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| | <StructureSection load='4ew9' size='340' side='right'caption='[[4ew9]], [[Resolution|resolution]] 1.60Å' scene=''> | | <StructureSection load='4ew9' size='340' side='right'caption='[[4ew9]], [[Resolution|resolution]] 1.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4ew9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Anaerocellum_thermophilum Anaerocellum thermophilum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EW9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4EW9 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4ew9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Caldicellulosiruptor_bescii_DSM_6725 Caldicellulosiruptor bescii DSM 6725]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EW9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4EW9 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ADA:ALPHA-D-GALACTOPYRANURONIC+ACID'>ADA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DGU:D-GALACTURONIC+ACID'>DGU</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=UNG:4-O-(4-DEOXY-BETA-L-THREO-HEX-4-ENOPYRANURONOSYL)-ALPHA-D-GALACTOPYRANURONIC+ACID'>UNG</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ADA:ALPHA-D-GALACTOPYRANURONIC+ACID'>ADA</scene>, <scene name='pdbligand=AQA:4-DEOXY-BETA-L-THREO-HEX-4-ENOPYRANURONIC+ACID'>AQA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DGU:D-GALACTURONIC+ACID'>DGU</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Athe_1854 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=521460 Anaerocellum thermophilum])</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=4ew9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ew9 OCA], [https://pdbe.org/4ew9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ew9 RCSB], [https://www.ebi.ac.uk/pdbsum/4ew9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ew9 ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pectate_lyase Pectate lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.2 4.2.2.2] </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=4ew9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ew9 OCA], [http://pdbe.org/4ew9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ew9 RCSB], [http://www.ebi.ac.uk/pdbsum/4ew9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ew9 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/B9MKT4_CALBD B9MKT4_CALBD] |
| | <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: Anaerocellum thermophilum]] | + | [[Category: Caldicellulosiruptor bescii DSM 6725]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Pectate lyase]]
| + | [[Category: Alahuhta PM]] |
| - | [[Category: Alahuhta, P M]] | + | [[Category: Lunin VV]] |
| - | [[Category: Lunin, V V]] | + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Parallel beta-helix]]
| + | |
| - | [[Category: Pl3]]
| + | |
| Structural highlights
4ew9 is a 2 chain structure with sequence from Caldicellulosiruptor bescii DSM 6725. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
B9MKT4_CALBD
Publication Abstract from PubMed
The unique active site of the Caldicellulosiruptor bescii family 3 pectate lyase catalytic module (PL3-cat) has been structurally described and synergistic digestion studies with C. bescii cellulase A have been performed on unpretreated biomass. The X-ray structure of PL3-cat was determined at 1.6 A resolution (PDB entry 4ew9) in complex with the products of trigalacturonic acid. Comparison with family 1 pectate lyase (PL1) structures shows that the active site of the PL3 catalytic module is considerably different. However, on superimposing the identical sugar rings at the -2 subsites conserved interactions could be identified. Interestingly, only one catalytic residue, the lysine that donates the proton to the carboxylate group in the beta-elimination reaction of PL1 (Lys108 in PL3-cat), is conserved in PL3 and there is no arginine to abstract the proton from the C5 carbon of the galactouronate ring. This suggests that the reaction mechanism of PL3 requires different catalytic residues. Most interestingly, comparison with other proton-abstraction reactions reveals that in PL3 the alpha-proton is abstracted by a lysine, in a striking similarity to enolases. These observations led us to propose that in PL3-cat Lys108 is the catalytic base, Glu84 is the catalytic acid and an acidified water molecule completes the anti beta-elimination reaction by protonating the O4 atom of the substrate. Also, our digestion experiments with unpretreated switchgrass show that the loadings of C. bescii cellobiohydrolase A (CelA) can be lowered by the addition of PL3 to the reaction mixture. This result suggests that PL3 can significantly improve the deconstruction of unpretreated biomass by allowing other enzymes to better access their preferred substrates.
The structure and mode of action of Caldicellulosiruptor bescii family 3 pectate lyase in biomass deconstruction.,Alahuhta M, Brunecky R, Chandrayan P, Kataeva I, Adams MW, Himmel ME, Lunin VV Acta Crystallogr D Biol Crystallogr. 2013 Apr;69(Pt 4):534-9. doi:, 10.1107/S0907444912050512. Epub 2013 Mar 9. PMID:23519661[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Alahuhta M, Brunecky R, Chandrayan P, Kataeva I, Adams MW, Himmel ME, Lunin VV. The structure and mode of action of Caldicellulosiruptor bescii family 3 pectate lyase in biomass deconstruction. Acta Crystallogr D Biol Crystallogr. 2013 Apr;69(Pt 4):534-9. doi:, 10.1107/S0907444912050512. Epub 2013 Mar 9. PMID:23519661 doi:http://dx.doi.org/10.1107/S0907444912050512
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