1pgp

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(New page: 200px<br /><applet load="1pgp" size="450" color="white" frame="true" align="right" spinBox="true" caption="1pgp, resolution 2.5&Aring;" /> '''CRYSTALLOGRAPHIC STUD...)
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[[Image:1pgp.jpg|left|200px]]<br /><applet load="1pgp" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1pgp, resolution 2.5&Aring;" />
 
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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'''<br />
 
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==Overview==
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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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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.
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<StructureSection load='1pgp' size='340' side='right'caption='[[1pgp]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1pgp]] 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=1PGP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PGP FirstGlance]. <br>
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</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>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6PG:6-PHOSPHOGLUCONIC+ACID'>6PG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1pgp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pgp OCA], [https://pdbe.org/1pgp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pgp RCSB], [https://www.ebi.ac.uk/pdbsum/1pgp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pgp ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pg/1pgp_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1pgp ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1PGP is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Ovis_aries Ovis aries] with 6PG and SO4 as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1PGP OCA].
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*[[6-phosphogluconate dehydrogenase 3D structures|6-phosphogluconate dehydrogenase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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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., Adams MJ, Ellis GH, Gover S, Naylor CE, Phillips C, Structure. 1994 Jul 15;2(7):651-68. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7922042 7922042]
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[[Category: Large Structures]]
[[Category: Ovis aries]]
[[Category: Ovis aries]]
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[[Category: Phosphogluconate dehydrogenase (decarboxylating)]]
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[[Category: Adams MJ]]
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[[Category: Single protein]]
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[[Category: Gover S]]
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[[Category: Adams, M.J.]]
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[[Category: Naylor CE]]
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[[Category: Gover, S.]]
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[[Category: Phillips C]]
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[[Category: Naylor, C.E.]]
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[[Category: Phillips, C.]]
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[[Category: 6PG]]
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[[Category: SO4]]
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[[Category: oxidoreductase (choh(d)-nadp+(a))]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 23:47:27 2007''
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Current revision

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

PDB ID 1pgp

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