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==Crystal Structure of GDP-mannose 4,6-dehydratase ternary complex with NADPH and GDP==
The line below this paragraph, containing "STRUCTURE_1n7h", creates the "Structure Box" on the page.
<StructureSection load='1n7h' size='340' side='right'caption='[[1n7h]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<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>
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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]] 1.8&#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=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></td></tr>
{{STRUCTURE_1n7h|  PDB=1n7h  |  SCENE= }}
<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>
 
</table>
'''Crystal Structure of GDP-mannose 4,6-dehydratase ternary complex with NADPH and GDP'''
== 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 ==
==Overview==
[[Image:Consurf_key_small.gif|200px|right]]
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.
Check<jmol>
 
  <jmolCheckbox>
==About this Structure==
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n7/1n7h_consurf.spt"</scriptWhenChecked>
1N7H is a [[Single protein]] structure of sequence from [http://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].  
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 
    <text>to colour the structure by Evolutionary Conservation</text>
==Reference==
  </jmolCheckbox>
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://www.ncbi.nlm.nih.gov/pubmed/12501186 12501186]
</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: Rossmann fold]]
[[Category: Sdr]]
[[Category: Short-chain dehydrogenase/reductase]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 02:11:22 2008''

Latest revision as of 10:53, 14 February 2024

Crystal Structure of GDP-mannose 4,6-dehydratase ternary complex with NADPH and GDPCrystal Structure of GDP-mannose 4,6-dehydratase ternary complex with NADPH and GDP

Structural highlights

1n7h is a 2 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.8Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GMD2_ARATH Catalyzes the conversion of GDP-D-mannose to GDP-4-dehydro-6-deoxy-D-mannose.[1] [2]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

  1. ↑ Bonin CP, Potter I, Vanzin GF, Reiter WD. The MUR1 gene of Arabidopsis thaliana encodes an isoform of GDP-D-mannose-4,6-dehydratase, catalyzing the first step in the de novo synthesis of GDP-L-fucose. Proc Natl Acad Sci U S A. 1997 Mar 4;94(5):2085-90. PMID:9050909
  2. ↑ Bonin CP, Freshour G, Hahn MG, Vanzin GF, Reiter WD. The GMD1 and GMD2 genes of Arabidopsis encode isoforms of GDP-D-mannose 4,6-dehydratase with cell type-specific expression patterns. Plant Physiol. 2003 Jun;132(2):883-92. Epub 2003 May 15. PMID:12805618 doi:http://dx.doi.org/10.1104/pp.103.022368

1n7h, resolution 1.80Å

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