1gfs: Difference between revisions

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<StructureSection load='1gfs' size='340' side='right'caption='[[1gfs]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
<StructureSection load='1gfs' size='340' side='right'caption='[[1gfs]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1gfs]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GFS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1GFS FirstGlance]. <br>
<table><tr><td colspan='2'>[[1gfs]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GFS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GFS FirstGlance]. <br>
</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">WCAG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1gfs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gfs OCA], [http://pdbe.org/1gfs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1gfs RCSB], [http://www.ebi.ac.uk/pdbsum/1gfs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1gfs ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1gfs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gfs OCA], [https://pdbe.org/1gfs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gfs RCSB], [https://www.ebi.ac.uk/pdbsum/1gfs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gfs ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/FCL_ECOLI FCL_ECOLI]] Catalyzes the two-step NADP-dependent conversion of GDP-4-dehydro-6-deoxy-D-mannose to GDP-fucose, involving an epimerase and a reductase reaction.<ref>PMID:9473059</ref> <ref>PMID:10480878</ref> <ref>PMID:11021971</ref>
[https://www.uniprot.org/uniprot/FCL_ECOLI FCL_ECOLI] Catalyzes the two-step NADP-dependent conversion of GDP-4-dehydro-6-deoxy-D-mannose to GDP-fucose, involving an epimerase and a reductase reaction.<ref>PMID:9473059</ref> <ref>PMID:10480878</ref> <ref>PMID:11021971</ref>  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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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=1gfs ConSurf].
</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=1gfs ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Background:. In all species examined, GDP-fucose is synthesized from GDP-mannose in a three-step reaction catalyzed by two enzymes, GDP-mannose 4,6 dehydratase and a dual function 3, 5-epimerase-4-reductase named GDP-fucose synthetase. In this latter aspect fucose biosynthesis differs from that of other deoxy and dideoxy sugars, in which the epimerase and reductase activities are present as separate enzymes. Defects in GDP-fucose biosynthesis have been shown to affect nodulation in bacteria, stem development in plants, and are associated with the immune defect leukocyte adhesion deficiency type II in humans. Results:. We have determined the structure of GDP-fucose synthetase from Escherichia coli at 2.2 A resolution. The structure of GDP-fucose synthetase is closely related to that of UDP-galactose 4-epimerase and more distantly to other members of the short-chain dehydrogenase/reductase family. We have also determined the structures of the binary complexes of GDP-fucose synthetase with its substrate NADPH and its product NADP+. The nicotinamide cofactors bind in the syn and anti conformations, respectively. Conclusions:. GDP-fucose synthetase binds its substrate, NADPH, in the proper orientation (syn) for transferring the 4-pro-S hydride of the nicotinamide. We have observed a single binding site in GDP-fucose synthetase for the second substrate, GDP-4-keto,6-deoxy-mannose. This implies that both the epimerization and reduction reactions occur at the same site in the enzyme. As is the case for all members of the short-chain family of dehydrogenase/reductases, GDP-fucose synthetase retains the Ser-Tyr-Lys catalytic triad. We propose that this catalytic triad functions in a mechanistically equivalent manner in both the epimerization and reduction reactions. Additionally, the X-ray structure has allowed us to identify other residues that are potentially required for substrate binding and catalysis.
GDP-fucose synthetase from Escherichia coli: structure of a unique member of the short-chain dehydrogenase/reductase family that catalyzes two distinct reactions at the same active site.,Somers WS, Stahl ML, Sullivan FX Structure. 1998 Dec 15;6(12):1601-12. PMID:9862812<ref>PMID:9862812</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1gfs" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Ecoli]]
[[Category: Escherichia coli K-12]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Somers, W S]]
[[Category: Somers WS]]
[[Category: Stahl, M L]]
[[Category: Stahl ML]]
[[Category: Sullivan, F X]]
[[Category: Sullivan FX]]
[[Category: Epimerase-reductase]]
[[Category: Gdp-fucose]]
[[Category: Lipopolysaccharide biosynthesis]]
[[Category: Nadp]]
[[Category: Oxidoreductase]]

Latest revision as of 10:25, 7 February 2024

GDP-FUCOSE SYNTHETASE FROM E. COLIGDP-FUCOSE SYNTHETASE FROM E. COLI

Structural highlights

1gfs is a 1 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.2Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

FCL_ECOLI Catalyzes the two-step NADP-dependent conversion of GDP-4-dehydro-6-deoxy-D-mannose to GDP-fucose, involving an epimerase and a reductase reaction.[1] [2] [3]

Evolutionary Conservation

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

References

  1. ↑ Andrianopoulos K, Wang L, Reeves PR. Identification of the fucose synthetase gene in the colanic acid gene cluster of Escherichia coli K-12. J Bacteriol. 1998 Feb;180(4):998-1001. PMID:9473059
  2. ↑ Menon S, Stahl M, Kumar R, Xu GY, Sullivan F. Stereochemical course and steady state mechanism of the reaction catalyzed by the GDP-fucose synthetase from Escherichia coli. J Biol Chem. 1999 Sep 17;274(38):26743-50. PMID:10480878
  3. ↑ Rosano C, Bisso A, Izzo G, Tonetti M, Sturla L, De Flora A, Bolognesi M. Probing the catalytic mechanism of GDP-4-keto-6-deoxy-d-mannose Epimerase/Reductase by kinetic and crystallographic characterization of site-specific mutants. J Mol Biol. 2000 Oct 13;303(1):77-91. PMID:11021971 doi:10.1006/jmbi.2000.4106

1gfs, resolution 2.20Å

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