1rya

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[[Image:1rya.jpg|left|200px]]<br /><applet load="1rya" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1rya, resolution 1.30&Aring;" />
 
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'''Crystal Structure of the E. coli GDP-mannose mannosyl hydrolase in complex with GDP and MG'''<br />
 
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==Overview==
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==Crystal Structure of the E. coli GDP-mannose mannosyl hydrolase in complex with GDP and MG==
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GDP-mannose glycosyl hydrolase (GDPMH) catalyzes the hydrolysis of GDP-mannose and GDP-glucose to GDP and sugar by substitution with inversion at C1 of the sugar. The enzyme has a modified Nudix motif and requires one divalent cation for activity. The 1.3 A X-ray structure of the GDPMH-Mg(2+)-GDP complex, together with kinetic, mutational, and NMR data, suggests a mechanism for the GDPMH reaction. Several residues and the divalent cation strongly promote the departure of the GDP leaving group, supporting a dissociative mechanism. Comparison of the GDPMH structure with that of a typical Nudix hydrolase suggests how sequence changes result in the switch of catalytic activity from P-O bond cleavage to C-O bond cleavage. Changes in the Nudix motif result in loss of binding of at least one Mg(2+) ion, and shortening of a loop by 6 residues shifts the catalytic base by approximately 10 A.
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<StructureSection load='1rya' size='340' side='right'caption='[[1rya]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1rya]] 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=1RYA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RYA FirstGlance]. <br>
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1RYA 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 <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=CL:'>CL</scene>, <scene name='pdbligand=GDP:'>GDP</scene> and <scene name='pdbligand=TRS:'>TRS</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RYA 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]] 1.3&#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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=1rya FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rya OCA], [https://pdbe.org/1rya PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rya RCSB], [https://www.ebi.ac.uk/pdbsum/1rya PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rya ProSAT]</span></td></tr>
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Structure and mechanism of GDP-mannose glycosyl hydrolase, a Nudix enzyme that cleaves at carbon instead of phosphorus., Gabelli SB, Bianchet MA, Azurmendi HF, Xia Z, Sarawat V, Mildvan AS, Amzel LM, Structure. 2004 Jun;12(6):927-35. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15274914 15274914]
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/GMM_ECOLI GMM_ECOLI] Hydrolyzes both GDP-mannose and GDP-glucose. Could participate in the regulation of cell wall biosynthesis by influencing the concentration of GDP-mannose or GDP-glucose in the cell. Might also be involved in the biosynthesis of the slime polysaccharide colanic acid.<ref>PMID:10913267</ref> <ref>PMID:7592609</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/ry/1rya_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=1rya 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: Amzel, L M.]]
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[[Category: Amzel LM]]
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[[Category: Bianchet, M A.]]
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[[Category: Bianchet MA]]
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[[Category: Gabelli, S B.]]
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[[Category: Gabelli SB]]
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[[Category: Legler, P M.]]
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[[Category: Legler PM]]
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[[Category: Mildvan, A S.]]
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[[Category: Mildvan AS]]
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[[Category: CL]]
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[[Category: GDP]]
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[[Category: MG]]
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[[Category: TRS]]
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[[Category: gdp-glucose]]
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[[Category: gdp-mannose]]
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[[Category: mannose]]
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[[Category: nudix]]
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[[Category: nudix mg-complex]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:55:51 2008''
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Current revision

Crystal Structure of the E. coli GDP-mannose mannosyl hydrolase in complex with GDP and MG

PDB ID 1rya

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