2gub

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{{Seed}}
 
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[[Image:2gub.png|left|200px]]
 
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==Crystal Structure of Metal Free D-Xylose Isomerase.==
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The line below this paragraph, containing "STRUCTURE_2gub", creates the "Structure Box" on the page.
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<StructureSection load='2gub' size='340' side='right'caption='[[2gub]], [[Resolution|resolution]] 1.80&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'>[[2gub]] 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=2GUB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GUB 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]] 1.8&#8491;</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=2gub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gub OCA], [https://pdbe.org/2gub PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gub RCSB], [https://www.ebi.ac.uk/pdbsum/2gub PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gub ProSAT]</span></td></tr>
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{{STRUCTURE_2gub| PDB=2gub | SCENE= }}
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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/gu/2gub_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=2gub 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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===Crystal Structure of Metal Free D-Xylose Isomerase.===
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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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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2gub" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_16707576}}, adds the Publication Abstract to the page
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*[[D-xylose isomerase 3D structures|D-xylose isomerase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 16707576 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_16707576}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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2GUB is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_rubiginosus Streptomyces rubiginosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GUB OCA].
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==Reference==
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<ref group="xtra">PMID:16707576</ref><references group="xtra"/>
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[[Category: Streptomyces rubiginosus]]
[[Category: Streptomyces rubiginosus]]
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[[Category: Xylose isomerase]]
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[[Category: Carrell HL]]
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[[Category: Carrell, H L.]]
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[[Category: Glusker JP]]
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[[Category: Glusker, J P.]]
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[[Category: Katz AK]]
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[[Category: Katz, A K.]]
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[[Category: Beta-alpha-barrel]]
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[[Category: Inactive enzyme]]
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[[Category: Metal-free]]
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[[Category: Sugar interconversion]]
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[[Category: Tim barrel]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 04:21:02 2009''
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Current revision

Crystal Structure of Metal Free D-Xylose Isomerase.

PDB ID 2gub

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