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| | ==Crystal structure of HiLPMO9B== | | ==Crystal structure of HiLPMO9B== |
| - | <StructureSection load='5nns' size='340' side='right' caption='[[5nns]], [[Resolution|resolution]] 2.10Å' scene=''> | + | <StructureSection load='5nns' size='340' side='right'caption='[[5nns]], [[Resolution|resolution]] 2.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5nns]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Heterobasidion_irregulare_tc_32-1 Heterobasidion irregulare tc 32-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NNS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NNS FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5nns]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Heterobasidion_irregulare_TC_32-1 Heterobasidion irregulare TC 32-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NNS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NNS FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKR:ACRYLIC+ACID'>AKR</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 2.1Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GH61B, HETIRDRAFT_166613 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=747525 Heterobasidion irregulare TC 32-1])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKR:ACRYLIC+ACID'>AKR</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></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=5nns FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nns OCA], [http://pdbe.org/5nns PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nns RCSB], [http://www.ebi.ac.uk/pdbsum/5nns PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nns ProSAT]</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=5nns FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nns OCA], [https://pdbe.org/5nns PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5nns RCSB], [https://www.ebi.ac.uk/pdbsum/5nns PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5nns ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/W4KMP1_HETIT W4KMP1_HETIT] Has endoglucanase activity on substrates containing beta-1,4 glycosidic bonds. Involved in the degradation of complex natural cellulosic substrates.[RuleBase:RU368122] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Heterobasidion irregulare tc 32-1]] | + | [[Category: Heterobasidion irregulare TC 32-1]] |
| - | [[Category: Dimarogona, M]] | + | [[Category: Large Structures]] |
| - | [[Category: Sandgren, M]] | + | [[Category: Dimarogona M]] |
| - | [[Category: Aa9]] | + | [[Category: Sandgren M]] |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Lpmo]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Polysaccharide oxidase]]
| + | |
| Structural highlights
5nns is a 2 chain structure with sequence from Heterobasidion irregulare TC 32-1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.1Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
W4KMP1_HETIT Has endoglucanase activity on substrates containing beta-1,4 glycosidic bonds. Involved in the degradation of complex natural cellulosic substrates.[RuleBase:RU368122]
Publication Abstract from PubMed
Lytic polysaccharide monooxygenases (LPMOs) are a group of recently discovered enzymes that play important roles in the decomposition of recalcitrant polysaccharides. Here, we report the biochemical, structural, and computational characterization of an LPMO from the white-rot fungus Heterobasidion irregulare (HiLPMO9B). This enzyme oxidizes cellulose at the C1 carbon of glycosidic linkages. The crystal structure of HiLPMO9B was determined at 2.1 A resolution using X-ray crystallography. Unlike the majority of the currently available C1-specific LPMO structures, the HiLPMO9B structure contains an extended L2 loop, connecting beta-strands beta2 and beta3 of the beta-sandwich structure. Molecular dynamics (MD) simulations suggest roles for both aromatic and acidic residues in the substrate binding of HiLPMO9B, with the main contribution from the residues located on the extended region of the L2 loop (Tyr20) and the LC loop (Asp205, Tyr207, and Glu210). Asp205 and Glu210 were found to be involved in the hydrogen bonding with the hydroxyl group of the C6 carbon of glucose moieties directly or via a water molecule. Two different binding orientations were observed over the course of the MD simulations. In each orientation, the active-site copper of this LPMO preferentially skewed toward the pyranose C1 of the glycosidic linkage over the targeted glycosidic bond. This study provides additional insight into cellulose binding by C1-specific LPMOs, giving a molecular-level picture of active site substrate interactions. DATABASE: The atomic coordinates and structure factors for HiLPMO9B have been deposited in the Protein Data Bank with accession code 5NNS.
Structural and molecular dynamics studies of a C1-oxidizing lytic polysaccharide monooxygenase from Heterobasidion irregulare reveal amino acids important for substrate recognition.,Liu B, Kognole AA, Wu M, Westereng B, Crowley MF, Kim S, Dimarogona M, Payne CM, Sandgren M FEBS J. 2018 Jun;285(12):2225-2242. doi: 10.1111/febs.14472. Epub 2018 Apr 24. PMID:29660793[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Liu B, Kognole AA, Wu M, Westereng B, Crowley MF, Kim S, Dimarogona M, Payne CM, Sandgren M. Structural and molecular dynamics studies of a C1-oxidizing lytic polysaccharide monooxygenase from Heterobasidion irregulare reveal amino acids important for substrate recognition. FEBS J. 2018 Jun;285(12):2225-2242. doi: 10.1111/febs.14472. Epub 2018 Apr 24. PMID:29660793 doi:http://dx.doi.org/10.1111/febs.14472
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