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.

1qw9

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 13:12, 16 December 2020

Crystal structure of a family 51 alpha-L-arabinofuranosidase in complex with 4-nitrophenyl-Ara

Structural highlights

1qw9 is a 2 chain structure with sequence from Atcc 12980. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	1pz3, 1pz2, 1qw8
Gene:	ABFA (ATCC 12980)
Activity:	Non-reducing end alpha-L-arabinofuranosidase, with EC number 3.2.1.55
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.

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^[5]

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

References

↑ 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
↑ 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
↑ 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
↑ 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
↑ 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

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/1qw9"

@@ Line 1: / Line 1: @@
 ==Crystal structure of a family 51 alpha-L-arabinofuranosidase in complex with 4-nitrophenyl-Ara==
-<StructureSection load='1qw9' size='340' side='right' caption='[[1qw9]], [[Resolution|resolution]] 1.20&Aring;' scene=''>
+<StructureSection load='1qw9' size='340' side='right'caption='[[1qw9]], [[Resolution|resolution]] 1.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1qw9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QW9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QW9 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1qw9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QW9 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1QW9 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=KHP:2-HYDROXYMETHYL-5-(4-NITRO-PHENOXY)-TETRAHYDRO-FURAN-3,4-DIOL'>KHP</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=KHP:2-HYDROXYMETHYL-5-(4-NITRO-PHENOXY)-TETRAHYDRO-FURAN-3,4-DIOL'>KHP</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1pz3|1pz3]], [[1pz2|1pz2]], [[1qw8|1qw8]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1pz3|1pz3]], [[1pz2|1pz2]], [[1qw8|1qw8]]</div></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 ATCC 12980])</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1qw9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qw9 OCA], [http://pdbe.org/1qw9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qw9 RCSB], [http://www.ebi.ac.uk/pdbsum/1qw9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1qw9 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=1qw9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qw9 OCA], [http://pdbe.org/1qw9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qw9 RCSB], [http://www.ebi.ac.uk/pdbsum/1qw9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1qw9 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 36: / Line 36: @@
 </StructureSection>
 [[Category: Atcc 12980]]
+[[Category: Large Structures]]
 [[Category: Non-reducing end alpha-L-arabinofuranosidase]]
 [[Category: Bassov, T]]

1qw9

From Proteopedia

Revision as of 13:12, 16 December 2020

Crystal structure of a family 51 alpha-L-arabinofuranosidase in complex with 4-nitrophenyl-Ara

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox