1kv8

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(New page: 200px<br /><applet load="1kv8" size="450" color="white" frame="true" align="right" spinBox="true" caption="1kv8, resolution 1.62&Aring;" /> '''Crystal Structure of...)
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[[Image:1kv8.jpg|left|200px]]<br /><applet load="1kv8" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1kv8, resolution 1.62&Aring;" />
 
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'''Crystal Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase'''<br />
 
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==Overview==
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==Crystal Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase==
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The 3-keto-L-gulonate 6-phosphate decarboxylase (KGPDC) encoded by the, ulaD gene in the Escherichia coli genome [Yew, W. S., and Gerlt, J. A., (2002) J. Bacteriol. 184, 302-306] and orotidine 5'-monophosphate, decarboxylase (OMPDC) are homologous (derived from a common ancestor) but, catalyze different reactions. The metal-independent decarboxylation, reaction catalyzed by OMPDC avoids the formation of a vinyl anion, intermediate; the Mg2+-dependent decarboxylation reaction catalyzed by, KGPDC involves the formation of an enediolate anion intermediate. Based on, the available structures of OMPDC, a sequence alignment allows the, predictions that (1) KGPDC is a dimer of (beta/alpha)8-barrels, with the, active sites located at the dimer interface; (2) KGPDC and OMPDC share an, aspartate residue at the end of the first beta-strand and an, Asp-x-Lys-x-x-Asp motif at the end of the third beta-strand with OMPDC;, but (3) KGPDC has a Glu instead of a Lys at the end of the second, beta-strand. The structure of KGPDC has been determined in the presence of, Mg2+ and the substrate analogue L-gulonate 6-phosphate and confirms these, predictions. The carboxylate functional groups at the ends of the first, second, and third beta-strands in KGPDC are ligands of the Mg2+; in OMPDC, the homologues of these residues participate in a hydrogen-bonded network, that facilitates the decarboxylation reaction. The 3-OH group of the, substrate analogue is coordinated to the Mg2+, supporting the hypothesis, that the mechanism of the decarboxylation catalyzed by KGPDC involves, stabilization of an enediolate anion intermediate. These structural, studies establish the existence of the OMPDC "suprafamily," in which, members catalyze reactions that occur in different metabolic pathways and, share no mechanistic relationship. The existence of this suprafamily, demonstrates that divergent evolution can be opportunistic, conscripting, active site features of a progenitor to catalyze unrelated functions., Accordingly, sequence or structure homology alone cannot be used to infer, the functions of new proteins discovered in genome projects.
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<StructureSection load='1kv8' size='340' side='right'caption='[[1kv8]], [[Resolution|resolution]] 1.62&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1kv8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KV8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KV8 FirstGlance]. <br>
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1KV8 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with PO4 and MG as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1KV8 OCA].
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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]] 1.62&#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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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==Reference==
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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=1kv8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kv8 OCA], [https://pdbe.org/1kv8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kv8 RCSB], [https://www.ebi.ac.uk/pdbsum/1kv8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kv8 ProSAT]</span></td></tr>
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Homologous (beta/alpha)8-barrel enzymes that catalyze unrelated reactions: orotidine 5'-monophosphate decarboxylase and 3-keto-L-gulonate 6-phosphate decarboxylase., Wise E, Yew WS, Babbitt PC, Gerlt JA, Rayment I, Biochemistry. 2002 Mar 26;41(12):3861-9. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11900527 11900527]
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/ULAD_ECOLI ULAD_ECOLI] Catalyzes the decarboxylation of 3-keto-L-gulonate-6-P into L-xylulose-5-P. Is involved in the anaerobic L-ascorbate utilization.<ref>PMID:11741871</ref>
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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/kv/1kv8_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=1kv8 ConSurf].
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<div style="clear:both"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Babbitt, P.C.]]
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[[Category: Babbitt PC]]
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[[Category: Gerlt, J.A.]]
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[[Category: Gerlt JA]]
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[[Category: Rayment, I.]]
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[[Category: Rayment I]]
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[[Category: Wise, E.]]
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[[Category: Wise E]]
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[[Category: Yew, W.S.]]
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[[Category: Yew WS]]
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[[Category: MG]]
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[[Category: PO4]]
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[[Category: beta/alpha-barrel]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 19:54:54 2007''
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Current revision

Crystal Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase

PDB ID 1kv8

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