6qkr: Difference between revisions

Revision as of 12:02, 24 January 2024

2-Naphthoyl-CoA Reductase-2-Naphthoyl-CoA complex(NCR-NCoA-soaked complex)

Structural highlights

6qkr is a 2 chain structure with sequence from Bacterium enrichment culture clone N47. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.2Å
Ligands:	FAD, FMN, J5H, SF4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

E1YD54_9DELT

Publication Abstract from PubMed

Hydride transfers play a crucial role in a multitude of biological redox reactions and are mediated by flavin, deazaflavin or nicotinamide adenine dinucleotide cofactors at standard redox potentials ranging from 0 to -340 mV. 2-Naphthoyl-CoA reductase, a key enzyme of oxygen-independent bacterial naphthalene degradation, uses a low-potential one-electron donor for the two-electron dearomatization of its substrate below the redox limit of known biological hydride transfer processes at E degrees ' = -493 mV. Here we demonstrate by X-ray structural analyses, QM/MM computational studies, and multiple spectroscopy/activity based titrations that highly cooperative electron transfer (n = 3) from a low-potential one-electron (FAD) to a two-electron (FMN) transferring flavin cofactor is the key to overcome the resonance stabilized aromatic system by hydride transfer in a highly hydrophobic pocket. The results evidence how the protein environment inversely functionalizes two flavins to switch from low-potential one-electron to hydride transfer at the thermodynamic limit of flavin redox chemistry.

Low potential enzymatic hydride transfer via highly cooperative and inversely functionalized flavin cofactors.,Willistein M, Bechtel DF, Muller CS, Demmer U, Heimann L, Kayastha K, Schunemann V, Pierik AJ, Ullmann GM, Ermler U, Boll M Nat Commun. 2019 May 6;10(1):2074. doi: 10.1038/s41467-019-10078-3. PMID:31061390^[1]

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

References

↑ Willistein M, Bechtel DF, Muller CS, Demmer U, Heimann L, Kayastha K, Schunemann V, Pierik AJ, Ullmann GM, Ermler U, Boll M. Low potential enzymatic hydride transfer via highly cooperative and inversely functionalized flavin cofactors. Nat Commun. 2019 May 6;10(1):2074. doi: 10.1038/s41467-019-10078-3. PMID:31061390 doi:https://dx.doi.org/10.1038/s41467-019-10078-3

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OCA

[1] Willistein M, Bechtel DF, Muller CS, Demmer U, Heimann L, Kayastha K, Schunemann V, Pierik AJ, Ullmann GM, Ermler U, Boll M. Low potential enzymatic hydride transfer via highly cooperative and inversely functionalized flavin cofactors. Nat Commun. 2019 May 6;10(1):2074. doi: 10.1038/s41467-019-10078-3. PMID:31061390 doi:https://dx.doi.org/10.1038/s41467-019-10078-3

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='6qkr' size='340' side='right'caption='[[6qkr]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6qkr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacterium_enrichment_culture_clone_n47 Bacterium enrichment culture clone n47]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QKR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6QKR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6qkr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacterium_enrichment_culture_clone_N47 Bacterium enrichment culture clone N47]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QKR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6QKR 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=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=J5H:~{S}-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl]+naphthalene-2-carbothioate'>J5H</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</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=6qkr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qkr OCA], [http://pdbe.org/6qkr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qkr RCSB], [http://www.ebi.ac.uk/pdbsum/6qkr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qkr ProSAT]</span></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=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=J5H:~{S}-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl]+naphthalene-2-carbothioate'>J5H</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=6qkr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qkr OCA], [https://pdbe.org/6qkr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6qkr RCSB], [https://www.ebi.ac.uk/pdbsum/6qkr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6qkr ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/E1YD54_9DELT E1YD54_9DELT]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Bacterium enrichment culture clone n47]]
+[[Category: Bacterium enrichment culture clone N47]]
 [[Category: Large Structures]]
-[[Category: Ermler, U]]
+[[Category: Ermler U]]
-[[Category: Kayastha, K]]
+[[Category: Kayastha K]]
-[[Category: 2-naphthoyl-coa]]
-[[Category: 2-naphthoyl-coa reductase]]
-[[Category: 4fe-4]]
-[[Category: Fad]]
-[[Category: Flavoprotein]]
-[[Category: Fmn]]
-[[Category: Hydride transfer]]
-[[Category: Monomer]]
-[[Category: Naphthalene]]
-[[Category: Reductase]]

6qkr: Difference between revisions

Revision as of 12:02, 24 January 2024

2-Naphthoyl-CoA Reductase-2-Naphthoyl-CoA complex(NCR-NCoA-soaked complex)

Structural highlights

Function

Publication Abstract from PubMed

References

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