain Z [auth D] mmCIF format, chain ZA [auth G] mmCIF format, chain Q [auth A]	AA [auth D] AB [auth G] BA [auth D] BB [auth G] CA [auth D] AA [auth D], AB [auth G], BA [auth D], BB [auth G], CA [auth D], CB [auth G], DA [auth D], EA [auth D], FB [auth H], HA [auth E], LA [auth J], MA [auth J], N [auth A], NA [auth J], O [auth A], OA [auth J], P [auth A], PA [auth J], Q [auth A], QA [auth J], R [auth A], S [auth A], TA [auth K], V [auth B], XA [auth G], YA [auth G], Z [auth D], ZA [auth G]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain AB [auth G] Focus chain BA [auth D] Focus chain BB [auth G] Focus chain CA [auth D] Focus chain CB [auth G] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FB [auth H] Focus chain HA [auth E] Focus chain LA [auth J] Focus chain MA [auth J] Focus chain N [auth A] Focus chain NA [auth J] Focus chain O [auth A] Focus chain OA [auth J] Focus chain P [auth A] Focus chain PA [auth J] Focus chain Q [auth A] Focus chain QA [auth J] Focus chain R [auth A] Focus chain S [auth A] Focus chain TA [auth K] Focus chain V [auth B] Focus chain XA [auth G] Focus chain YA [auth G] Focus chain Z [auth D] Focus chain ZA [auth G] Interactions & Density Focus chain AA [auth D] Focus chain AB [auth G] Focus chain BA [auth D] Focus chain BB [auth G] Focus chain CA [auth D] Focus chain CB [auth G] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FB [auth H] Focus chain HA [auth E] Focus chain LA [auth J] Focus chain MA [auth J] Focus chain N [auth A] Focus chain NA [auth J] Focus chain O [auth A] Focus chain OA [auth J] Focus chain P [auth A] Focus chain PA [auth J] Focus chain Q [auth A] Focus chain QA [auth J] Focus chain R [auth A] Focus chain S [auth A] Focus chain TA [auth K] Focus chain V [auth B] Focus chain XA [auth G] Focus chain YA [auth G] Focus chain Z [auth D] Focus chain ZA [auth G]
FES (Subject of Investigation/LOI) Query on FES Download:Ideal Coordinates CCD File SDF format, chain KA [auth J] SDF format, chain M [auth A] SDF format, chain WA [auth G] SDF format, chain Y [auth D] MOL2 format, chain KA [auth J] MOL2 format, chain M [auth A] MOL2 format, chain WA [auth G] MOL2 format, chain Y [auth D] mmCIF format, chain KA [auth J] mmCIF format, chain M [auth A] mmCIF format, chain WA [auth G] mmCIF format, chain Y [auth D]	KA [auth J], M [auth A], WA [auth G], Y [auth D]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain KA [auth J] Focus chain M [auth A] Focus chain WA [auth G] Focus chain Y [auth D] Interactions & Density Focus chain KA [auth J] Focus chain M [auth A] Focus chain WA [auth G] Focus chain Y [auth D]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain GB [auth H] SDF format, chain IA [auth E] SDF format, chain UA [auth K] SDF format, chain W [auth B] MOL2 format, chain GB [auth H] MOL2 format, chain IA [auth E] MOL2 format, chain UA [auth K] MOL2 format, chain W [auth B] mmCIF format, chain GB [auth H] mmCIF format, chain IA [auth E] mmCIF format, chain UA [auth K] mmCIF format, chain W [auth B]	GB [auth H], IA [auth E], UA [auth K], W [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain GB [auth H] Focus chain IA [auth E] Focus chain UA [auth K] Focus chain W [auth B] Interactions & Density Focus chain GB [auth H] Focus chain IA [auth E] Focus chain UA [auth K] Focus chain W [auth B]