3emc

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
m (Protected "3emc" [edit=sysop:move=sysop])
Line 1: Line 1:
-
[[Image:3emc.png|left|200px]]
+
==Crystal structure of XynB, an intracellular xylanase from Paenibacillus barcinonensis==
 +
<StructureSection load='3emc' size='340' side='right' caption='[[3emc]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[3emc]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Paenibacillus_barcinonensis Paenibacillus barcinonensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EMC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EMC FirstGlance]. <br>
 +
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene><br>
 +
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3emq|3emq]], [[3emz|3emz]]</td></tr>
 +
<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">xynB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=198119 Paenibacillus barcinonensis])</td></tr>
 +
<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3emc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3emc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3emc RCSB], [http://www.ebi.ac.uk/pdbsum/3emc PDBsum]</span></td></tr>
 +
<table>
 +
== 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/em/3emc_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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/chain_selection.php?pdb_ID=2ata ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Paenibacillus barcinonensis is a soil bacterium bearing a complex set of enzymes for xylan degradation, including several secreted enzymes and Xyn10B, one of the few intracellular xylanases reported to date. The crystal structure of Xyn10B has been determined by x-ray analysis. The enzyme folds into the typical (beta/alpha)(8) barrel of family 10 glycosyl hydrolases (GH10), with additional secondary structure elements within the beta/alpha motifs. One of these loops -L7- located at the beta7 C terminus, was essential for xylanase activity as its partial deletion yielded an inactive enzyme. The loop contains residues His(249)-Glu(250), which shape a pocket opened to solvent in close proximity to the +2 subsite, which has not been described in other GH10 enzymes. This wide cavity at the +2 subsite, where methyl-2,4-pentanediol from the crystallization medium was found, is a noteworthy feature of Xyn10B, as compared with the narrow crevice described for other GH10 xylanases. Docking analysis showed that this open cavity can accommodate glucuronic acid decorations of xylo-oligosaccharides. Co-crystallization experiments with conduramine derivative inhibitors supported the importance of this open cavity at the +2 subsite for Xyn10B activity. Several mutant derivatives of Xyn10B with improved thermal stability were obtained by forced evolution. Among them, mutant xylanases S15L and M93V showed increased half-life, whereas the double mutant S15L/M93V exhibited a further increase in stability, showing a 20-fold higher heat resistance than the wild type xylanase. All the mutations obtained were located on the surface of Xyn10B. Replacement of a Ser by a Leu residue in mutant xylanase S15L can increase hydrophobic packing efficiency and fill a superficial indentation of the protein, giving rise to a more compact structure of the enzyme.
-
<!--
+
Structural insights into the specificity of Xyn10B from Paenibacillus barcinonensis and its improved stability by forced protein evolution.,Gallardo O, Pastor FI, Polaina J, Diaz P, Lysek R, Vogel P, Isorna P, Gonzalez B, Sanz-Aparicio J J Biol Chem. 2010 Jan 22;285(4):2721-33. Epub 2009 Nov 23. PMID:19940147<ref>PMID:19940147</ref>
-
The line below this paragraph, containing "STRUCTURE_3emc", creates the "Structure Box" on the page.
+
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
-
or leave the SCENE parameter empty for the default display.
+
-
-->
+
-
{{STRUCTURE_3emc| PDB=3emc | SCENE= }}
+
-
===Crystal structure of XynB, an intracellular xylanase from Paenibacillus barcinonensis===
+
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-
 
+
</div>
-
 
+
== References ==
-
<!--
+
<references/>
-
The line below this paragraph, {{ABSTRACT_PUBMED_19940147}}, adds the Publication Abstract to the page
+
__TOC__
-
(as it appears on PubMed at http://www.pubmed.gov), where 19940147 is the PubMed ID number.
+
</StructureSection>
-
-->
+
-
{{ABSTRACT_PUBMED_19940147}}
+
-
 
+
-
==About this Structure==
+
-
[[3emc]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Paenibacillus_barcinonensis Paenibacillus barcinonensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EMC OCA].
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:019940147</ref><references group="xtra"/>
+
[[Category: Endo-1,4-beta-xylanase]]
[[Category: Endo-1,4-beta-xylanase]]
[[Category: Paenibacillus barcinonensis]]
[[Category: Paenibacillus barcinonensis]]

Revision as of 09:45, 21 May 2014

Crystal structure of XynB, an intracellular xylanase from Paenibacillus barcinonensis

3emc, resolution 2.10Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://proteopedia.org/wiki/index.php/3emc"
Views
Personal tools
Navigation
Toolbox