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| - | [[Image:1e7r.jpg|left|200px]]<br /><applet load="1e7r" size="450" color="white" frame="true" align="right" spinBox="true" | |
| - | caption="1e7r, resolution 1.6Å" /> | |
| - | '''GDP 4-KETO-6-DEOXY-D-MANNOSE EPIMERASE REDUCTASE Y136E'''<br /> | |
| | | | |
| - | ==Overview== | + | ==GDP 4-keto-6-deoxy-D-mannose epimerase reductase Y136E== |
| - | GDP-4-keto-6-deoxy-d-mannose epimerase/reductase is a bifunctional enzyme, responsible for the last step in the biosynthesis of GDP-l-fucose, the, substrate of fucosyl transferases. Several cell-surface antigens, including the leukocyte Lewis system and cell-surface antigens in, pathogenic bacteria, depend on the availability of GDP-l-fucose for their, expression. Therefore, the enzyme is a potential target for therapy in, pathological states depending on selectin-mediated cell-to-cell, interactions. Previous crystallographic investigations have shown that, GDP-4-keto-6-deoxy-d-mannose epimerase/reductase belongs to the, short-chain dehydrogenase/reductase protein homology family. The enzyme, active-site region is at the interface of an N-terminal NADPH-binding, domain and a C-terminal domain, held to bind the substrate. The design, expression and functional characterization of seven site-specific mutant, forms of GDP-4-keto-6-deoxy-d-mannose epimerase/reductase are reported, here. In parallel, the crystal structures of the native holoenzyme and of, three mutants (Ser107Ala, Tyr136Glu and Lys140Arg) have been investigated, and refined at 1. 45-1.60 A resolution, based on synchrotron data, (R-factors range between 12.6 % and 13.9 %). The refined protein models, show that besides the active-site residues Ser107, Tyr136 and Lys140, whose mutations impair the overall enzymatic activity and may affect the, coenzyme binding mode, side-chains capable of proton exchange, located, around the expected substrate (GDP-4-keto-6-deoxy-d-mannose) binding, pocket, are selectively required during the epimerization and reduction, steps. Among these, Cys109 and His179 may play a primary role in proton, exchange between the enzyme and the epimerization catalytic intermediates., Finally, the additional role of mutated active-site residues involved in, substrate recognition and in enzyme stability has been analyzed. | + | <StructureSection load='1e7r' size='340' side='right'caption='[[1e7r]], [[Resolution|resolution]] 1.60Å' scene=''> |
| | + | == Structural highlights == |
| | + | <table><tr><td colspan='2'>[[1e7r]] 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=1E7R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1E7R FirstGlance]. <br> |
| | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6Å</td></tr> |
| | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>, <scene name='pdbligand=UVW:ACETYLPHOSPHATE'>UVW</scene></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=1e7r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e7r OCA], [https://pdbe.org/1e7r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1e7r RCSB], [https://www.ebi.ac.uk/pdbsum/1e7r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e7r ProSAT]</span></td></tr> |
| | + | </table> |
| | + | == Function == |
| | + | [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 == |
| | + | [[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/e7/1e7r_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=1e7r ConSurf]. |
| | + | <div style="clear:both"></div> |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | GDP-4-keto-6-deoxy-d-mannose epimerase/reductase is a bifunctional enzyme responsible for the last step in the biosynthesis of GDP-l-fucose, the substrate of fucosyl transferases. Several cell-surface antigens, including the leukocyte Lewis system and cell-surface antigens in pathogenic bacteria, depend on the availability of GDP-l-fucose for their expression. Therefore, the enzyme is a potential target for therapy in pathological states depending on selectin-mediated cell-to-cell interactions. Previous crystallographic investigations have shown that GDP-4-keto-6-deoxy-d-mannose epimerase/reductase belongs to the short-chain dehydrogenase/reductase protein homology family. The enzyme active-site region is at the interface of an N-terminal NADPH-binding domain and a C-terminal domain, held to bind the substrate. The design, expression and functional characterization of seven site-specific mutant forms of GDP-4-keto-6-deoxy-d-mannose epimerase/reductase are reported here. In parallel, the crystal structures of the native holoenzyme and of three mutants (Ser107Ala, Tyr136Glu and Lys140Arg) have been investigated and refined at 1. 45-1.60 A resolution, based on synchrotron data (R-factors range between 12.6 % and 13.9 %). The refined protein models show that besides the active-site residues Ser107, Tyr136 and Lys140, whose mutations impair the overall enzymatic activity and may affect the coenzyme binding mode, side-chains capable of proton exchange, located around the expected substrate (GDP-4-keto-6-deoxy-d-mannose) binding pocket, are selectively required during the epimerization and reduction steps. Among these, Cys109 and His179 may play a primary role in proton exchange between the enzyme and the epimerization catalytic intermediates. Finally, the additional role of mutated active-site residues involved in substrate recognition and in enzyme stability has been analyzed. |
| | | | |
| - | ==About this Structure==
| + | Probing the catalytic mechanism of GDP-4-keto-6-deoxy-d-mannose Epimerase/Reductase by kinetic and crystallographic characterization of site-specific mutants.,Rosano C, Bisso A, Izzo G, Tonetti M, Sturla L, De Flora A, Bolognesi M J Mol Biol. 2000 Oct 13;303(1):77-91. PMID:11021971<ref>PMID:11021971</ref> |
| - | 1E7R 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 SO4, NAP, UVW and TRS as [http://en.wikipedia.org/wiki/ligands ligands]. Known structural/functional Sites: <scene name='pdbsite=AC1:Nap Binding Site For Chain A'>AC1</scene>, <scene name='pdbsite=AC2:Uvw Binding Site For Chain A'>AC2</scene> and <scene name='pdbsite=CAT:Catalytic Triad Residue GLU A136 Is Mutated The Native B ...'>CAT</scene>. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1E7R OCA].
| + | |
| | | | |
| - | ==Reference==
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| - | Probing the catalytic mechanism of GDP-4-keto-6-deoxy-d-mannose Epimerase/Reductase by kinetic and crystallographic characterization of site-specific mutants., Rosano C, Bisso A, Izzo G, Tonetti M, Sturla L, De Flora A, Bolognesi M, J Mol Biol. 2000 Oct 13;303(1):77-91. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11021971 11021971]
| + | </div> |
| | + | <div class="pdbe-citations 1e7r" style="background-color:#fffaf0;"></div> |
| | + | == References == |
| | + | <references/> |
| | + | __TOC__ |
| | + | </StructureSection> |
| | [[Category: Escherichia coli]] | | [[Category: Escherichia coli]] |
| - | [[Category: Single protein]] | + | [[Category: Large Structures]] |
| - | [[Category: Bolognesi, M.]] | + | [[Category: Bolognesi M]] |
| - | [[Category: Izzo, G.]] | + | [[Category: Izzo G]] |
| - | [[Category: Rosano, C.]] | + | [[Category: Rosano C]] |
| - | [[Category: NAP]]
| + | |
| - | [[Category: SO4]]
| + | |
| - | [[Category: TRS]]
| + | |
| - | [[Category: UVW]]
| + | |
| - | [[Category: epimerase/reductase]]
| + | |
| - | [[Category: red]]
| + | |
| - | [[Category: sdr]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Dec 18 15:02:37 2007''
| + | |
| Structural highlights
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.
Publication Abstract from PubMed
GDP-4-keto-6-deoxy-d-mannose epimerase/reductase is a bifunctional enzyme responsible for the last step in the biosynthesis of GDP-l-fucose, the substrate of fucosyl transferases. Several cell-surface antigens, including the leukocyte Lewis system and cell-surface antigens in pathogenic bacteria, depend on the availability of GDP-l-fucose for their expression. Therefore, the enzyme is a potential target for therapy in pathological states depending on selectin-mediated cell-to-cell interactions. Previous crystallographic investigations have shown that GDP-4-keto-6-deoxy-d-mannose epimerase/reductase belongs to the short-chain dehydrogenase/reductase protein homology family. The enzyme active-site region is at the interface of an N-terminal NADPH-binding domain and a C-terminal domain, held to bind the substrate. The design, expression and functional characterization of seven site-specific mutant forms of GDP-4-keto-6-deoxy-d-mannose epimerase/reductase are reported here. In parallel, the crystal structures of the native holoenzyme and of three mutants (Ser107Ala, Tyr136Glu and Lys140Arg) have been investigated and refined at 1. 45-1.60 A resolution, based on synchrotron data (R-factors range between 12.6 % and 13.9 %). The refined protein models show that besides the active-site residues Ser107, Tyr136 and Lys140, whose mutations impair the overall enzymatic activity and may affect the coenzyme binding mode, side-chains capable of proton exchange, located around the expected substrate (GDP-4-keto-6-deoxy-d-mannose) binding pocket, are selectively required during the epimerization and reduction steps. Among these, Cys109 and His179 may play a primary role in proton exchange between the enzyme and the epimerization catalytic intermediates. Finally, the additional role of mutated active-site residues involved in substrate recognition and in enzyme stability has been analyzed.
Probing the catalytic mechanism of GDP-4-keto-6-deoxy-d-mannose Epimerase/Reductase by kinetic and crystallographic characterization of site-specific mutants.,Rosano C, Bisso A, Izzo G, Tonetti M, Sturla L, De Flora A, Bolognesi M J Mol Biol. 2000 Oct 13;303(1):77-91. PMID:11021971[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ 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
- ↑ 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
- ↑ 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
- ↑ 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
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