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2d44

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Crystal structure of arabinofuranosidase complexed with arabinofuranosyl-alpha-1,2-xylobiose

Structural highlights

2d44 is a 1 chain structure with sequence from Aspergillus luchuensis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.3Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ABFB_ASPKW Alpha-L-arabinofuranosidase involved in the degradation of arabinoxylan, a major component of plant hemicellulose. Able to hydrolyze 1,5-, 1,3- and 1,2-alpha-linkages not only in L-arabinofuranosyl oligosaccharides, but also in polysaccharides containing terminal non-reducing L-arabinofuranoses in side chains, like L-arabinan, arabinogalactan and arabinoxylan.^[1] ^[2]

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

Alpha-L-arabinofuranosidase catalyses the hydrolysis of the alpha-1,2-, alpha-1,3-, and alpha-1,5-L-arabinofuranosidic bonds in L-arabinose-containing hemicelluloses such as arabinoxylan. AkAbf54 (the glycoside hydrolase family 54 alpha-L-arabinofuranosidase from Aspergillus kawachii) consists of two domains, a catalytic and an arabinose-binding domain. The latter has been named AkCBM42 [family 42 CBM (carbohydrate-binding module) of AkAbf54] because homologous domains are classified into CBM family 42. In the complex between AkAbf54 and arabinofuranosyl-alpha-1,2-xylobiose, the arabinose moiety occupies the binding pocket of AkCBM42, whereas the xylobiose moiety is exposed to the solvent. AkCBM42 was found to facilitate the hydrolysis of insoluble arabinoxylan, because mutants at the arabinose binding site exhibited markedly decreased activity. The results of binding assays and affinity gel electrophoresis showed that AkCBM42 interacts with arabinose-substituted, but not with unsubstituted, hemicelluloses. Isothermal titration calorimetry and frontal affinity chromatography analyses showed that the association constant of AkCBM42 with the arabinose moiety is approximately 10(3) M(-1). These results indicate that AkCBM42 binds the non-reducing-end arabinofuranosidic moiety of hemicellulose. To our knowledge, this is the first example of a CBM that can specifically recognize the side-chain monosaccharides of branched hemicelluloses.

The family 42 carbohydrate-binding module of family 54 alpha-L-arabinofuranosidase specifically binds the arabinofuranose side chain of hemicellulose.,Miyanaga A, Koseki T, Miwa Y, Mese Y, Nakamura S, Kuno A, Hirabayashi J, Matsuzawa H, Wakagi T, Shoun H, Fushinobu S Biochem J. 2006 Nov 1;399(3):503-11. PMID:16846393^[3]

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

References

↑ Miyanaga A, Koseki T, Matsuzawa H, Wakagi T, Shoun H, Fushinobu S. Crystal structure of a family 54 alpha-L-arabinofuranosidase reveals a novel carbohydrate-binding module that can bind arabinose. J Biol Chem. 2004 Oct 22;279(43):44907-14. Epub 2004 Aug 3. PMID:15292273 doi:10.1074/jbc.M405390200
↑ Koseki T, Okuda M, Sudoh S, Kizaki Y, Iwano K, Aramaki I, Matsuzawa H. Role of two alpha-L-arabinofuranosidases in arabinoxylan degradation and characteristics of the encoding genes from shochu koji molds, Aspergillus kawachii and Aspergillus awamori. J Biosci Bioeng. 2003;96(3):232-41. doi: 10.1016/s1389-1723(03)80187-1. PMID:16233515 doi:http://dx.doi.org/10.1016/s1389-1723(03)80187-1
↑ Miyanaga A, Koseki T, Miwa Y, Mese Y, Nakamura S, Kuno A, Hirabayashi J, Matsuzawa H, Wakagi T, Shoun H, Fushinobu S. The family 42 carbohydrate-binding module of family 54 alpha-L-arabinofuranosidase specifically binds the arabinofuranose side chain of hemicellulose. Biochem J. 2006 Nov 1;399(3):503-11. PMID:16846393 doi:10.1042/BJ20060567

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/2d44"

@@ Line 1: / Line 1: @@
 ==Crystal structure of arabinofuranosidase complexed with arabinofuranosyl-alpha-1,2-xylobiose==
-<StructureSection load='2d44' size='340' side='right' caption='[[2d44]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<StructureSection load='2d44' size='340' side='right'caption='[[2d44]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2d44]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspka Aspka]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D44 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D44 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2d44]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_luchuensis Aspergillus luchuensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D44 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D44 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AHR:ALPHA-L-ARABINOFURANOSE'>AHR</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 2.3&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1wd3|1wd3]], [[1wd4|1wd4]], [[2d43|2d43]]</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=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Non-reducing_end_alpha-L-arabinofuranosidase Non-reducing end alpha-L-arabinofuranosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.55 3.2.1.55] </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=2d44 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d44 OCA], [https://pdbe.org/2d44 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d44 RCSB], [https://www.ebi.ac.uk/pdbsum/2d44 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d44 ProSAT]</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=2d44 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d44 OCA], [http://pdbe.org/2d44 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d44 RCSB], [http://www.ebi.ac.uk/pdbsum/2d44 PDBsum]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/ABFB_ASPKW ABFB_ASPKW] Alpha-L-arabinofuranosidase involved in the degradation of arabinoxylan, a major component of plant hemicellulose. Able to hydrolyze 1,5-, 1,3- and 1,2-alpha-linkages not only in L-arabinofuranosyl oligosaccharides, but also in polysaccharides containing terminal non-reducing L-arabinofuranoses in side chains, like L-arabinan, arabinogalactan and arabinoxylan.<ref>PMID:15292273</ref> <ref>PMID:16233515</ref>
 == 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/d4/2d44_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d4/2d44_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 31: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Aspka]]
+[[Category: Aspergillus luchuensis]]
-[[Category: Non-reducing end alpha-L-arabinofuranosidase]]
+[[Category: Large Structures]]
-[[Category: Fushinobu, S]]
+[[Category: Fushinobu S]]
-[[Category: Koseki, T]]
+[[Category: Koseki T]]
-[[Category: Matsuzawa, H]]
+[[Category: Matsuzawa H]]
-[[Category: Miwa, Y]]
+[[Category: Miwa Y]]
-[[Category: Miyanaga, A]]
+[[Category: Miyanaga A]]
-[[Category: Shoun, H]]
+[[Category: Shoun H]]
-[[Category: Wakagi, T]]
+[[Category: Wakagi T]]
-[[Category: 2-xylobiose complex]]
-[[Category: Arabinofuranosyl-alpha-1]]
-[[Category: Hydrolase]]

2d44

From Proteopedia

Current revision

Crystal structure of arabinofuranosidase complexed with arabinofuranosyl-alpha-1,2-xylobiose

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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