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2xis

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(New page: 200px<br /><applet load="2xis" size="450" color="white" frame="true" align="right" spinBox="true" caption="2xis, resolution 1.71&Aring;" /> '''A METAL-MEDIATED HYD...)
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[[Image:2xis.jpg|left|200px]]<br /><applet load="2xis" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2xis, resolution 1.71&Aring;" />
 
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'''A METAL-MEDIATED HYDRIDE SHIFT MECHANISM FOR XYLOSE ISOMERASE BASED ON THE 1.6 ANGSTROMS STREPTOMYCES RUBIGINOSUS STRUCTURES WITH XYLITOL AND D-XYLOSE'''<br />
 
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==Overview==
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==A METAL-MEDIATED HYDRIDE SHIFT MECHANISM FOR XYLOSE ISOMERASE BASED ON THE 1.6 ANGSTROMS STREPTOMYCES RUBIGINOSUS STRUCTURES WITH XYLITOL AND D-XYLOSE==
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The crystal structure of recombinant Streptomyces rubiginosus D-xylose, isomerase (D-xylose keto-isomerase, EC 5.3.1.5) solved by the multiple, isomorphous replacement technique has been refined to R = 0.16 at 1.64 A, resolution. As observed in an earlier study at 4.0 A (Carrell et al., J., Biol. Chem. 259: 3230-3236, 1984), xylose isomerase is a tetramer composed, of four identical subunits. The monomer consists of an eight-stranded, parallel beta-barrel surrounded by eight helices with an extended, C-terminal tail that provides extensive contacts with a neighboring, monomer. The active site pocket is defined by an opening in the barrel, whose entrance is lined with hydrophobic residues while the bottom of the, pocket consists mainly of glutamate, aspartate, and histidine residues, coordinated to two manganese ions. The structures of the enzyme in the, presence of MnCl2, the inhibitor xylitol, and the substrate D-xylose in, the presence and absence of MnCl2 have also been refined to R = 0.14 at, 1.60 A, R = 0.15 at 1.71 A, R = 0.15 at 1.60 A, and R = 0.14 at 1.60 A, respectively. Both the ring oxygen of the cyclic alpha-D-xylose and its C1, hydroxyl are within hydrogen bonding distance of NE2 of His-54 in the, structure crystallized in the presence of D-xylose. Both the inhibitor, xylitol, and the extended form of the substrate, D-xylose, bind such that, the C2 and C4 OH groups interact with one of the two divalent cations, found in the active site and the C1 OH with the other cation. The, remainder of the OH groups hydrogen bond with neighboring amino acid side, chains. A detailed mechanism for D-xylose isomerase is proposed. Upon, binding of cyclic alpha-D-xylose to xylose isomerase, His-54 acts as the, catalytic base in a ring opening reaction. The ring opening step is, followed by binding of D-xylose, involving two divalent cations, in an, extended conformation. The isomerization of D-xylose to D-xylulose, involves a metal-mediated 1,2-hydride shift. The final step in the, mechanism is a ring closure to produce alpha-D-xylulose. The ring closing, is the reverse of the ring opening step. This mechanism accounts for the, majority of xylose isomerase's biochemical properties, including (1) the, lack of solvent exchange between the 2-position of D-xylose and the, 1-pro-R position of D-xylulose, (2) the chemical modification of histidine, and lysine, (3) the pH vs. activity profile, and (4) the requirement for, two divalent cations in the mechanism.
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<StructureSection load='2xis' size='340' side='right'caption='[[2xis]], [[Resolution|resolution]] 1.71&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2xis]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_rubiginosus Streptomyces rubiginosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XIS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XIS 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]] 1.71&#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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=XYL:D-XYLITOL'>XYL</scene></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=2xis FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xis OCA], [https://pdbe.org/2xis PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xis RCSB], [https://www.ebi.ac.uk/pdbsum/2xis PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xis ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/XYLA_STRRU XYLA_STRRU] Involved in D-xylose catabolism.
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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/xi/2xis_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=2xis ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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2XIS is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_rubiginosus Streptomyces rubiginosus] with XYL and MG as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Xylose_isomerase Xylose isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.5 5.3.1.5] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2XIS OCA].
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*[[D-xylose isomerase 3D structures|D-xylose isomerase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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A metal-mediated hydride shift mechanism for xylose isomerase based on the 1.6 A Streptomyces rubiginosus structures with xylitol and D-xylose., Whitlow M, Howard AJ, Finzel BC, Poulos TL, Winborne E, Gilliland GL, Proteins. 1991;9(3):153-73. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=2006134 2006134]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Streptomyces rubiginosus]]
[[Category: Streptomyces rubiginosus]]
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[[Category: Xylose isomerase]]
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[[Category: Howard AJ]]
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[[Category: Howard, A.J.]]
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[[Category: Whitlow M]]
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[[Category: Whitlow, M.]]
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[[Category: MG]]
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[[Category: XYL]]
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[[Category: isomerase(intramolecular oxidoreductse)]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 19:30:46 2007''
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Current revision

A METAL-MEDIATED HYDRIDE SHIFT MECHANISM FOR XYLOSE ISOMERASE BASED ON THE 1.6 ANGSTROMS STREPTOMYCES RUBIGINOSUS STRUCTURES WITH XYLITOL AND D-XYLOSE

PDB ID 2xis

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