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| <StructureSection load='1x39' size='340' side='right'caption='[[1x39]], [[Resolution|resolution]] 1.80Å' scene=''> | | <StructureSection load='1x39' size='340' side='right'caption='[[1x39]], [[Resolution|resolution]] 1.80Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
- | <table><tr><td colspan='2'>[[1x39]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Hordeum_vulgare Hordeum vulgare]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X39 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1X39 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1x39]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Hordeum_vulgare Hordeum vulgare]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X39 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1X39 FirstGlance]. <br> |
- | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IDE:(5R,6R,7S,8S)-3-(ANILINOMETHYL)-5,6,7,8-TETRAHYDRO-5-(HYDROXYMETHYL)-IMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL'>IDE</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</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]] 1.8Å</td></tr> |
- | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1lq2|1lq2]], [[1x38|1x38]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IDE:(5R,6R,7S,8S)-3-(ANILINOMETHYL)-5,6,7,8-TETRAHYDRO-5-(HYDROXYMETHYL)-IMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL'>IDE</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr> |
- | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucan_1,3-beta-glucosidase Glucan 1,3-beta-glucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.58 3.2.1.58] </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=1x39 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x39 OCA], [https://pdbe.org/1x39 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1x39 RCSB], [https://www.ebi.ac.uk/pdbsum/1x39 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1x39 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=1x39 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x39 OCA], [http://pdbe.org/1x39 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1x39 RCSB], [http://www.ebi.ac.uk/pdbsum/1x39 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1x39 ProSAT]</span></td></tr> | + | |
| </table> | | </table> |
| + | == Function == |
| + | [https://www.uniprot.org/uniprot/Q9XEI3_HORVV Q9XEI3_HORVV] |
| == Evolutionary Conservation == | | == Evolutionary Conservation == |
| [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| __TOC__ | | __TOC__ |
| </StructureSection> | | </StructureSection> |
- | [[Category: Glucan 1,3-beta-glucosidase]] | |
| [[Category: Hordeum vulgare]] | | [[Category: Hordeum vulgare]] |
| [[Category: Large Structures]] | | [[Category: Large Structures]] |
- | [[Category: Fincher, G B]] | + | [[Category: Fincher GB]] |
- | [[Category: Hrmova, M]] | + | [[Category: Hrmova M]] |
- | [[Category: Smith, B J]] | + | [[Category: Smith BJ]] |
- | [[Category: Streltsov, V A]] | + | [[Category: Streltsov VA]] |
- | [[Category: Varghese, J N]] | + | [[Category: Varghese JN]] |
- | [[Category: Vasella, A]] | + | [[Category: Vasella A]] |
- | [[Category: 2-domain fold]]
| + | |
- | [[Category: Hydrolase]]
| + | |
- | [[Category: Ligand-protein complex]]
| + | |
| Structural highlights
1x39 is a 1 chain structure with sequence from Hordeum vulgare. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| Method: | X-ray diffraction, Resolution 1.8Å |
Ligands: | , , , , , , , |
Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
Q9XEI3_HORVV
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
The interactions of a transition state mimic anilinomethyl glucoimidazole (AmGlcIm), with a K(i) constant of 0.6 x 10(-)(9) M and a Gibbs free energy value of -53.5 kJ/mol, with a family GH3 beta-d-glucan glucohydrolase from barley have been analyzed crystallographically and by ab initio quantum mechanical modeling. AmGlcIm binds 3 times more tightly to the beta-d-glucan glucohydrolase than a previously investigated phenyl glucoimidazole. In the enzyme-AmGlcIm complex, an additional residue, Tyr253, and a water molecule positioned between subsites -1 and +1 are recruited for binding. Analyses of the two binary complexes reveal the following. (i) An intricate network exists in which hydrogen bonds between the enzyme's catalytic pocket residues Lys206, His207, Tyr253, Asp285, and Glu491 and the glucoimidazoles are shorter by 0.15-0.53 A, compared with distances of hydrogen bonds in the Michaelis complex. (ii) The "glucose" moiety of the glucoimidazoles adopts a (4)E conformation that is vital for the low-nanomolar binding. (iii) The N1 atoms of the glucoimidazoles are positioned nearly optimally for in-line protonation by the Oepsilon1 atom of the catalytic acid/base Glu491. (iv) The enzyme derives binding energies from both glycone and aglycone components of the glucoimidazoles. (iv) The prevalent libration motion of the two domains of the enzyme could play a significant role during induced fit closure in the active site. (v) Modeling based on the structural data predicts that protons could be positioned on the N1 atoms of the glucoimidazoles, and the catalytic acid/base Glu491 could carry an overall negative charge. (vi) The enzyme-AmGlcIm complex reveals the likely structure of an early transition state during hydrolysis. Finally, the high-resolution structures enabled us to define minimal structures of oligosaccharides attached to Asn221, Asn498, and Asn600 N-glycosylation sites.
Structural rationale for low-nanomolar binding of transition state mimics to a family GH3 beta-D-glucan glucohydrolase from barley.,Hrmova M, Streltsov VA, Smith BJ, Vasella A, Varghese JN, Fincher GB Biochemistry. 2005 Dec 20;44(50):16529-39. PMID:16342944[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Hrmova M, Streltsov VA, Smith BJ, Vasella A, Varghese JN, Fincher GB. Structural rationale for low-nanomolar binding of transition state mimics to a family GH3 beta-D-glucan glucohydrolase from barley. Biochemistry. 2005 Dec 20;44(50):16529-39. PMID:16342944 doi:http://dx.doi.org/10.1021/bi0514818
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