5l1n: Difference between revisions
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The | ==Pyrococcus horikoshii CoA Disulfide Reductase Quadruple Mutant== | ||
<StructureSection load='5l1n' size='340' side='right'caption='[[5l1n]], [[Resolution|resolution]] 3.60Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5l1n]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5L1N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5L1N 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]] 3.6Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</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=5l1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l1n OCA], [https://pdbe.org/5l1n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5l1n RCSB], [https://www.ebi.ac.uk/pdbsum/5l1n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5l1n ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/NCPPR_PYRHO NCPPR_PYRHO] Catalyzes the NAD(P)H-dependent reduction of polysulfide, CoA-polysulfides, and CoA persulfide, as well as the reduction of a range of other small persulfides, including TNB and glutathione persulfides. The likely in vivo substrates are di-, poly-, and persulfide derivatives of coenzyme A, although polysulfide itself is also efficiently reduced (PubMed:23530771). Shows coenzyme A disulfide reductase (CoADR) activity with both NADH and NADPH, with a preference for NADPH (PubMed:15720393). May also play a role in the reduction of elemental sulfur (PubMed:23530771).<ref>PMID:15720393</ref> <ref>PMID:23530771</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Within the family of pyridine nucleotide disulfide oxidoreductase (PNDOR), enzymes are a group of single-cysteine containing FAD-dependent reductases that utilize a tightly bound coenzyme A to assist in the NAD(P)H-dependent reduction of di-, per-, and polysulfide substrates in bacteria and archaea. For many of these homodimeric enzymes, it has proved difficult to determine the substrate specificity and metabolic function based on sequence and genome analysis alone. Coenzyme A-disulfide reductase (CoADR) isolated from Pyrococcus horikoshii (phCoADR) reduces Co-A per- and polysulfides, but, unlike other highly homologous members of this group, is a poor CoA disulfide reductase. The phCoADR structure has a narrower access channel for CoA substrates, which suggested that this restriction might be responsible for the enzyme's poor activity toward the bulky CoA disulfide substrate. To test this hypothesis, the substrate channel was widened by making four mutations along the channel wall (Y65A, Y66A, P67G, and H367G). The structure of the quadruple mutant shows a widened substrate channel, which is supported by a fourfold increase in kcat for the NAD(P)H-dependent reduction of CoA disulfide and enhanced activity toward the substrate at lower temperatures. Anaerobic titrations of the enzyme with NADH revealed a half-site reactivity not observed with the wild-type enzyme in which one subunit of the enzyme could be fully reduced to an EH4 state, while the other remained in an EH2 or EH2.NADH state. These results suggest that for these closely related enzymes, substrate channel morphology is an important determinant of substrate specificity, and homology modeling will be the preferred technique for predicting function among PNDORs. | |||
A broader active site in Pyrococcus horikoshii CoA disulfide reductase accommodates larger substrates and reveals evidence of subunit asymmetry.,Sea K, Lee J, To D, Chen B, Sazinsky MH, Crane EJ 3rd FEBS Open Bio. 2018 Jun 9;8(7):1083-1092. doi: 10.1002/2211-5463.12439., eCollection 2018 Jul. PMID:29988575<ref>PMID:29988575</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 5l1n" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Coenzyme A-Disulfide Reductase|Coenzyme A-Disulfide Reductase]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Pyrococcus horikoshii OT3]] | |||
[[Category: Chen B]] | |||
[[Category: Crane III EJ]] | |||
[[Category: Sazinsky MH]] | |||
[[Category: Sea K]] | |||
Latest revision as of 15:47, 4 October 2023
Pyrococcus horikoshii CoA Disulfide Reductase Quadruple MutantPyrococcus horikoshii CoA Disulfide Reductase Quadruple Mutant
Structural highlights
FunctionNCPPR_PYRHO Catalyzes the NAD(P)H-dependent reduction of polysulfide, CoA-polysulfides, and CoA persulfide, as well as the reduction of a range of other small persulfides, including TNB and glutathione persulfides. The likely in vivo substrates are di-, poly-, and persulfide derivatives of coenzyme A, although polysulfide itself is also efficiently reduced (PubMed:23530771). Shows coenzyme A disulfide reductase (CoADR) activity with both NADH and NADPH, with a preference for NADPH (PubMed:15720393). May also play a role in the reduction of elemental sulfur (PubMed:23530771).[1] [2] Publication Abstract from PubMedWithin the family of pyridine nucleotide disulfide oxidoreductase (PNDOR), enzymes are a group of single-cysteine containing FAD-dependent reductases that utilize a tightly bound coenzyme A to assist in the NAD(P)H-dependent reduction of di-, per-, and polysulfide substrates in bacteria and archaea. For many of these homodimeric enzymes, it has proved difficult to determine the substrate specificity and metabolic function based on sequence and genome analysis alone. Coenzyme A-disulfide reductase (CoADR) isolated from Pyrococcus horikoshii (phCoADR) reduces Co-A per- and polysulfides, but, unlike other highly homologous members of this group, is a poor CoA disulfide reductase. The phCoADR structure has a narrower access channel for CoA substrates, which suggested that this restriction might be responsible for the enzyme's poor activity toward the bulky CoA disulfide substrate. To test this hypothesis, the substrate channel was widened by making four mutations along the channel wall (Y65A, Y66A, P67G, and H367G). The structure of the quadruple mutant shows a widened substrate channel, which is supported by a fourfold increase in kcat for the NAD(P)H-dependent reduction of CoA disulfide and enhanced activity toward the substrate at lower temperatures. Anaerobic titrations of the enzyme with NADH revealed a half-site reactivity not observed with the wild-type enzyme in which one subunit of the enzyme could be fully reduced to an EH4 state, while the other remained in an EH2 or EH2.NADH state. These results suggest that for these closely related enzymes, substrate channel morphology is an important determinant of substrate specificity, and homology modeling will be the preferred technique for predicting function among PNDORs. A broader active site in Pyrococcus horikoshii CoA disulfide reductase accommodates larger substrates and reveals evidence of subunit asymmetry.,Sea K, Lee J, To D, Chen B, Sazinsky MH, Crane EJ 3rd FEBS Open Bio. 2018 Jun 9;8(7):1083-1092. doi: 10.1002/2211-5463.12439., eCollection 2018 Jul. PMID:29988575[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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