4yry: Difference between revisions

Revision as of 08:28, 3 May 2023

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

Structural highlights

4yry is a 4 chain structure with sequence from Thermotoga maritima. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	FAD, FES, NAD, PO4, SF4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PYRKH_THEMA

Publication Abstract from PubMed

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 E. 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) and 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 centre of the NfnAB complex and the site of electron bifurcation. Arg187 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 radical/FAD pair required for ferredoxin reduction. A mechanism of FAD-coupled electron bifurcation by NfnAB is proposed.

Insights into Flavin-based Electron Bifurcation via the NADH- dependent Reduced Ferredoxin: NADP oxidoreductase Structure.,Demmer JK, Huang H, Wang S, Demmer U, Thauer RK, Ermler U J Biol Chem. 2015 Jul 2. pii: jbc.M115.656520. PMID:26139605^[1]

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

References

↑ Demmer JK, Huang H, Wang S, Demmer U, Thauer RK, Ermler U. Insights into Flavin-based Electron Bifurcation via the NADH- dependent Reduced Ferredoxin: NADP oxidoreductase Structure. J Biol Chem. 2015 Jul 2. pii: jbc.M115.656520. PMID:26139605 doi:https://dx.doi.org/10.1074/jbc.M115.656520

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Demmer JK, Huang H, Wang S, Demmer U, Thauer RK, Ermler U. Insights into Flavin-based Electron Bifurcation via the NADH- dependent Reduced Ferredoxin: NADP oxidoreductase Structure. J Biol Chem. 2015 Jul 2. pii: jbc.M115.656520. PMID:26139605 doi:https://dx.doi.org/10.1074/jbc.M115.656520

[1]

@@ Line 1: / Line 1: @@
 ==Insights into flavin-based electron bifurcation via the NADH-dependent reduced ferredoxin-NADP oxidoreductase structure==
-<StructureSection load='4yry' size='340' side='right' caption='[[4yry]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+<StructureSection load='4yry' size='340' side='right'caption='[[4yry]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4yry]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43589 Atcc 43589]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YRY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YRY FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4yry]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YRY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YRY FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
+</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=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TM_1639 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 ATCC 43589]), THEMA_06045 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 ATCC 43589])</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=4yry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yry OCA], [https://pdbe.org/4yry PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yry RCSB], [https://www.ebi.ac.uk/pdbsum/4yry PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yry ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4yry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yry OCA], [http://pdbe.org/4yry PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yry RCSB], [http://www.ebi.ac.uk/pdbsum/4yry PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4yry ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/PYRKH_THEMA PYRKH_THEMA]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 17: / Line 18: @@
 </div>
 <div class="pdbe-citations 4yry" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Dihydroorotate dehydrogenase 3D structures|Dihydroorotate dehydrogenase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Atcc 43589]]
+[[Category: Large Structures]]
-[[Category: Demmer, J K]]
+[[Category: Thermotoga maritima]]
-[[Category: Demmer, U]]
+[[Category: Demmer JK]]
-[[Category: Ermler, U]]
+[[Category: Demmer U]]
-[[Category: Huang, H]]
+[[Category: Ermler U]]
-[[Category: Thauer, R K]]
+[[Category: Huang H]]
-[[Category: Wang, S]]
+[[Category: Thauer RK]]
-[[Category: Oxidoreductase]]
+[[Category: Wang S]]

4yry: Difference between revisions

Revision as of 08:28, 3 May 2023

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

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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