4YLF: Insights Into Flavin-based Electron Bifurcation Via The Nadh-dependent Reduced Ferredoxin-nadp Oxidoreductase Structure

Citation:
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.
PDB ID: 4YLFDownload
MMDB ID: 130715
PDB Deposition Date: 2015/3/5
Updated in MMDB: 2015/09
Experimental Method:
x-ray diffraction
Resolution: 2.3  Å
Source Organism:
Similar Structures:
Biological Unit for 4YLF: dimeric; determined by author and by software (PISA)
Molecular Components in 4YLF
Label Count Molecule
Proteins (2 molecules)
1
Dihydroorotate Dehydrogenase B (Nad(+)), Electron Transfer Subunit Homolog(Gene symbol: TM1639)
Molecule annotation
1
Dihydropyrimidine Dehydrogenase Subunit a
Molecule annotation
Chemicals (6 molecules)
1
1
2
2
3
2
4
1
* Click molecule labels to explore molecular sequence information.

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