6a8i: Difference between revisions

Latest revision as of 09:21, 22 November 2023

Crystal structure of endo-arabinanase ABN-TS D147N mutant in complex with arabinohexaose

Structural highlights

6a8i is a 2 chain structure with sequence from Geobacillus thermodenitrificans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.9Å
Ligands:	AHR, CA
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

IABN_GEOTD Involved in the degradation of arabinan and is a key enzyme in the complete degradation of the plant cell wall. Catalyzes the cleavage of endo alpha-(1->5)-L-arabinofuranosyl residues in debranched arabinan.^[1]

Publication Abstract from PubMed

The thermostable endo-1,5-alpha-L-arabinanase from Bacillus thermodenitrificans TS-3 (ABN-TS) hydrolyzes the alpha-1,5-L-arabinofuranoside linkages of arabinan. In this study, the crystal structures of inactive ABN-TS mutants, D27A and D147N, were determined in complex with arabino-oligosaccharides. The crystal structures revealed that ABN-TS has at least six subsites in the deep V-shaped cleft formed across one face of the propeller structure. The structural features indicate that substrate recognition is profoundly influenced by the remote subsites as well as by the subsites surrounding the active center. The `open' structure of the substrate-binding cleft of the endo-acting ABN-TS is suitable for the random binding of several sugar units in polymeric substrates.

Structures of endo-1,5-alpha-L-arabinanase mutants from Bacillus thermodenitrificans TS-3 in complex with arabino-oligosaccharides.,Yamaguchi A, Sogabe Y, Fukuoka S, Sakai T, Tada T Acta Crystallogr F Struct Biol Commun. 2018 Dec 1;74(Pt 12):774-780. doi:, 10.1107/S2053230X18015947. Epub 2018 Nov 26. PMID:30511671^[2]

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

References

↑ Takao M, Yamaguchi A, Yoshikawa K, Terashita T, Sakai T. Molecular cloning of the gene encoding thermostable endo-1,5-alpha-L-arabinase of Bacillus thermodenitrificans TS-3 and its expression in Bacillus subtilis. Biosci Biotechnol Biochem. 2002 Feb;66(2):430-3. PMID:11999422
↑ Yamaguchi A, Sogabe Y, Fukuoka S, Sakai T, Tada T. Structures of endo-1,5-alpha-L-arabinanase mutants from Bacillus thermodenitrificans TS-3 in complex with arabino-oligosaccharides. Acta Crystallogr F Struct Biol Commun. 2018 Dec 1;74(Pt 12):774-780. doi:, 10.1107/S2053230X18015947. Epub 2018 Nov 26. PMID:30511671 doi:https://dx.doi.org/10.1107/S2053230X18015947

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OCA

[1] Takao M, Yamaguchi A, Yoshikawa K, Terashita T, Sakai T. Molecular cloning of the gene encoding thermostable endo-1,5-alpha-L-arabinase of Bacillus thermodenitrificans TS-3 and its expression in Bacillus subtilis. Biosci Biotechnol Biochem. 2002 Feb;66(2):430-3. PMID:11999422

[2] Yamaguchi A, Sogabe Y, Fukuoka S, Sakai T, Tada T. Structures of endo-1,5-alpha-L-arabinanase mutants from Bacillus thermodenitrificans TS-3 in complex with arabino-oligosaccharides. Acta Crystallogr F Struct Biol Commun. 2018 Dec 1;74(Pt 12):774-780. doi:, 10.1107/S2053230X18015947. Epub 2018 Nov 26. PMID:30511671 doi:https://dx.doi.org/10.1107/S2053230X18015947

[1]

[2]

@@ Line 3: / Line 3: @@
 <StructureSection load='6a8i' size='340' side='right'caption='[[6a8i]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6a8i]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_thermodenitrificans"_klaushofer_and_hollaus_1970 "bacillus thermodenitrificans" klaushofer and hollaus 1970]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A8I OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6A8I FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6a8i]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_thermodenitrificans Geobacillus thermodenitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A8I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6A8I FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=AHR:ALPHA-L-ARABINOFURANOSE'>AHR</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]] 1.9&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">abn-ts ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33940 "Bacillus thermodenitrificans" Klaushofer and Hollaus 1970])</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></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=6a8i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a8i OCA], [https://pdbe.org/6a8i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6a8i RCSB], [https://www.ebi.ac.uk/pdbsum/6a8i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6a8i 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=6a8i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a8i OCA], [http://pdbe.org/6a8i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6a8i RCSB], [http://www.ebi.ac.uk/pdbsum/6a8i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6a8i ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/IABN_GEOTD IABN_GEOTD]] Involved in the degradation of arabinan and is a key enzyme in the complete degradation of the plant cell wall. Catalyzes the cleavage of endo alpha-(1->5)-L-arabinofuranosyl residues in debranched arabinan.<ref>PMID:11999422</ref>
+[https://www.uniprot.org/uniprot/IABN_GEOTD IABN_GEOTD] Involved in the degradation of arabinan and is a key enzyme in the complete degradation of the plant cell wall. Catalyzes the cleavage of endo alpha-(1->5)-L-arabinofuranosyl residues in debranched arabinan.<ref>PMID:11999422</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 27: / Line 26: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus thermodenitrificans klaushofer and hollaus 1970]]
+[[Category: Geobacillus thermodenitrificans]]
-[[Category: Arabinan endo-1,5-alpha-L-arabinosidase]]
 [[Category: Large Structures]]
-[[Category: Tada, T]]
+[[Category: Tada T]]
-[[Category: Yamaguchi, A]]
+[[Category: Yamaguchi A]]
-[[Category: Arabinanase]]
-[[Category: Gh43]]
-[[Category: Glycoside hydrolase]]
-[[Category: Hydrolase]]
-[[Category: Thermostable enzyme]]

6a8i: Difference between revisions

Latest revision as of 09:21, 22 November 2023

Crystal structure of endo-arabinanase ABN-TS D147N mutant in complex with arabinohexaose

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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