This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2bvv

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 06:28, 16 May 2018

SUGAR RING DISTORTION IN THE GLYCOSYL-ENZYME INTERMEDIATE OF A FAMILY G/11 XYLANASE.

Structural highlights

2bvv is a 1 chain structure with sequence from Atcc 24. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Activity:	Endo-1,4-beta-xylanase, with EC number 3.2.1.8
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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 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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Sidhu G, Withers SG, Nguyen NT, McIntosh LP, Ziser L, Brayer GD. Sugar ring distortion in the glycosyl-enzyme intermediate of a family G/11 xylanase. Biochemistry. 1999 Apr 27;38(17):5346-54. PMID:10220321 doi:10.1021/bi982946f

1 Structural highlights
2 Evolutionary Conservation
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2bvv"

@@ Line 1: / Line 1: @@
 ==SUGAR RING DISTORTION IN THE GLYCOSYL-ENZYME INTERMEDIATE OF A FAMILY G/11 XYLANASE.==
 <StructureSection load='2bvv' size='340' side='right' caption='[[2bvv]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
@@ Line 4: / Line 5: @@
 <table><tr><td colspan='2'>[[2bvv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_24 Atcc 24]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BVV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BVV FirstGlance]. <br>
 </td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </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=2bvv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bvv OCA], [http://pdbe.org/2bvv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2bvv RCSB], [http://www.ebi.ac.uk/pdbsum/2bvv PDBsum]</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=2bvv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bvv OCA], [http://pdbe.org/2bvv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2bvv RCSB], [http://www.ebi.ac.uk/pdbsum/2bvv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2bvv ProSAT]</span></td></tr>
 </table>
 == Evolutionary Conservation ==
@@ Line 10: / Line 11: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bv/2bvv_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bv/2bvv_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>

2bvv

From Proteopedia

Revision as of 06:28, 16 May 2018

SUGAR RING DISTORTION IN THE GLYCOSYL-ENZYME INTERMEDIATE OF A FAMILY G/11 XYLANASE.

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox