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| | <StructureSection load='5ayv' size='340' side='right'caption='[[5ayv]], [[Resolution|resolution]] 1.65Å' scene=''> | | <StructureSection load='5ayv' size='340' side='right'caption='[[5ayv]], [[Resolution|resolution]] 1.65Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5ayv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_kodakaraensis_(strain_kod1) Pyrococcus kodakaraensis (strain kod1)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AYV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AYV FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5ayv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis_KOD1 Thermococcus kodakarensis KOD1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AYV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AYV FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=KPL:KETOPANTOATE'>KPL</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</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]] 1.647Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TK1968 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=69014 Pyrococcus kodakaraensis (strain KOD1)])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=KPL:KETOPANTOATE'>KPL</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-dehydropantoate_2-reductase 2-dehydropantoate 2-reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.169 1.1.1.169] </span></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=5ayv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ayv OCA], [https://pdbe.org/5ayv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ayv RCSB], [https://www.ebi.ac.uk/pdbsum/5ayv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ayv 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=5ayv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ayv OCA], [http://pdbe.org/5ayv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ayv RCSB], [http://www.ebi.ac.uk/pdbsum/5ayv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ayv ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/Q5JGC2_THEKO Q5JGC2_THEKO]] Catalyzes the NADPH-dependent reduction of ketopantoate into pantoic acid.[RuleBase:RU362068] | + | [https://www.uniprot.org/uniprot/PANE_THEKO PANE_THEKO] Catalyzes the NAD(P)H-dependent reduction of ketopantoate into pantoic acid. Prefers NADH rather than NADPH as the electron donor.<ref>PMID:23941541</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: 2-dehydropantoate 2-reductase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Aikawa, Y]] | + | [[Category: Thermococcus kodakarensis KOD1]] |
| - | [[Category: Miki, K]] | + | [[Category: Aikawa Y]] |
| - | [[Category: Nishitani, Y]]
| + | [[Category: Miki K]] |
| - | [[Category: Coenzyme some]] | + | [[Category: Nishitani Y]] |
| - | [[Category: Feedback inhibition]] | + | |
| - | [[Category: Ketopantoate reductase]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
5ayv is a 2 chain structure with sequence from Thermococcus kodakarensis KOD1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.647Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
PANE_THEKO Catalyzes the NAD(P)H-dependent reduction of ketopantoate into pantoic acid. Prefers NADH rather than NADPH as the electron donor.[1]
Publication Abstract from PubMed
Coenzyme A (CoA) plays essential roles in a variety of metabolic pathways in all three domains of life. The biosynthesis pathway of CoA is strictly regulated by feedback inhibition. In bacteria and eukaryotes, pantothenate kinase is the target of feedback inhibition by CoA. Recent biochemical studies have identified ketopantoate reductase (KPR), which catalyzes the NAD(P)H-dependent reduction of 2-oxopantoate to pantoate, as a target of the feedback inhibition by CoA in archaea. However the mechanism for recognition of CoA by KPR is still unknown. Here we report the crystal structure of KPR from Thermococcus kodakarensis in complex with CoA and 2-oxopantoate. CoA occupies the binding site of NAD(P)H, explaining the competitive inhibition by CoA. Our structure reveals a disulfide bond between CoA and Cys84 that indicates an irreversible inhibition upon binding of CoA. The structure also suggests the cooperative binding of CoA and 2-oxopantoate that triggers a conformational closure and seems to facilitate the disulfide bond formation. Our findings provide novel insights into the mechanism that regulates biosynthesis of CoA in archaea. This article is protected by copyright. All rights reserved.
Crystal structure of archaeal ketopantoate reductase complexed with coenzyme A and 2-oxopantoate provides structural insights into feedback regulation.,Aikawa Y, Nishitani Y, Tomita H, Atomi H, Miki K Proteins. 2016 Jan 12. doi: 10.1002/prot.24984. PMID:26757028[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Tomita H, Imanaka T, Atomi H. Identification and characterization of an archaeal ketopantoate reductase and its involvement in regulation of coenzyme A biosynthesis. Mol Microbiol. 2013 Oct;90(2):307-21. PMID:23941541 doi:10.1111/mmi.12363
- ↑ Aikawa Y, Nishitani Y, Tomita H, Atomi H, Miki K. Crystal structure of archaeal ketopantoate reductase complexed with coenzyme A and 2-oxopantoate provides structural insights into feedback regulation. Proteins. 2016 Jan 12. doi: 10.1002/prot.24984. PMID:26757028 doi:http://dx.doi.org/10.1002/prot.24984
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