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==Crystal structure of a family 51 alpha-L-arabinofuranosidase in complex with Ara-alpha(1,3)-Xyl==
==Crystal structure of a family 51 alpha-L-arabinofuranosidase in complex with Ara-alpha(1,3)-Xyl==
<StructureSection load='1qw8' size='340' side='right' caption='[[1qw8]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
<StructureSection load='1qw8' size='340' side='right'caption='[[1qw8]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1qw8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QW8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QW8 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1qw8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QW8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QW8 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=KHO:4-(3,4-DIHYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-2-YLOXY)-TETRAHYDRO-PYRAN-2,3,5-TRIOL'>KHO</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]] 1.8&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1pz3|1pz3]], [[1pz2|1pz2]], [[1qw9|1qw9]]</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=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ABFA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 Geobacillus stearothermophilus])</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=1qw8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qw8 OCA], [https://pdbe.org/1qw8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qw8 RCSB], [https://www.ebi.ac.uk/pdbsum/1qw8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qw8 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/Alpha-N-arabinofuranosidase Alpha-N-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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1qw8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qw8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qw8 RCSB], [http://www.ebi.ac.uk/pdbsum/1qw8 PDBsum]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/ABFA_BACST ABFA_BACST]] Involved in the degradation of arabinan and is a key enzyme in the complete degradation of the plant cell wall. Catalyzes the cleavage of terminal alpha-(1->5)-arabinofuranosyl bonds in different hemicellulosic homopolysaccharides (branched and debranched arabinans). It acts preferentially on aryl-alpha-L-arabinofuranosides, and is much less effective on aryl-beta-D-xylopyranosides.<ref>PMID:7887599</ref> <ref>PMID:11943144</ref> <ref>PMID:12221104</ref> <ref>PMID:14517232</ref>
[https://www.uniprot.org/uniprot/IABF_GEOSE IABF_GEOSE] Involved in the degradation of arabinan and is a key enzyme in the complete degradation of the plant cell wall. Catalyzes the cleavage of terminal alpha-(1->5)-arabinofuranosyl bonds in different hemicellulosic homopolysaccharides (branched and debranched arabinans). It acts preferentially on aryl-alpha-L-arabinofuranosides, and is much less effective on aryl-beta-D-xylopyranosides.<ref>PMID:11943144</ref> <ref>PMID:12221104</ref> <ref>PMID:14517232</ref> <ref>PMID:7887599</ref>  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qw/1qw8_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qw/1qw8_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </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].
</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/main_output.php?pdb_ID=1qw8 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
High-resolution crystal structures of alpha-L-arabinofuranosidase from Geobacillus stearothermophilus T-6, a family 51 glycosidase, are described. The enzyme is a hexamer, and each monomer is organized into two domains: a (beta/alpha)8-barrel and a 12-stranded beta sandwich with jelly-roll topology. The structures of the Michaelis complexes with natural and synthetic substrates, and of the transient covalent arabinofuranosyl-enzyme intermediate represent two stable states in the double displacement mechanism, and allow thorough examination of the catalytic mechanism. The arabinofuranose sugar is tightly bound and distorted by an extensive network of hydrogen bonds. The two catalytic residues are 4.7 A apart, and together with other conserved residues contribute to the stabilization of the oxocarbenium ion-like transition state via charge delocalization and specific protein-substrate interactions. The enzyme is an anti-protonator, and a 1.7 A electrophilic migration of the anomeric carbon takes place during the hydrolysis.
Crystal structure and snapshots along the reaction pathway of a family 51 alpha-L-arabinofuranosidase.,Hovel K, Shallom D, Niefind K, Belakhov V, Shoham G, Baasov T, Shoham Y, Schomburg D EMBO J. 2003 Oct 1;22(19):4922-32. PMID:14517232<ref>PMID:14517232</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Alpha-N-arabinofuranosidase]]
[[Category: Geobacillus stearothermophilus]]
[[Category: Geobacillus stearothermophilus]]
[[Category: Bassov, T]]
[[Category: Large Structures]]
[[Category: Belakhov, V]]
[[Category: Bassov T]]
[[Category: Hoevel, K]]
[[Category: Belakhov V]]
[[Category: Niefind, K]]
[[Category: Hoevel K]]
[[Category: Schomburg, D]]
[[Category: Niefind K]]
[[Category: Shallom, D]]
[[Category: Schomburg D]]
[[Category: Shoham, G]]
[[Category: Shallom D]]
[[Category: Shoham, Y]]
[[Category: Shoham G]]
[[Category: Hydrolase]]
[[Category: Shoham Y]]

Latest revision as of 11:18, 14 February 2024

Crystal structure of a family 51 alpha-L-arabinofuranosidase in complex with Ara-alpha(1,3)-XylCrystal structure of a family 51 alpha-L-arabinofuranosidase in complex with Ara-alpha(1,3)-Xyl

Structural highlights

1qw8 is a 2 chain structure with sequence from Geobacillus stearothermophilus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.8Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

IABF_GEOSE Involved in the degradation of arabinan and is a key enzyme in the complete degradation of the plant cell wall. Catalyzes the cleavage of terminal alpha-(1->5)-arabinofuranosyl bonds in different hemicellulosic homopolysaccharides (branched and debranched arabinans). It acts preferentially on aryl-alpha-L-arabinofuranosides, and is much less effective on aryl-beta-D-xylopyranosides.[1] [2] [3] [4]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

  1. ↑ Shallom D, Belakhov V, Solomon D, Gilead-Gropper S, Baasov T, Shoham G, Shoham Y. The identification of the acid-base catalyst of alpha-arabinofuranosidase from Geobacillus stearothermophilus T-6, a family 51 glycoside hydrolase. FEBS Lett. 2002 Mar 13;514(2-3):163-7. PMID:11943144
  2. ↑ Shallom D, Belakhov V, Solomon D, Shoham G, Baasov T, Shoham Y. Detailed kinetic analysis and identification of the nucleophile in alpha-L-arabinofuranosidase from Geobacillus stearothermophilus T-6, a family 51 glycoside hydrolase. J Biol Chem. 2002 Nov 15;277(46):43667-73. Epub 2002 Sep 6. PMID:12221104 doi:http://dx.doi.org/10.1074/jbc.M208285200
  3. ↑ Hovel K, Shallom D, Niefind K, Belakhov V, Shoham G, Baasov T, Shoham Y, Schomburg D. Crystal structure and snapshots along the reaction pathway of a family 51 alpha-L-arabinofuranosidase. EMBO J. 2003 Oct 1;22(19):4922-32. PMID:14517232 doi:10.1093/emboj/cdg494
  4. ↑ Gilead S, Shoham Y. Purification and characterization of alpha-L-arabinofuranosidase from Bacillus stearothermophilus T-6. Appl Environ Microbiol. 1995 Jan;61(1):170-4. PMID:7887599

1qw8, resolution 1.80Å

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