6jfj
From Proteopedia
(Difference between revisions)
| (One intermediate revision not shown.) | |||
| Line 3: | Line 3: | ||
<StructureSection load='6jfj' size='340' side='right'caption='[[6jfj]], [[Resolution|resolution]] 1.93Å' scene=''> | <StructureSection load='6jfj' size='340' side='right'caption='[[6jfj]], [[Resolution|resolution]] 1.93Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[6jfj]] is a 1 chain structure with sequence from [ | + | <table><tr><td colspan='2'>[[6jfj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Paenibacillus_barengoltzii Paenibacillus barengoltzii]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5ww2 5ww2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JFJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JFJ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand= | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.932Å</td></tr> |
| - | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PRD_900009:alpha-maltotriose'>PRD_900009</scene>, <scene name='pdbligand=PRD_900030:alpha-maltopentaose'>PRD_900030</scene>, <scene name='pdbligand=TAM:TRIS(HYDROXYETHYL)AMINOMETHANE'>TAM</scene></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=6jfj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jfj OCA], [https://pdbe.org/6jfj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jfj RCSB], [https://www.ebi.ac.uk/pdbsum/6jfj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jfj ProSAT]</span></td></tr> | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | |
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/A0A0C5GWS2_9BACL A0A0C5GWS2_9BACL] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Pullulanase (EC 3.2.1.41) is a well known starch-debranching enzyme that catalyzes the cleavage of alpha-1,6-glycosidic linkages in alpha-glucans such as starch and pullulan. Crystal structures of a type I pullulanase from Paenibacillus barengoltzii (PbPulA) and of PbPulA in complex with maltopentaose (G5), maltohexaose (G6)/alpha-cyclodextrin (alpha-CD) and beta-cyclodextrin (beta-CD) were determined in order to better understand substrate binding to this enzyme. PbPulA belongs to glycoside hydrolase (GH) family 13 subfamily 14 and is composed of three domains (CBM48, A and C). Three carbohydrate-binding sites identified in PbPulA were located in CBM48, near the active site and in domain C, respectively. The binding site in CBM48 was specific for beta-CD, while that in domain C has not been reported for other pullulanases. The domain C binding site had higher affinity for alpha-CD than for G6; a small motif (FGGEH) seemed to be one of the major determinants for carbohydrate binding in this domain. Structure-based mutations of several surface-exposed aromatic residues in CBM48 and domain C had a debilitating effect on the activity of the enzyme. These results suggest that both CBM48 and domain C play a role in binding substrates. The crystal forms described contribute to the understanding of pullulanase domain-carbohydrate interactions. | ||
| + | |||
| + | Structural basis of carbohydrate binding in domain C of a type I pullulanase from Paenibacillus barengoltzii.,Huang P, Wu S, Yang S, Yan Q, Jiang Z Acta Crystallogr D Struct Biol. 2020 May 1;76(Pt 5):447-457. doi:, 10.1107/S205979832000409X. Epub 2020 Apr 23. PMID:32355041<ref>PMID:32355041</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 6jfj" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: Atcc baa-1209]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: | + | [[Category: Paenibacillus barengoltzii]] |
| - | [[Category: Huang | + | [[Category: Huang P]] |
| - | [[Category: Jiang | + | [[Category: Jiang ZQ]] |
| - | [[Category: Qin | + | [[Category: Qin Z]] |
| - | [[Category: Wu | + | [[Category: Wu SW]] |
| - | [[Category: Yang | + | [[Category: Yang SQ]] |
| - | [[Category: You | + | [[Category: You X]] |
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
Current revision
Crystal structure of Pullulanase from Paenibacillus barengoltzii complex with maltohexaose and alpha-cyclodextrin
| |||||||||||
Categories: Large Structures | Paenibacillus barengoltzii | Huang P | Jiang ZQ | Qin Z | Wu SW | Yang SQ | You X
