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3d61

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Revision as of 21:37, 5 August 2016

Crystal Structure Analysis of 1,5-alpha-arabinanase catalytic mutant (AbnBD147A) complexed to arabinobiose

Structural highlights

3d61 is a 1 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:	3cu9, 3d5y, 3d5z, 3d60
Gene:	abn (ATCC 12980)
Activity:	Arabinan endo-1,5-alpha-L-arabinosidase, with EC number 3.2.1.99
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[IABN_GEOSE] 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 debranched arabinan, linear arabinan and short arabino-oligosaccharides (degree of polymerization from 2 to 8). It exhibits marginal activity toward sugar beet arabinan.^[1]

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

Arabinanases are glycosidases that hydrolyse alpha-(1-->5)- arabinofuranosidic linkages found in the backbone of the pectic polysaccharide arabinan. Here we describe the biochemical characterization and the enzyme-substrate crystal structure of an inverting family 43 arabinanase from Geobacillus stearothermophilus T-6 (AbnB). Based on viscosity and reducing power measurements, and based on product analysis for the hydrolysis of linear arabinan by AbnB, the enzyme works in an endo mode of action. Isothermal titration calorimetry studies of a catalytic mutant with various arabino-oligosaccharides suggested that the enzyme active site can accommodate at least five arabinose units. The crystal structure of AbnB was determined at 1.06 A (1 A=0.1 nm) resolution, revealing a single five-bladed-beta-propeller fold domain. Co-crystallization of catalytic mutants of the enzyme with different substrates allowed us to obtain complex structures of AbnBE201A with arabinotriose and AbnBD147A with arabinobiose. Based on the crystal structures of AbnB together with its substrates, the position of the three catalytic carboxylates: Asp27, the general base; Glu201, the general acid; and Asp147, the pKa modulator, is in agreement with their putative catalytic roles. In the complex structure of AbnBE201A with arabinotriose, a single water molecule is located 2.8 A from Asp27 and 3.7 A from the anomeric carbon. The position of this water molecule is kept via hydrogen bonding with a conserved tyrosine (Tyr229) that is 2.6 A distant from it. The location of this molecule suggests that it can function as the catalytic water molecule in the hydrolysis reaction, resulting in the inversion of the anomeric configuration of the product.

Crystal structure of an inverting GH 43 1,5-alpha-L-arabinanase from Geobacillus stearothermophilus complexed with its substrate.,Alhassid A, Ben-David A, Tabachnikov O, Libster D, Naveh E, Zolotnitsky G, Shoham Y, Shoham G Biochem J. 2009 Jul 29;422(1):73-82. PMID:19505290^[2]

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

References

↑ Alhassid A, Ben-David A, Tabachnikov O, Libster D, Naveh E, Zolotnitsky G, Shoham Y, Shoham G. Crystal structure of an inverting GH 43 1,5-alpha-L-arabinanase from Geobacillus stearothermophilus complexed with its substrate. Biochem J. 2009 Jul 29;422(1):73-82. PMID:19505290 doi:10.1042/BJ20090180
↑ Alhassid A, Ben-David A, Tabachnikov O, Libster D, Naveh E, Zolotnitsky G, Shoham Y, Shoham G. Crystal structure of an inverting GH 43 1,5-alpha-L-arabinanase from Geobacillus stearothermophilus complexed with its substrate. Biochem J. 2009 Jul 29;422(1):73-82. PMID:19505290 doi:10.1042/BJ20090180

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3d61"

@@ Line 1: / Line 1: @@
 ==Crystal Structure Analysis of 1,5-alpha-arabinanase catalytic mutant (AbnBD147A) complexed to arabinobiose==
 <StructureSection load='3d61' size='340' side='right' caption='[[3d61]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3d61]] is a 1 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=3D61 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3D61 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3d61]] is a 1 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=3D61 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3D61 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=AHR:ALPHA-L-ARABINOFURANOSE'>AHR</scene>, <scene name='pdbligand=FUB:BETA-L-ARABINOFURANOSE'>FUB</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3cu9|3cu9]], [[3d5y|3d5y]], [[3d5z|3d5z]], [[3d60|3d60]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">abn ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 Geobacillus stearothermophilus])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">abn ([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/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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3d61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d61 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3d61 RCSB], [http://www.ebi.ac.uk/pdbsum/3d61 PDBsum]</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=3d61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d61 OCA], [http://pdbe.org/3d61 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3d61 RCSB], [http://www.ebi.ac.uk/pdbsum/3d61 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3d61 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/B3EYM8_BACST B3EYM8_BACST]] 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 debranched arabinan, linear arabinan and short arabino-oligosaccharides (degree of polymerization from 2 to 8). It exhibits marginal activity toward sugar beet arabinan.<ref>PMID:19505290</ref>
+[[http://www.uniprot.org/uniprot/IABN_GEOSE IABN_GEOSE]] 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 debranched arabinan, linear arabinan and short arabino-oligosaccharides (degree of polymerization from 2 to 8). It exhibits marginal activity toward sugar beet arabinan.<ref>PMID:19505290</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 19: / Line 20: @@
     <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].
+</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=3d61 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 29: / Line 30: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3d61" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 37: / Line 39: @@
 </StructureSection>
 [[Category: Arabinan endo-1,5-alpha-L-arabinosidase]]
-[[Category: Geobacillus stearothermophilus]]
+[[Category: Atcc 12980]]
 [[Category: Alhassid, A]]
 [[Category: David, A Ben]]
@@ Line 44: / Line 46: @@
 [[Category: Arabinanase]]
 [[Category: Beta-propeller]]
+[[Category: Geobacillus stearothermophilus]]
 [[Category: Glycosyl hydrolase]]
 [[Category: Hydrolase]]

3d61

From Proteopedia

Revision as of 21:37, 5 August 2016

Crystal Structure Analysis of 1,5-alpha-arabinanase catalytic mutant (AbnBD147A) complexed to arabinobiose

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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