2gve

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[[Image:2gve.gif|left|200px]]<br /><applet load="2gve" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2gve, resolution 2.2&Aring;" />
 
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'''Time-of-Flight Neutron Diffraction Structure of D-Xylose Isomerase'''<br />
 
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==Overview==
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==Time-of-Flight Neutron Diffraction Structure of D-Xylose Isomerase==
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<StructureSection load='2gve' size='340' side='right'caption='[[2gve]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2gve]] 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=2GVE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GVE 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">Neutron Diffraction, [[Resolution|Resolution]] 2.2&#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=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</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=2gve FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gve OCA], [https://pdbe.org/2gve PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gve RCSB], [https://www.ebi.ac.uk/pdbsum/2gve PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gve 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/gv/2gve_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=2gve 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 ==
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.
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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2GVE 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 <scene name='pdbligand=CO:'>CO</scene> and <scene name='pdbligand=DOD:'>DOD</scene> 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://oca.weizmann.ac.il/oca-bin/ocashort?id=2GVE 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 2gve" 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: Coates, L.]]
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[[Category: Glusker, J P.]]
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[[Category: Hanson, B L.]]
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[[Category: Katz, A K.]]
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[[Category: Langan, P.]]
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[[Category: Li, X.]]
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[[Category: Schoenborn, B P.]]
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[[Category: CO]]
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[[Category: DOD]]
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[[Category: protonation states of residues]]
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[[Category: tim barrel-beta-alpha-barrels]]
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[[Category: two metal binding sites]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:35:49 2008''
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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: Coates L]]
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[[Category: Glusker JP]]
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[[Category: Hanson BL]]
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[[Category: Katz AK]]
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[[Category: Langan P]]
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[[Category: Li X]]
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[[Category: Schoenborn BP]]

Current revision

Time-of-Flight Neutron Diffraction Structure of D-Xylose Isomerase

PDB ID 2gve

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