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| | <StructureSection load='2glk' size='340' side='right'caption='[[2glk]], [[Resolution|resolution]] 0.94Å' scene=''> | | <StructureSection load='2glk' size='340' side='right'caption='[[2glk]], [[Resolution|resolution]] 0.94Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2glk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"actinomyces_rubiginosus"_preobrazhenskaya_et_al._in_gauze_et_al._1957 "actinomyces rubiginosus" preobrazhenskaya et al. in gauze et al. 1957]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GLK FirstGlance]. <br> | + | <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> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></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]] 0.94Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1xib|1xib]]</td></tr> | + | <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> |
| - | <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=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> |
| - | <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=2glk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2glk OCA], [http://pdbe.org/2glk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2glk RCSB], [http://www.ebi.ac.uk/pdbsum/2glk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2glk 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/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Actinomyces rubiginosus preobrazhenskaya et al. in gauze et al. 1957]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Xylose isomerase]] | + | [[Category: Streptomyces rubiginosus]] |
| - | [[Category: Bunick, G J]] | + | [[Category: Bunick GJ]] |
| - | [[Category: Carrell, H L]] | + | [[Category: Carrell HL]] |
| - | [[Category: Glusker, J P]] | + | [[Category: Glusker JP]] |
| - | [[Category: Hanson, B L]] | + | [[Category: Hanson BL]] |
| - | [[Category: Harp, J M]] | + | [[Category: Harp JM]] |
| - | [[Category: Katz, A K]] | + | [[Category: Katz AK]] |
| - | [[Category: Beta-alpha-barrel]]
| + | |
| - | [[Category: Isomerase]]
| + | |
| - | [[Category: Tim barrel]]
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| - | [[Category: Two metal binding site]]
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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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