4YLF | pdb_00004ylf

Insights into flavin-based electron bifurcation via the NADH-dependent reduced ferredoxin-NADP oxidoreductase structure

PDB DOI: https://doi.org/10.2210/pdb4YLF/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermotoga maritima MSB8
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-03-05 Released: 2015-07-08
Deposition Author(s): Ermler, U., Thauer, R.K., Demmer, J.K., Huang, H., Wang, S., Demmer, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.219 (Depositor), 0.229 (DCC)
R-Value Work:
0.187 (Depositor)
R-Value Observed:
0.191 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Insights into Flavin-based Electron Bifurcation via the NADH-dependent Reduced Ferredoxin:NADP Oxidoreductase Structure.

Demmer, J.K., Huang, H., Wang, S., Demmer, U., Thauer, R.K., Ermler, U.

(2015) J Biological Chem 290: 21985-21995

PubMed: 26139605 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1074/jbc.M115.656520
Primary Citation Related Structures:
4YLF, 4YRY

PubMed Abstract:
NADH-dependent reduced ferredoxin:NADP oxidoreductase (NfnAB) is found in the cytoplasm of various anaerobic bacteria and archaea. The enzyme reversibly catalyzes the endergonic reduction of ferredoxin with NADPH driven by the exergonic transhydrogenation from NADPH onto NAD(+). Coupling is most probably accomplished via the mechanism of flavin-based electron bifurcation. To understand this process on a structural basis, we heterologously produced the NfnAB complex of Thermotoga maritima in Escherichia coli, provided kinetic evidence for its bifurcating behavior, and determined its x-ray structure in the absence and presence of NADH. The structure of NfnAB reveals an electron transfer route including the FAD (a-FAD), the [2Fe-2S] cluster of NfnA and the FAD (b-FAD), and the two [4Fe-4S] clusters of NfnB. Ferredoxin is presumably docked onto NfnB close to the [4Fe-4S] cluster distal to b-FAD. NAD(H) binds to a-FAD and NADP(H) consequently to b-FAD, which is positioned in the center of the NfnAB complex and the site of electron bifurcation. Arg(187) is hydrogen-bonded to N5 and O4 of the bifurcating b-FAD and might play a key role in adjusting a low redox potential of the FADH(•)/FAD pair required for ferredoxin reduction. A mechanism of FAD-coupled electron bifurcation by NfnAB is proposed.

Organizational Affiliation

From the Max-Planck-Institut für Biophysik, D-60438 Frankfurt am Main, Germany and the Max-Planck-Institut für Terrestrische Mikrobiologie, D-35043 Marburg, Germany.

Macromolecule Content

Total Structure Weight: 169.57 kDa
Atom Count: 11,843
Modeled Residue Count: 1,475
Deposited Residue Count: 1,488
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit homolog	A, C	276	Thermotoga maritima MSB8	Mutation(s): 0 Gene Names: TM_1639
UniProt
Find proteins for Q9X1X4 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X1X4 Go to UniProtKB: Q9X1X4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9X1X4
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydropyrimidine dehydrogenase subunit A	B, D	468	Thermotoga maritima MSB8	Mutation(s): 0 Gene Names: THEMA_06045
UniProt
Find proteins for Q9X1X5 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X1X5 Go to UniProtKB: Q9X1X5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9X1X5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain O [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain O [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain O [auth D]	F [auth A], I [auth B], K [auth C], O [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain O [auth D]
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain M [auth D] SDF format, chain N [auth D] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D]	G [auth B], H [auth B], M [auth D], N [auth D]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain H [auth B] Focus chain M [auth D] Focus chain N [auth D] Interactions & Density Focus chain G [auth B] Focus chain H [auth B] Focus chain M [auth D] Focus chain N [auth D]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth C] MOL2 format, chain E [auth A] MOL2 format, chain L [auth C] mmCIF format, chain E [auth A] mmCIF format, chain L [auth C]	E [auth A], L [auth C]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth C] Interactions & Density Focus chain E [auth A] Focus chain L [auth C]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain P [auth D] MOL2 format, chain J [auth B] MOL2 format, chain P [auth D] mmCIF format, chain J [auth B] mmCIF format, chain P [auth D]	J [auth B], P [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain J [auth B] Focus chain P [auth D] Interactions & Density Focus chain J [auth B] Focus chain P [auth D]