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3lb9

From Proteopedia

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Crystal structure of the B. circulans cpA123 circular permutant

Structural highlights

3lb9 is a 3 chain structure with sequence from Niallia circulans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

XYNA_NIACI

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 20 kDa Bacillus circulans Bcx is a well-studied endoxylanase with a beta-jellyroll fold that places its N- and C-termini in salt bridge contact. Initial experiments verified that Bcx could be circularly permuted by PCR methods to introduce new termini in loop regions while linking its native termini directly or via one or two glycines. Subsequently, a library of circular permutants, generated by random DNase cleavage of the circularized Bcx gene, was screened for xylanase activity on xylan in Congo Red-stained agar. Analysis of 35 unique active circular permutants revealed that, while many of the new termini were introduced in external loops as anticipated, a surprising number were also located within beta-strands. Furthermore, several permutations placed key catalytic residues at or near the new termini with minimal deleterious effects on activity and, in one case, a 4-fold increase. The structure of one permutant was determined by X-ray crystallography, whereas three others were probed by NMR spectroscopy. These studies revealed that the overall conformation of Bcx changed very little in response to circular permutation, with effects largely being limited to increased local mobility near the new and the linked old termini and to a decrease in global stability against thermal denaturation. This library of circularly permuted xylanases provides an excellent set of new start points for directed evolution of this commercially important enzyme, as well as valuable constructs for intein-mediated replacement of key catalytic residues with unnatural analogues. Such approaches should permit new insights into the mechanism of enzymatic glycoside hydrolysis.

Circular permutation of Bacillus circulans xylanase: a kinetic and structural study.,Reitinger S, Yu Y, Wicki J, Ludwiczek M, D'Angelo I, Baturin S, Okon M, Strynadka NC, Lutz S, Withers SG, McIntosh LP Biochemistry. 2010 Mar 23;49(11):2464-74. PMID:20163191^[1]

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

References

↑ Reitinger S, Yu Y, Wicki J, Ludwiczek M, D'Angelo I, Baturin S, Okon M, Strynadka NC, Lutz S, Withers SG, McIntosh LP. Circular permutation of Bacillus circulans xylanase: a kinetic and structural study. Biochemistry. 2010 Mar 23;49(11):2464-74. PMID:20163191 doi:10.1021/bi100036f

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3lb9"

@@ Line 1: / Line 1: @@
 ==Crystal structure of the B. circulans cpA123 circular permutant==
-<StructureSection load='3lb9' size='340' side='right' caption='[[3lb9]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
+<StructureSection load='3lb9' size='340' side='right'caption='[[3lb9]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3lb9]] is a 3 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=3LB9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LB9 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3lb9]] is a 3 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=3LB9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LB9 FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1hv1|1hv1]]</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]] 3&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">xlnA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1397 ATCC 24])</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=3lb9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lb9 OCA], [https://pdbe.org/3lb9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lb9 RCSB], [https://www.ebi.ac.uk/pdbsum/3lb9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lb9 ProSAT]</span></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=3lb9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lb9 OCA], [http://pdbe.org/3lb9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3lb9 RCSB], [http://www.ebi.ac.uk/pdbsum/3lb9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3lb9 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/lb/3lb9_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lb/3lb9_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 32: / Line 32: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 24]]
+[[Category: Large Structures]]
-[[Category: Endo-1,4-beta-xylanase]]
+[[Category: Niallia circulans]]
-[[Category: Angelo, I D]]
+[[Category: D'Angelo I]]
-[[Category: Ludwiczek, M]]
+[[Category: Ludwiczek M]]
-[[Category: Mcintosh, L P]]
+[[Category: Mcintosh LP]]
-[[Category: Reitinger, S]]
+[[Category: Reitinger S]]
-[[Category: Strynadka, N]]
+[[Category: Strynadka N]]
-[[Category: Withers, S G]]
+[[Category: Withers SG]]
-[[Category: Bcx]]
-[[Category: Glycosidase]]
-[[Category: Hydrolase]]
-[[Category: Permutation]]
-[[Category: Xylan degradation]]

3lb9

From Proteopedia

Current revision

Crystal structure of the B. circulans cpA123 circular permutant

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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