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1xyc

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[[Image:1xyc.gif|left|200px]]
 
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==X-RAY CRYSTALLOGRAPHIC STRUCTURES OF D-XYLOSE ISOMERASE-SUBSTRATE COMPLEXES POSITION THE SUBSTRATE AND PROVIDE EVIDENCE FOR METAL MOVEMENT DURING CATALYSIS==
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The line below this paragraph, containing "STRUCTURE_1xyc", creates the "Structure Box" on the page.
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<StructureSection load='1xyc' size='340' side='right'caption='[[1xyc]], [[Resolution|resolution]] 2.19&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1xyc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_olivochromogenes Streptomyces olivochromogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XYC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XYC FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 2.19&#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=3MF:3-O-METHYLFRUCTOSE+IN+LINEAR+FORM'>3MF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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{{STRUCTURE_1xyc| PDB=1xyc | SCENE= }}
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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=1xyc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xyc OCA], [https://pdbe.org/1xyc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xyc RCSB], [https://www.ebi.ac.uk/pdbsum/1xyc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xyc ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/XYLA_STROL XYLA_STROL] 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/xy/1xyc_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=1xyc ConSurf].
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<div style="clear:both"></div>
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'''X-RAY CRYSTALLOGRAPHIC STRUCTURES OF D-XYLOSE ISOMERASE-SUBSTRATE COMPLEXES POSITION THE SUBSTRATE AND PROVIDE EVIDENCE FOR METAL MOVEMENT DURING CATALYSIS'''
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==See Also==
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*[[D-xylose isomerase 3D structures|D-xylose isomerase 3D structures]]
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__TOC__
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==Overview==
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</StructureSection>
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The X-ray crystallographic structures of the metal-activated enzyme xylose isomerase from Streptomyces olivochromogenes with the substrates D-glucose, 3-O-methyl-D-glucose and in the absence of substrate were determined to 1.96-, 2.19-, and 1.81-A resolution and refined to R-factors of 16.6%, 15.9%, and 16.1%, respectively. Xylose isomerase catalyzes the interconversion between glucose and fructose (xylose and xylulose under physiological conditions) by utilizing two metal cofactors to promote a hydride shift; the metals are bridged by a glutamate residue. This puts xylose isomerase in the small but rapidly growing family of enzymes with a bridged bimetallic active site, in which both metals are involved in the chemical transformation. The substrate 3-O-methylglucose was chosen in order to position the glucose molecule in the observed electron density unambiguously. Of the two essential magnesium ions per active site, Mg-2 was observed to occupy two alternate positions, separated by 1.8 A, in the substrate-soaked structures. The deduced movement was not observed in the structure without substrate present and is attributed to a step following substrate binding but prior to isomerization. The substrates glucose and 3-O-methylglucose are observed in their linear extended forms and make identical interactions with the enzyme by forming ligands to Mg-1 through O2 and O4 and by forming hydrogen bonds with His53 through O5 and Lys182 through O1. Mg-2 has a water ligand that is interpreted in the crystal structure in the absence of substrate as a hydroxide ion and in the presence of substrate as a water molecule. This hydroxide ion may act as a base to deprotonate the glucose O2 and subsequently protonate the product fructose O1 concomitant with hydride transfer. Calculations of the solvent-accessible surface of possible dimers, with and without the alpha-helical C-terminal domain, suggest that the tetramer is the active form of this xylose isomerase.
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[[Category: Large Structures]]
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==About this Structure==
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1XYC is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_olivochromogenes Streptomyces olivochromogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XYC OCA].
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==Reference==
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X-ray crystallographic structures of D-xylose isomerase-substrate complexes position the substrate and provide evidence for metal movement during catalysis., Lavie A, Allen KN, Petsko GA, Ringe D, Biochemistry. 1994 May 10;33(18):5469-80. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8180169 8180169]
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[[Category: Single protein]]
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[[Category: Streptomyces olivochromogenes]]
[[Category: Streptomyces olivochromogenes]]
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[[Category: Xylose isomerase]]
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[[Category: Allen KN]]
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[[Category: Allen, K N.]]
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[[Category: Lavie A]]
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[[Category: Lavie, A.]]
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[[Category: Petsko GA]]
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[[Category: Petsko, G A.]]
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[[Category: Ringe D]]
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[[Category: Ringe, D.]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 15:39:44 2008''
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Current revision

X-RAY CRYSTALLOGRAPHIC STRUCTURES OF D-XYLOSE ISOMERASE-SUBSTRATE COMPLEXES POSITION THE SUBSTRATE AND PROVIDE EVIDENCE FOR METAL MOVEMENT DURING CATALYSIS

PDB ID 1xyc

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