1n7h: Difference between revisions

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New page: left|200px<br /><applet load="1n7h" size="450" color="white" frame="true" align="right" spinBox="true" caption="1n7h, resolution 1.8Å" /> '''Crystal Structure of ...
 
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[[Image:1n7h.jpg|left|200px]]<br /><applet load="1n7h" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1n7h, resolution 1.8&Aring;" />
'''Crystal Structure of GDP-mannose 4,6-dehydratase ternary complex with NADPH and GDP'''<br />


==Overview==
==Crystal Structure of GDP-mannose 4,6-dehydratase ternary complex with NADPH and GDP==
GDP-D-mannose 4,6-dehydratase catalyzes the first step in the de novo, synthesis of GDP-L-fucose, the activated form of L-fucose, which is a, component of glycoconjugates in plants known to be important to the, development and strength of stem tissues. We have determined the, three-dimensional structure of the MUR1 dehydratase isoform from, Arabidopsis thaliana complexed with its NADPH cofactor as well as with the, ligands GDP and GDP-D-rhamnose. MUR1 is a member of the, nucleoside-diphosphosugar modifying subclass of the short-chain, dehydrogenase/reductase enzyme family, having homologous structures and a, conserved catalytic triad of Lys, Tyr, and Ser/Thr residues. MUR1 is the, first member of this subfamily to be observed as a tetramer, the interface, of which reveals a close and intimate overlap of neighboring, NADP(+)-binding sites. The GDP moiety of the substrate also binds in an, unusual syn conformation. The protein-ligand interactions around the, hexose moiety of the substrate support the importance of the conserved, triad residues and an additional Glu side chain serving as a general base, for catalysis. Phe and Arg side chains close to the hexose ring may serve, to confer substrate specificity at the O2 position. In the, MUR1/GDP-D-rhamnose complex, a single unique monomer within the protein, tetramer that has an unoccupied substrate site highlights the, conformational changes that accompany substrate binding and may suggest, the existence of negative cooperativity in MUR1 function.
<StructureSection load='1n7h' size='340' side='right'caption='[[1n7h]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[1n7h]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N7H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N7H FirstGlance]. <br>
1N7H is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] with NDP and GDP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/GDP-mannose_4,6-dehydratase GDP-mannose 4,6-dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.47 4.2.1.47] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1N7H OCA].  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
 
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></td></tr>
==Reference==
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1n7h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n7h OCA], [https://pdbe.org/1n7h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n7h RCSB], [https://www.ebi.ac.uk/pdbsum/1n7h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n7h ProSAT]</span></td></tr>
Structure of the MUR1 GDP-mannose 4,6-dehydratase from Arabidopsis thaliana: implications for ligand binding and specificity., Mulichak AM, Bonin CP, Reiter WD, Garavito RM, Biochemistry. 2002 Dec 31;41(52):15578-89. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12501186 12501186]
</table>
== Function ==
[https://www.uniprot.org/uniprot/GMD2_ARATH GMD2_ARATH] Catalyzes the conversion of GDP-D-mannose to GDP-4-dehydro-6-deoxy-D-mannose.<ref>PMID:9050909</ref> <ref>PMID:12805618</ref>
== 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/n7/1n7h_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=1n7h ConSurf].
<div style="clear:both"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Arabidopsis thaliana]]
[[Category: Arabidopsis thaliana]]
[[Category: GDP-mannose 4,6-dehydratase]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Bonin CP]]
[[Category: Bonin, C.P.]]
[[Category: Garavito RM]]
[[Category: Garavito, R.M.]]
[[Category: Mulichak AM]]
[[Category: Mulichak, A.M.]]
[[Category: Reiter W-D]]
[[Category: Reiter, W.D.]]
[[Category: GDP]]
[[Category: NDP]]
[[Category: rossmann fold]]
[[Category: sdr]]
[[Category: short-chain dehydrogenase/reductase]]
 
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