3c2v: Difference between revisions

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-[[Image:3c2v.jpg|left|200px]]
- {{Structure
+==Crystal structure of the quinolinate phosphoribosyl transferase (BNA6) from Saccharomyces cerevisiae complexed with PRPP and the inhibitor phthalate==
-|PDB= 3c2v |SIZE=350|CAPTION= <scene name='initialview01'>3c2v</scene>, resolution 2.290&Aring;
+<StructureSection load='3c2v' size='340' side='right'caption='[[3c2v]], [[Resolution|resolution]] 2.29&Aring;' scene=''>
-|SITE= <scene name='pdbsite=AC1:Prp+Binding+Site+For+Residue+A+300'>AC1</scene> and <scene name='pdbsite=AC2:Pht+Binding+Site+For+Residue+A+301'>AC2</scene>
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=PHT:PHTHALIC+ACID'>PHT</scene>, <scene name='pdbligand=PRP:ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC+ACID'>PRP</scene>
+<table><tr><td colspan='2'>[[3c2v]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C2V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C2V FirstGlance]. <br>
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Nicotinate-nucleotide_diphosphorylase_(carboxylating) Nicotinate-nucleotide diphosphorylase (carboxylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.19 2.4.2.19] </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]] 2.29&#8491;</td></tr>
-|GENE= BNA6, QPT1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PHT:PHTHALIC+ACID'>PHT</scene>, <scene name='pdbligand=PRP:ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC+ACID'>PRP</scene></td></tr>
-|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cd01572 QPRTase], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=COG0157 NadC]</span>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3c2v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c2v OCA], [https://pdbe.org/3c2v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c2v RCSB], [https://www.ebi.ac.uk/pdbsum/3c2v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c2v ProSAT]</span></td></tr>
-|RELATEDENTRY=[[3c2r|3C2R]], [[3c2o|3C2O]], [[3c2f|3C2F]], [[3c2e|3C2E]], [[3c2d|3C2D]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3c2v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c2v OCA], [http://www.ebi.ac.uk/pdbsum/3c2v PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=3c2v RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/NADC_YEAST NADC_YEAST] Involved in the catabolism of quinolinic acid (QA) (By similarity).
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c2/3c2v_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=3c2v ConSurf].
+<div style="clear:both"></div>
-'''Crystal structure of the quinolinate phosphoribosyl transferase (BNA6) from Saccharomyces cerevisiae complexed with PRPP and the inhibitor phthalate'''
+==See Also==
+*[[Phosphoribosyltransferase 3D structures|Phosphoribosyltransferase 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-Quinolinic acid phosphoribosyl transferase (QAPRTase, EC 2.4.2.19) is a 32 kDa enzyme encoded by the BNA6 gene in yeast and catalyzes the formation of nicotinate mononucleotide from quinolinate and 5-phosphoribosyl-1-pyrophosphate (PRPP). QAPRTase plays a key role in the tryptophan degradation pathway via kynurenine, leading to the de novo biosynthesis of NAD (+) and clearing the neurotoxin quinolinate. To improve our understanding of the specificity of the eukaryotic enzyme and the course of events associated with catalysis, we have determined the crystal structures of the apo and singly bound forms with the substrates quinolinate and PRPP. This reveals that the enzyme folds in a manner similar to that of various prokaryotic forms which are approximately 30% identical in sequence. In addition, the structure of the Michaelis complex is approximated by PRPP and the quinolinate analogue phthalate bound to the active site. These results allow insight into the kinetic mechanism of QAPRTase and provide an understanding of structural diversity in the active site of the Saccharomyces cerevisiae enzyme when compared to prokaryotic homologues.
+[[Category: Large Structures]]
-==About this Structure==
-C2V is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C2V OCA].
-==Reference==
-Comprehensive X-ray Structural Studies of the Quinolinate Phosphoribosyl Transferase (BNA6) from Saccharomyces cerevisiae., di Luccio E, Wilson DK, Biochemistry. 2008 Apr 1;47(13):4039-50. Epub 2008 Mar 6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18321072 18321072]
-[[Category: Nicotinate-nucleotide diphosphorylase (carboxylating)]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Single protein]]
+[[Category: Wilson DK]]
-[[Category: Luccio, E di.]]
+[[Category: Di Luccio E]]
-[[Category: Wilson, D K.]]
-[[Category: bna6]]
-[[Category: cytoplasm]]
-[[Category: glycosyltransferase]]
-[[Category: mechanism]]
-[[Category: nucleus]]
-[[Category: phthalate]]
-[[Category: prpp]]
-[[Category: prtase]]
-[[Category: pyridine nucleotide biosynthesis]]
-[[Category: qprtase]]
-[[Category: quinolinate]]
-[[Category: transferase]]
-[[Category: x-ray structure]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr  2 11:59:54 2008''