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| | ==Crystal structure of AMP phosphorylase C-terminal deletion mutant in complex with substrates== | | ==Crystal structure of AMP phosphorylase C-terminal deletion mutant in complex with substrates== |
| - | <StructureSection load='4ga6' size='340' side='right' caption='[[4ga6]], [[Resolution|resolution]] 2.21Å' scene=''> | + | <StructureSection load='4ga6' size='340' side='right'caption='[[4ga6]], [[Resolution|resolution]] 2.21Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4ga6]] 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=4GA6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GA6 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4ga6]] 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=4GA6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GA6 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ga4|4ga4]], [[4ga5|4ga5]]</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=4ga6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ga6 OCA], [https://pdbe.org/4ga6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ga6 RCSB], [https://www.ebi.ac.uk/pdbsum/4ga6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ga6 ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">deoA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=69014 Pyrococcus kodakaraensis (strain KOD1)])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thymidine_phosphorylase Thymidine phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.4 2.4.2.4] </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=4ga6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ga6 OCA], [http://pdbe.org/4ga6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ga6 RCSB], [http://www.ebi.ac.uk/pdbsum/4ga6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ga6 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/AMPPA_THEKO AMPPA_THEKO] Catalyzes the conversion of AMP and phosphate to adenine and ribose 1,5-bisphosphate (R15P). Exhibits phosphorylase activity toward CMP, dCMP and UMP in addition to AMP. Functions in an archaeal AMP degradation pathway, together with R15P isomerase and RubisCO.<ref>PMID:17303759</ref> <ref>PMID:23065974</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: Thymidine phosphorylase]] | + | [[Category: Large Structures]] |
| - | [[Category: Aono, R]] | + | [[Category: Thermococcus kodakarensis KOD1]] |
| - | [[Category: Atomi, H]] | + | [[Category: Aono R]] |
| - | [[Category: Imanaka, T]] | + | [[Category: Atomi H]] |
| - | [[Category: Miki, K]] | + | [[Category: Imanaka T]] |
| - | [[Category: Nakamura, A]] | + | [[Category: Miki K]] |
| - | [[Category: Nishitani, Y]] | + | [[Category: Nakamura A]] |
| - | [[Category: Sato, T]] | + | [[Category: Nishitani Y]] |
| - | [[Category: Phosphorolysis]]
| + | [[Category: Sato T]] |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
AMPPA_THEKO Catalyzes the conversion of AMP and phosphate to adenine and ribose 1,5-bisphosphate (R15P). Exhibits phosphorylase activity toward CMP, dCMP and UMP in addition to AMP. Functions in an archaeal AMP degradation pathway, together with R15P isomerase and RubisCO.[1] [2]
Publication Abstract from PubMed
AMP phosphorylase (AMPpase) catalyzes the initial reaction in a novel AMP metabolic pathway recently found in archaea, converting AMP and phosphate into adenine and ribose 1,5-bisphosphate. Gel-filtration chromatography revealed that AMPpase from Thermococcus kodakarensis (Tk-AMPpase) forms an exceptionally large macromolecular structure (>40-mers) in solution. To investigate its unique multimerization feature, we determined the first crystal structures of Tk-AMPpase, in the apo-form and in complex with substrates. Structures of two truncated forms of Tk-AMPpase (Tk-AMPpaseDeltaN84 and Tk-AMPpaseDeltaC10) clarified that this multimerization is achieved by two dimer interfaces within a single molecule: one by the central domain and the other by the C-terminal domain, which consists of an unexpected domain-swapping interaction. The N-terminal domain, characteristic of archaeal enzymes, is essential for enzymatic activity, participating in multimerization as well as domain closure of the active site upon substrate binding. Moreover, biochemical analysis demonstrated that the macromolecular assembly of Tk-AMPpase contributes to its high thermostability, essential for an enzyme from a hyperthermophile. Our findings unveil a unique archaeal nucleotide phosphorylase that is distinct in both function and structure from previously known members of the nucleoside phosphorylase II family.
Structure analysis of archaeal AMP phosphorylase reveals two unique modes of dimerization.,Nishitani Y, Aono R, Nakamura A, Sato T, Atomi H, Imanaka T, Miki K J Mol Biol. 2013 Aug 9;425(15):2709-21. doi: 10.1016/j.jmb.2013.04.026. Epub 2013, May 7. PMID:23659790[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Sato T, Atomi H, Imanaka T. Archaeal type III RuBisCOs function in a pathway for AMP metabolism. Science. 2007 Feb 16;315(5814):1003-6. PMID:17303759 doi:http://dx.doi.org/10.1126/science.1135999
- ↑ Aono R, Sato T, Yano A, Yoshida S, Nishitani Y, Miki K, Imanaka T, Atomi H. Enzymatic characterization of AMP phosphorylase and ribose-1,5-bisphosphate isomerase functioning in an archaeal AMP metabolic pathway. J Bacteriol. 2012 Dec;194(24):6847-55. doi: 10.1128/JB.01335-12. Epub 2012 Oct, 12. PMID:23065974 doi:http://dx.doi.org/10.1128/JB.01335-12
- ↑ Nishitani Y, Aono R, Nakamura A, Sato T, Atomi H, Imanaka T, Miki K. Structure analysis of archaeal AMP phosphorylase reveals two unique modes of dimerization. J Mol Biol. 2013 Aug 9;425(15):2709-21. doi: 10.1016/j.jmb.2013.04.026. Epub 2013, May 7. PMID:23659790 doi:http://dx.doi.org/10.1016/j.jmb.2013.04.026
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