2glk

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(New page: 200px<br /><applet load="2glk" size="450" color="white" frame="true" align="right" spinBox="true" caption="2glk, resolution 0.94&Aring;" /> '''High-resolution stud...)
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[[Image:2glk.gif|left|200px]]<br /><applet load="2glk" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2glk, resolution 0.94&Aring;" />
 
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'''High-resolution study of D-Xylose isomerase, 0.94A resolution.'''<br />
 
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==Overview==
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==High-resolution study of D-Xylose isomerase, 0.94A resolution.==
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Time-of-flight neutron diffraction has been used to locate hydrogen atoms, that define the ionization states of amino acids in crystals of D-xylose, isomerase. This enzyme, from Streptomyces rubiginosus, is one of the, largest enzymes studied to date at high resolution (1.8 A) by this method., We have determined the position and orientation of a metal ion-bound water, molecule that is located in the active site of the enzyme; this water has, been thought to be involved in the isomerization step in which D-xylose is, converted to D-xylulose or D-glucose to D-fructose. It is shown to be, water (rather than a hydroxyl group) under the conditions of measurement, (pH 8.0). Our analyses also reveal that one lysine probably has an, -NH(2)-terminal group (rather than NH(3)(+)). The ionization state of each, histidine residue also was determined. High-resolution x-ray studies (at, 0.94 A) indicate disorder in some side chains when a truncated substrate, is bound and suggest how some side chains might move during catalysis., This combination of time-of-flight neutron diffraction and x-ray, diffraction can contribute greatly to the elucidation of enzyme, mechanisms.
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<StructureSection load='2glk' size='340' side='right'caption='[[2glk]], [[Resolution|resolution]] 0.94&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2glk]] 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=2GLK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GLK 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]] 0.94&#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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=2glk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2glk OCA], [https://pdbe.org/2glk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2glk RCSB], [https://www.ebi.ac.uk/pdbsum/2glk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2glk 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/gl/2glk_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=2glk ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Time-of-flight neutron diffraction has been used to locate hydrogen atoms that define the ionization states of amino acids in crystals of D-xylose isomerase. This enzyme, from Streptomyces rubiginosus, is one of the largest enzymes studied to date at high resolution (1.8 A) by this method. We have determined the position and orientation of a metal ion-bound water molecule that is located in the active site of the enzyme; this water has been thought to be involved in the isomerization step in which D-xylose is converted to D-xylulose or D-glucose to D-fructose. It is shown to be water (rather than a hydroxyl group) under the conditions of measurement (pH 8.0). Our analyses also reveal that one lysine probably has an -NH(2)-terminal group (rather than NH(3)(+)). The ionization state of each histidine residue also was determined. High-resolution x-ray studies (at 0.94 A) indicate disorder in some side chains when a truncated substrate is bound and suggest how some side chains might move during catalysis. This combination of time-of-flight neutron diffraction and x-ray diffraction can contribute greatly to the elucidation of enzyme mechanisms.
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==About this Structure==
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Locating active-site hydrogen atoms in D-xylose isomerase: time-of-flight neutron diffraction.,Katz AK, Li X, Carrell HL, Hanson BL, Langan P, Coates L, Schoenborn BP, Glusker JP, Bunick GJ Proc Natl Acad Sci U S A. 2006 May 30;103(22):8342-7. Epub 2006 May 17. PMID:16707576<ref>PMID:16707576</ref>
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2GLK 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 MN and GOL 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=2GLK OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Locating active-site hydrogen atoms in D-xylose isomerase: time-of-flight neutron diffraction., Katz AK, Li X, Carrell HL, Hanson BL, Langan P, Coates L, Schoenborn BP, Glusker JP, Bunick GJ, Proc Natl Acad Sci U S A. 2006 May 30;103(22):8342-7. Epub 2006 May 17. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16707576 16707576]
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</div>
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[[Category: Single protein]]
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<div class="pdbe-citations 2glk" style="background-color:#fffaf0;"></div>
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[[Category: Streptomyces rubiginosus]]
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[[Category: Xylose isomerase]]
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[[Category: Bunick, G.J.]]
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[[Category: Carrell, H.L.]]
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[[Category: Glusker, J.P.]]
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[[Category: Hanson, B.L.]]
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[[Category: Harp, J.M.]]
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[[Category: Katz, A.K.]]
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[[Category: GOL]]
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[[Category: MN]]
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[[Category: beta-alpha-barrels]]
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[[Category: tim barrel]]
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[[Category: two metal binding sites]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 11:15:49 2007''
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==See Also==
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*[[D-xylose isomerase 3D structures|D-xylose isomerase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Streptomyces rubiginosus]]
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[[Category: Bunick GJ]]
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[[Category: Carrell HL]]
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[[Category: Glusker JP]]
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[[Category: Hanson BL]]
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[[Category: Harp JM]]
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[[Category: Katz AK]]

Current revision

High-resolution study of D-Xylose isomerase, 0.94A resolution.

PDB ID 2glk

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