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1db3

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(New page: 200px<br /><applet load="1db3" size="450" color="white" frame="true" align="right" spinBox="true" caption="1db3, resolution 2.3&Aring;" /> '''E.COLI GDP-MANNOSE 4,...)
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[[Image:1db3.gif|left|200px]]<br /><applet load="1db3" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1db3, resolution 2.3&Aring;" />
 
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'''E.COLI GDP-MANNOSE 4,6-DEHYDRATASE'''<br />
 
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==Overview==
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==E.COLI GDP-MANNOSE 4,6-DEHYDRATASE==
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Background: GDP-mannose 4,6 dehydratase (GMD) catalyzes the conversion of, GDP-(D)-mannose to GDP-4-keto, 6-deoxy-(D)-mannose. This is the first and, regulatory step in the de novo biosynthesis of GDP-(L)-fucose. Fucose, forms part of a number of glycoconjugates, including the ABO blood groups, and the selectin ligand sialyl Lewis X. Defects in GDP-fucose metabolism, have been linked to leukocyte adhesion deficiency type II (LADII)., Results: The structure of the GDP-mannose 4,6 dehydratase apo enzyme has, been determined and refined using data to 2.3 A resolution. GMD is a, homodimeric protein with each monomer composed of two domains. The larger, N-terminal domain binds the NADP(H) cofactor in a classical Rossmann fold, and the C-terminal domain harbors the sugar-nucleotide binding site. We, have determined the GMD dissociation constants for NADP, NADPH and, GDP-mannose. Each GMD monomer binds one cofactor and one substrate, molecule, suggesting that both subunits are catalytically competent., GDP-fucose acts as a competitive inhibitor, suggesting that it binds to, the same site as GDP-mannose, providing a mechanism for the feedback, inhibition of fucose biosynthesis. Conclusions: The X-ray structure of GMD, reveals that it is a member of the short-chain dehydrogenase/reductase, (SDR) family of proteins. We have modeled the binding of NADP and, GDP-mannose to the enzyme and mutated four of the active-site residues to, determine their function. The combined modeling and mutagenesis data, suggests that at position 133 threonine substitutes serine as part of the, serine-tyrosine-lysine catalytic triad common to the SDR family and Glu, 135 functions as an active-site base.
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<StructureSection load='1db3' size='340' side='right'caption='[[1db3]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1db3]] is a 1 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=1DB3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DB3 FirstGlance]. <br>
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1DB3 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. 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=1DB3 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]] 2.3&#8491;</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=1db3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1db3 OCA], [https://pdbe.org/1db3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1db3 RCSB], [https://www.ebi.ac.uk/pdbsum/1db3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1db3 ProSAT]</span></td></tr>
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==Reference==
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</table>
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Structural and kinetic analysis of Escherichia coli GDP-mannose 4,6 dehydratase provides insights into the enzyme's catalytic mechanism and regulation by GDP-fucose., Somoza JR, Menon S, Schmidt H, Joseph-McCarthy D, Dessen A, Stahl ML, Somers WS, Sullivan FX, Structure. 2000 Feb 15;8(2):123-35. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10673432 10673432]
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== Function ==
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[https://www.uniprot.org/uniprot/GM4D_ECOLI GM4D_ECOLI]
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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/db/1db3_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=1db3 ConSurf].
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<div style="clear:both"></div>
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__TOC__
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</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: GDP-mannose 4,6-dehydratase]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Menon S]]
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[[Category: Menon, S.]]
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[[Category: Somers WS]]
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[[Category: Somers, W.S.]]
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[[Category: Somoza JR]]
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[[Category: Somoza, J.R.]]
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[[Category: Sullivan FX]]
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[[Category: Sullivan, F.X.]]
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[[Category: dehydratase]]
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[[Category: gdp-fucose]]
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[[Category: gdp-mannose]]
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[[Category: nadp]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:08:06 2007''
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Current revision

E.COLI GDP-MANNOSE 4,6-DEHYDRATASE

PDB ID 1db3

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