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1pgo

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CRYSTALLOGRAPHIC STUDY OF COENZYME, COENZYME ANALOGUE AND SUBSTRATE BINDING IN 6-PHOSPHOGLUCONATE DEHYDROGENASE: IMPLICATIONS FOR NADP SPECIFICITY AND THE ENZYME MECHANISM

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Retrieved from "http://52.214.119.220/wiki/index.php/1pgo"

Categories: Large Structures | Ovis aries | Adams MJ | Gover S | Phillips C

@@ Line 1: / Line 1: @@
-[[Image:1pgo.jpg|left|200px]]
- {{Structure
+==CRYSTALLOGRAPHIC STUDY OF COENZYME, COENZYME ANALOGUE AND SUBSTRATE BINDING IN 6-PHOSPHOGLUCONATE DEHYDROGENASE: IMPLICATIONS FOR NADP SPECIFICITY AND THE ENZYME MECHANISM==
-|PDB= 1pgo |SIZE=350|CAPTION= <scene name='initialview01'>1pgo</scene>, resolution 2.5&Aring;
+<StructureSection load='1pgo' size='340' side='right'caption='[[1pgo]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
+<table><tr><td colspan='2'>[[1pgo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ovis_aries Ovis aries]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PGO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PGO FirstGlance]. <br>
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphogluconate_dehydrogenase_(decarboxylating) Phosphogluconate dehydrogenase (decarboxylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.44 1.1.1.44] </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]] 2.5&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</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=1pgo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pgo OCA], [https://pdbe.org/1pgo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pgo RCSB], [https://www.ebi.ac.uk/pdbsum/1pgo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pgo ProSAT]</span></td></tr>
-|RELATEDENTRY=
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1pgo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pgo OCA], [http://www.ebi.ac.uk/pdbsum/1pgo PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1pgo RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/6PGD_SHEEP 6PGD_SHEEP] Catalyzes the oxidative decarboxylation of 6-phosphogluconate to ribulose 5-phosphate and CO(2), with concomitant reduction of NADP to NADPH.
+== 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/pg/1pgo_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=1pgo ConSurf].
+<div style="clear:both"></div>
-'''CRYSTALLOGRAPHIC STUDY OF COENZYME, COENZYME ANALOGUE AND SUBSTRATE BINDING IN 6-PHOSPHOGLUCONATE DEHYDROGENASE: IMPLICATIONS FOR NADP SPECIFICITY AND THE ENZYME MECHANISM'''
+==See Also==
+*[[6-phosphogluconate dehydrogenase|6-phosphogluconate dehydrogenase]]
+*[[6-phosphogluconate dehydrogenase 3D structures|6-phosphogluconate dehydrogenase 3D structures]]
-==Overview==
+__TOC__
-BACKGROUND: The nicotinamide adenine dinucleotide phosphate (NADP)-dependent oxidative decarboxylase, 6-phosphogluconate dehydrogenase, is a major source of reduced coenzyme for synthesis. Enzymes later in the pentose phosphate pathway convert the reaction product, ribulose 5-phosphate, to ribose 5-phosphate. Crystallographic study of complexes with coenzyme and substrate explain the NADP dependence which determines the enzyme's metabolic role and support the proposed general base-general acid mechanism. RESULTS: The refined structures of binary coenzyme/analogue complexes show that Arg33 is ordered by binding the 2'-phosphate, and provides one face of the adenine site. The nicotinamide, while less tightly bound, is more extended when reduced than when oxidized. All substrate binding residues are conserved; the 3-hydroxyl of 6-phosphogluconate is hydrogen bonded to N zeta of Lys183 and the 3-hydrogen points towards the oxidized nicotinamide. The 6-phosphate replaces a tightly bound sulphate in the apo-enzyme. CONCLUSIONS: NADP specificity is achieved primarily by Arg33 which binds the 2'-phosphate but, in its absence, obscures the adenine pocket. The bound oxidized nicotinamide is syn; hydride transfer from bound substrate to the nicotinamide si- face is achieved with a small movement of the nicotinamide nucleotide. Lys183 may act as general base. A water bound to Gly130 in the coenzyme domain is the most likely acid required in decarboxylation. The dihydronicotinamide ring of NADPH competes for ligands with the 1-carboxyl of 6-phosphogluconate.
+</StructureSection>
+[[Category: Large Structures]]
-==About this Structure==
-PGO is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Ovis_aries Ovis aries]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PGO OCA].
-==Reference==
-Crystallographic study of coenzyme, coenzyme analogue and substrate binding in 6-phosphogluconate dehydrogenase: implications for NADP specificity and the enzyme mechanism., Adams MJ, Ellis GH, Gover S, Naylor CE, Phillips C, Structure. 1994 Jul 15;2(7):651-68. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/7922042 7922042]
 [[Category: Ovis aries]]
-[[Category: Phosphogluconate dehydrogenase (decarboxylating)]]
+[[Category: Adams MJ]]
-[[Category: Single protein]]
+[[Category: Gover S]]
-[[Category: Adams, M J.]]
+[[Category: Phillips C]]
-[[Category: Gover, S.]]
-[[Category: Phillips, C.]]
-[[Category: oxidoreductase (choh(d)-nadp+(a))]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:59:27 2008''

1pgo

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CRYSTALLOGRAPHIC STUDY OF COENZYME, COENZYME ANALOGUE AND SUBSTRATE BINDING IN 6-PHOSPHOGLUCONATE DEHYDROGENASE: IMPLICATIONS FOR NADP SPECIFICITY AND THE ENZYME MECHANISM

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Evolutionary Conservation

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