1bvv: Difference between revisions

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-[[Image:1bvv.gif|left|200px]]<br />
-<applet load="1bvv" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1bvv, resolution 1.8&Aring;" />
-'''SUGAR RING DISTORTION IN THE GLYCOSYL-ENZYME INTERMEDIATE OF A FAMILY G/11 XYLANASE'''<br />
-==Overview==
+==SUGAR RING DISTORTION IN THE GLYCOSYL-ENZYME INTERMEDIATE OF A FAMILY G/11 XYLANASE==
-The 1.8 A resolution structure of the glycosyl-enzyme intermediate formed, on the retaining beta-1,4-xylanase from Bacillus circulans has been, determined using X-ray crystallographic techniques. The 2-fluoro-xylose, residue bound in the -1 subsite adopts a 2,5B (boat) conformation, allowing atoms C5, O5, C1, and C2 of the sugar to achieve coplanarity as, required at the oxocarbenium ion-like transition states of the, double-displacement catalytic mechanism. Comparison of this structure to, that of a mutant of this same enzyme noncovalently complexed with, xylotetraose [Wakarchuk et al. (1994) Protein Sci. 3, 467-475] reveals a, number of differences beyond the distortion of the sugar moiety. Most, notably, a bifurcated hydrogen bond interaction is formed in the, glycosyl-enzyme intermediate involving Heta of Tyr69, the endocyclic, oxygen (O5) of the xylose residue in the -1 subsite, and Oepsilon2 of the, catalytic nucleophile, Glu78. To gain additional understanding of the role, of Tyr69 at the active site of this enzyme, we also determined the 1.5 A, resolution structure of the catalytically inactive Tyr69Phe mutant., Interestingly, no significant structural perturbation due to the loss of, the phenolic group is observed. These results suggest that the, interactions involving the phenolic group of Tyr69, O5 of the proximal, saccharide, and Glu78 Oepsilon2 are important for the catalytic mechanism, of this enzyme, and it is proposed that, through charge redistribution, these interactions serve to stabilize the oxocarbenium-like ion of the, transition state. Studies of the covalent glycosyl-enzyme intermediate of, this xylanase also provide insight into specificity, as contacts with C5, of the xylose moiety exclude sugars with hydroxymethyl substituents, and, the mechanism of catalysis, including aspects of stereoelectronic theory, as applied to glycoside hydrolysis.
+<StructureSection load='1bvv' size='340' side='right'caption='[[1bvv]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1bvv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Niallia_circulans Niallia circulans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BVV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BVV FirstGlance]. <br>
+</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>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DFX:1,2-DEOXY-2-FLUORO-XYLOPYRANOSE'>DFX</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></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=1bvv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bvv OCA], [https://pdbe.org/1bvv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bvv RCSB], [https://www.ebi.ac.uk/pdbsum/1bvv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bvv ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/XYNA_NIACI XYNA_NIACI]
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bv/1bvv_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=1bvv ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The 1.8 A resolution structure of the glycosyl-enzyme intermediate formed on the retaining beta-1,4-xylanase from Bacillus circulans has been determined using X-ray crystallographic techniques. The 2-fluoro-xylose residue bound in the -1 subsite adopts a 2,5B (boat) conformation, allowing atoms C5, O5, C1, and C2 of the sugar to achieve coplanarity as required at the oxocarbenium ion-like transition states of the double-displacement catalytic mechanism. Comparison of this structure to that of a mutant of this same enzyme noncovalently complexed with xylotetraose [Wakarchuk et al. (1994) Protein Sci. 3, 467-475] reveals a number of differences beyond the distortion of the sugar moiety. Most notably, a bifurcated hydrogen bond interaction is formed in the glycosyl-enzyme intermediate involving Heta of Tyr69, the endocyclic oxygen (O5) of the xylose residue in the -1 subsite, and Oepsilon2 of the catalytic nucleophile, Glu78. To gain additional understanding of the role of Tyr69 at the active site of this enzyme, we also determined the 1.5 A resolution structure of the catalytically inactive Tyr69Phe mutant. Interestingly, no significant structural perturbation due to the loss of the phenolic group is observed. These results suggest that the interactions involving the phenolic group of Tyr69, O5 of the proximal saccharide, and Glu78 Oepsilon2 are important for the catalytic mechanism of this enzyme, and it is proposed that, through charge redistribution, these interactions serve to stabilize the oxocarbenium-like ion of the transition state. Studies of the covalent glycosyl-enzyme intermediate of this xylanase also provide insight into specificity, as contacts with C5 of the xylose moiety exclude sugars with hydroxymethyl substituents, and the mechanism of catalysis, including aspects of stereoelectronic theory as applied to glycoside hydrolysis.
-==About this Structure==
+Sugar ring distortion in the glycosyl-enzyme intermediate of a family G/11 xylanase.,Sidhu G, Withers SG, Nguyen NT, McIntosh LP, Ziser L, Brayer GD Biochemistry. 1999 Apr 27;38(17):5346-54. PMID:10220321<ref>PMID:10220321</ref>
-BVV is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_circulans Bacillus circulans] with XYP and DFX as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] Structure known Active Sites: ABC and NUC. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1BVV OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Sugar ring distortion in the glycosyl-enzyme intermediate of a family G/11 xylanase., Sidhu G, Withers SG, Nguyen NT, McIntosh LP, Ziser L, Brayer GD, Biochemistry. 1999 Apr 27;38(17):5346-54. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10220321 10220321]
+</div>
-[[Category: Bacillus circulans]]
+<div class="pdbe-citations 1bvv" style="background-color:#fffaf0;"></div>
-[[Category: Endo-1,4-beta-xylanase]]
+== References ==
-[[Category: Single protein]]
+<references/>
-[[Category: Brayer, G.D.]]
+__TOC__
-[[Category: Sidhu, G.]]
+</StructureSection>
-[[Category: DFX]]
+[[Category: Large Structures]]
-[[Category: XYP]]
+[[Category: Niallia circulans]]
-[[Category: boat conformation]]
+[[Category: Brayer GD]]
-[[Category: glycosidase]]
+[[Category: Sidhu G]]
-[[Category: glycosyl-enzyme intermediate]]
-[[Category: hydrolase]]
-[[Category: xylan degradation]]
-[[Category: xylanase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov  5 14:25:13 2007''