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| | <StructureSection load='2gub' size='340' side='right'caption='[[2gub]], [[Resolution|resolution]] 1.80Å' scene=''> | | <StructureSection load='2gub' size='340' side='right'caption='[[2gub]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2gub]] is a 1 chain structure with 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]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GUB FirstGlance]. <br> | + | <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> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1xib|1xib]], [[2glk|2glk]]</td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
| + | <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> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2gub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gub OCA], [http://pdbe.org/2gub PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2gub RCSB], [http://www.ebi.ac.uk/pdbsum/2gub PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2gub ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/XYLA_STRRU XYLA_STRRU]] Involved in D-xylose catabolism. | + | [https://www.uniprot.org/uniprot/XYLA_STRRU XYLA_STRRU] Involved in D-xylose catabolism. |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | ==See Also== | | ==See Also== |
| - | *[[D-xylose isomerase|D-xylose isomerase]] | + | *[[D-xylose isomerase 3D structures|D-xylose isomerase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| | [[Category: Streptomyces rubiginosus]] | | [[Category: Streptomyces rubiginosus]] |
| - | [[Category: Xylose isomerase]]
| + | [[Category: Carrell HL]] |
| - | [[Category: Carrell, H L]] | + | [[Category: Glusker JP]] |
| - | [[Category: Glusker, J P]] | + | [[Category: Katz AK]] |
| - | [[Category: Katz, A K]] | + | |
| - | [[Category: Beta-alpha-barrel]]
| + | |
| - | [[Category: Inactive enzyme]]
| + | |
| - | [[Category: Isomerase]]
| + | |
| - | [[Category: Metal-free]]
| + | |
| - | [[Category: Sugar interconversion]]
| + | |
| - | [[Category: Tim barrel]]
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| Structural highlights
Function
XYLA_STRRU Involved in D-xylose catabolism.
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Katz AK, Li X, Carrell HL, Hanson BL, Langan P, Coates L, Schoenborn BP, Glusker JP, Bunick GJ. Locating active-site hydrogen atoms in D-xylose isomerase: time-of-flight neutron diffraction. Proc Natl Acad Sci U S A. 2006 May 30;103(22):8342-7. Epub 2006 May 17. PMID:16707576
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