5jca: Difference between revisions

Latest revision as of 12:23, 13 August 2026

NADP(H) bound NADH-dependent Ferredoxin:NADP Oxidoreductase (NfnI) from Pyrococcus furiosus

Structural highlights

5jca is a 2 chain structure with sequence from Pyrococcus furiosus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.5Å
Ligands:	FAD, FES, GOL, MG, NDP
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SUDHA_PYRFU A bifunctional enzyme that catalyzes the reduction of elemental sulfur or polysulfide to hydrogen sulfide with NADPH as electron donor. Also functions as a reduced ferredoxin:NADP oxidoreductase with a very high affinity for reduced ferredoxin. Exhibits a broad specificity for various physiological and non-physiological substrates with varied reduction potentials such as methyl viologen, benzyl viologen, FAD, FMN, methylene blue, 2,6-dichlorophenolindophenol (DCIP), cytochrome C and ferricyanide with highest preference for benzyl viologen. Does not reduce fumarate, succinate, nitrate, nitrite, sulfate, sulfite or protons. Does not possess any hydrogenase activity or NADPH-dependent glutamate synthase activity.^[1] ^[2] [REFERENCE:4]

Publication Abstract from PubMed

The recently realized biochemical phenomenon of energy conservation through electron bifurcation provides biology with an elegant means to maximize utilization of metabolic energy. The mechanism of coordinated coupling of exergonic and endergonic oxidation-reduction reactions by a single enzyme complex has been elucidated through optical and paramagnetic spectroscopic studies revealing unprecedented features. Pairs of electrons are bifurcated over more than 1 volt of electrochemical potential by generating a low-potential, highly energetic, unstable flavin semiquinone and directing electron flow to an iron-sulfur cluster with a highly negative potential to overcome the barrier of the endergonic half reaction. The unprecedented range of thermodynamic driving force that is generated by flavin-based electron bifurcation accounts for unique chemical reactions that are catalyzed by these enzymes.

Mechanistic insights into energy conservation by flavin-based electron bifurcation.,Lubner CE, Jennings DP, Mulder DW, Schut GJ, Zadvornyy OA, Hoben JP, Tokmina-Lukaszewska M, Berry L, Nguyen DM, Lipscomb GL, Bothner B, Jones AK, Miller AF, King PW, Adams MWW, Peters JW Nat Chem Biol. 2017 Apr 10. doi: 10.1038/nchembio.2348. PMID:28394885^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Hagen WR, Silva PJ, Amorim MA, Hagedoorn PL, Wassink H, Haaker H, Robb FT. Novel structure and redox chemistry of the prosthetic groups of the iron-sulfur flavoprotein sulfide dehydrogenase from Pyrococcus furiosus; evidence for a [2Fe-2S] cluster with Asp(Cys)3 ligands. J Biol Inorg Chem. 2000 Aug;5(4):527-34. PMID:10968624
↑ Ma K, Adams MW. Sulfide dehydrogenase from the hyperthermophilic archaeon Pyrococcus furiosus: a new multifunctional enzyme involved in the reduction of elemental sulfur. J Bacteriol. 1994 Nov;176(21):6509-17. PMID:7961401
↑ Lubner CE, Jennings DP, Mulder DW, Schut GJ, Zadvornyy OA, Hoben JP, Tokmina-Lukaszewska M, Berry L, Nguyen DM, Lipscomb GL, Bothner B, Jones AK, Miller AF, King PW, Adams MWW, Peters JW. Mechanistic insights into energy conservation by flavin-based electron bifurcation. Nat Chem Biol. 2017 Apr 10. doi: 10.1038/nchembio.2348. PMID:28394885 doi:https://dx.doi.org/10.1038/nchembio.2348

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Hagen WR, Silva PJ, Amorim MA, Hagedoorn PL, Wassink H, Haaker H, Robb FT. Novel structure and redox chemistry of the prosthetic groups of the iron-sulfur flavoprotein sulfide dehydrogenase from Pyrococcus furiosus; evidence for a [2Fe-2S] cluster with Asp(Cys)3 ligands. J Biol Inorg Chem. 2000 Aug;5(4):527-34. PMID:10968624

[2] Ma K, Adams MW. Sulfide dehydrogenase from the hyperthermophilic archaeon Pyrococcus furiosus: a new multifunctional enzyme involved in the reduction of elemental sulfur. J Bacteriol. 1994 Nov;176(21):6509-17. PMID:7961401

[3] Lubner CE, Jennings DP, Mulder DW, Schut GJ, Zadvornyy OA, Hoben JP, Tokmina-Lukaszewska M, Berry L, Nguyen DM, Lipscomb GL, Bothner B, Jones AK, Miller AF, King PW, Adams MWW, Peters JW. Mechanistic insights into energy conservation by flavin-based electron bifurcation. Nat Chem Biol. 2017 Apr 10. doi: 10.1038/nchembio.2348. PMID:28394885 doi:https://dx.doi.org/10.1038/nchembio.2348

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[2]

[3]

@@ Line 5: / Line 5: @@
 <table><tr><td colspan='2'>[[5jca]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JCA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JCA FirstGlance]. <br>
 </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5&#8491;</td></tr>
-<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></td></tr>
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5jca FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jca OCA], [https://pdbe.org/5jca PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jca RCSB], [https://www.ebi.ac.uk/pdbsum/5jca PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jca ProSAT]</span></td></tr>
 </table>

5jca: Difference between revisions

Latest revision as of 12:23, 13 August 2026

NADP(H) bound NADH-dependent Ferredoxin:NADP Oxidoreductase (NfnI) from Pyrococcus furiosus

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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