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.

2x8s

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Crystal Structure of the Abn2 D171A mutant in complex with arabinotriose

Structural highlights

2x8s is a 2 chain structure with sequence from Bacillus subtilis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.5Å
Ligands:	, , , , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

EABN2_BACSU Involved in the degradation of arabinan and is a key enzyme in the complete degradation of the plant cell wall. Catalyzes the internal cleavage of alpha-(1->5)-L-arabinofuranosyl residues of the alpha-1,5-L-arabinan to produce arabino-oligosaccharides and L-arabinose. It is also active toward linear branched sugar beet arabinan, and pectin from apple.^[1] ^[2]

Publication Abstract from PubMed

Endo-1,5-alpha-l-arabinanases are glycosyl hydrolases that are able to cleave the glycosidic bonds of alpha-1,5-l-arabinan, releasing arabino-oligosaccharides and l-arabinose. Two extracellular endo-1,5-alpha-l-arabinanases have been isolated from Bacillus subtilis, BsArb43A and BsArb43B (formally named AbnA and Abn2, respectively). BsArb43B shows low sequence identity with previously characterized 1,5-alpha-l-arabinanases and is a much larger enzyme. Here we describe the 3D structure of native BsArb43B, biochemical and structure characterization of two BsArb43B mutant proteins (H318A and D171A), and the 3D structure of the BsArb43B D171A mutant enzyme in complex with arabinohexose. The 3D structure of BsArb43B is different from that of other structurally characterized endo-1,5-alpha-l-arabinanases, as it comprises two domains, an N-terminal catalytic domain, with a 3D fold similar to that observed for other endo-1,5-alpha-l-arabinanases, and an additional C-terminal domain. Moreover, this work also provides experimental evidence for the presence of a cluster containing a calcium ion in the catalytic domain, and the importance of this calcium ion in the enzymatic mechanism of BsArb43B.

New evidence for the role of calcium in the glycosidase reaction of GH43 arabinanases.,De Sanctis D, Inacio JM, Lindley PF, De Sa-Nogueira I, Bento I FEBS J. 2010 Sep 10. doi: 10.1111/j.1742-4658.2010.07870.x. PMID:20883454^[3]

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

References

↑ Inacio JM, de Sa-Nogueira I. Characterization of abn2 (yxiA), encoding a Bacillus subtilis GH43 arabinanase, Abn2, and its role in arabino-polysaccharide degradation. J Bacteriol. 2008 Jun;190(12):4272-80. Epub 2008 Apr 11. PMID:18408032 doi:http://dx.doi.org/JB.00162-08
↑ De Sanctis D, Inacio JM, Lindley PF, De Sa-Nogueira I, Bento I. New evidence for the role of calcium in the glycosidase reaction of GH43 arabinanases. FEBS J. 2010 Sep 10. doi: 10.1111/j.1742-4658.2010.07870.x. PMID:20883454 doi:10.1111/j.1742-4658.2010.07870.x
↑ De Sanctis D, Inacio JM, Lindley PF, De Sa-Nogueira I, Bento I. New evidence for the role of calcium in the glycosidase reaction of GH43 arabinanases. FEBS J. 2010 Sep 10. doi: 10.1111/j.1742-4658.2010.07870.x. PMID:20883454 doi:10.1111/j.1742-4658.2010.07870.x

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2x8s"

@@ Line 3: / Line 3: @@
 <StructureSection load='2x8s' size='340' side='right'caption='[[2x8s]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2x8s]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2X8S OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2X8S FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2x8s]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2X8S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2X8S FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AHR:ALPHA-L-ARABINOFURANOSE'>AHR</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 1.5&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2x8t|2x8t]], [[2x8f|2x8f]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AHR:ALPHA-L-ARABINOFURANOSE'>AHR</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Arabinan_endo-1,5-alpha-L-arabinosidase Arabinan endo-1,5-alpha-L-arabinosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.99 3.2.1.99] </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=2x8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2x8s OCA], [https://pdbe.org/2x8s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2x8s RCSB], [https://www.ebi.ac.uk/pdbsum/2x8s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2x8s ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2x8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2x8s OCA], [http://pdbe.org/2x8s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2x8s RCSB], [http://www.ebi.ac.uk/pdbsum/2x8s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2x8s ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/EABN2_BACSU EABN2_BACSU]] Involved in the degradation of arabinan and is a key enzyme in the complete degradation of the plant cell wall. Catalyzes the internal cleavage of alpha-(1->5)-L-arabinofuranosyl residues of the alpha-1,5-L-arabinan to produce arabino-oligosaccharides and L-arabinose. It is also active toward linear branched sugar beet arabinan, and pectin from apple.<ref>PMID:18408032</ref> <ref>PMID:20883454</ref>
+[https://www.uniprot.org/uniprot/EABN2_BACSU EABN2_BACSU] Involved in the degradation of arabinan and is a key enzyme in the complete degradation of the plant cell wall. Catalyzes the internal cleavage of alpha-(1->5)-L-arabinofuranosyl residues of the alpha-1,5-L-arabinan to produce arabino-oligosaccharides and L-arabinose. It is also active toward linear branched sugar beet arabinan, and pectin from apple.<ref>PMID:18408032</ref> <ref>PMID:20883454</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 27: / Line 26: @@
 __TOC__
 </StructureSection>
-[[Category: Vibrio subtilis ehrenberg 1835]]
+[[Category: Bacillus subtilis]]
-[[Category: Arabinan endo-1,5-alpha-L-arabinosidase]]
 [[Category: Large Structures]]
-[[Category: Bento, I]]
+[[Category: Bento I]]
-[[Category: Inacio, J M]]
+[[Category: Inacio JM]]
-[[Category: Lindley, P F]]
+[[Category: Lindley PF]]
-[[Category: Sa-Nogueira, I de]]
+[[Category: De Sa-Nogueira I]]
-[[Category: DeSanctis, D]]
+[[Category: DeSanctis D]]
-[[Category: Hydrolase]]

2x8s

From Proteopedia

Current revision

Crystal Structure of the Abn2 D171A mutant in complex with arabinotriose

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox