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| - | [[Image:1ibs.jpg|left|200px]] | |
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| - | {{Structure
| + | ==PHOSPHORIBOSYLDIPHOSPHATE SYNTHETASE IN COMPLEX WITH CADMIUM IONS== |
| - | |PDB= 1ibs |SIZE=350|CAPTION= <scene name='initialview01'>1ibs</scene>, resolution 2.8Å
| + | <StructureSection load='1ibs' size='340' side='right'caption='[[1ibs]], [[Resolution|resolution]] 2.80Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=ABM:METHYL+PHOSPHONIC+ACID+ADENOSINE+ESTER'>ABM</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> | + | <table><tr><td colspan='2'>[[1ibs]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IBS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IBS FirstGlance]. <br> |
| - | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribose-phosphate_diphosphokinase Ribose-phosphate diphosphokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.6.1 2.7.6.1] </span>
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8Å</td></tr> |
| - | |GENE= PRS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ABM:METHYL+PHOSPHONIC+ACID+ADENOSINE+ESTER'>ABM</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | |DOMAIN=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ibs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ibs OCA], [https://pdbe.org/1ibs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ibs RCSB], [https://www.ebi.ac.uk/pdbsum/1ibs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ibs ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=[[1dkr|1DKR]], [[1dku|1DKU]]
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ibs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ibs OCA], [http://www.ebi.ac.uk/pdbsum/1ibs PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ibs RCSB]</span>
| + | == Function == |
| - | }}
| + | [https://www.uniprot.org/uniprot/KPRS_BACSU KPRS_BACSU] |
| - | | + | == Evolutionary Conservation == |
| - | '''PHOSPHORIBOSYLDIPHOSPHATE SYNTHETASE IN COMPLEX WITH CADMIUM IONS'''
| + | [[Image:Consurf_key_small.gif|200px|right]] |
| - | | + | Check<jmol> |
| - | | + | <jmolCheckbox> |
| - | ==Overview== | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ib/1ibs_consurf.spt"</scriptWhenChecked> |
| - | The binding sites for the two cations essential for the catalytic function of 5-phospho-D-ribosyl alpha-1-diphosphate (PRPP) synthases have been identified from the structure of the Bacillus subtilis phosphoribosyldiphosphate synthetase (PRPPsase) with bound Cd(2+). The structure determined from X-ray diffraction data to 2.8-A resolution reveals the same hexameric arrangement of the subunits that was observed in the complexes of the enzyme with the activator sulfate and the allosteric inhibitor ADP. Two cation binding sites were localized in each of the two domains of the subunits that compose the hexamer; each domain of the subunit has an associated cation. In addition to the bound Cd(2+), the Cd(2+)-PRPPsase structure contains a sulfate ion in the regulatory site, a sulfate ion at the ribose-5-phosphate binding site, and an AMP moiety at the ATP binding site. Comparison of the Cd(2+)-PRPPsase to the structures of the PRPPsase complexed with sulfate and mADP reveals the structural rearrangement induced by the binding of the free cation, which is essential for the initiation of the reaction. The comparison to the cPRPP complex of glutamine phosphoribosylpyrophosphate amidotransferase from Escherichia coli, a type I phosphoribosyltransferase, provided information about the binding of PRPP. This strongly indicates that the binding of both substrates must lead to a stabilized conformation of the loop region, which remains unresolved in the known PRPPsase complex structures.
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| - | | + | <text>to colour the structure by Evolutionary Conservation</text> |
| - | ==About this Structure== | + | </jmolCheckbox> |
| - | 1IBS is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IBS OCA].
| + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1ibs ConSurf]. |
| - | | + | <div style="clear:both"></div> |
| - | ==Reference== | + | __TOC__ |
| - | Binding of cations in Bacillus subtilis phosphoribosyldiphosphate synthetase and their role in catalysis., Eriksen TA, Kadziola A, Larsen S, Protein Sci. 2002 Feb;11(2):271-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11790837 11790837]
| + | </StructureSection> |
| | [[Category: Bacillus subtilis]] | | [[Category: Bacillus subtilis]] |
| - | [[Category: Ribose-phosphate diphosphokinase]] | + | [[Category: Large Structures]] |
| - | [[Category: Single protein]]
| + | [[Category: Eriksen TA]] |
| - | [[Category: Eriksen, T A.]] | + | [[Category: Kadziola A]] |
| - | [[Category: Kadziola, A.]] | + | [[Category: Larsen S]] |
| - | [[Category: Larsen, S.]] | + | |
| - | [[Category: domain duplication]]
| + | |
| - | [[Category: open alpha beta structure]]
| + | |
| - | [[Category: phosphoribosyltransferase type i fold]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:17:31 2008''
| + | |
