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| | ==PECTIN LYASE B== | | ==PECTIN LYASE B== |
| - | <StructureSection load='1qcx' size='340' side='right' caption='[[1qcx]], [[Resolution|resolution]] 1.70Å' scene=''> | + | <StructureSection load='1qcx' size='340' side='right'caption='[[1qcx]], [[Resolution|resolution]] 1.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1qcx]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspergillus_niger Aspergillus niger]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QCX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QCX FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1qcx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_niger Aspergillus niger]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QCX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QCX FirstGlance]. <br> |
| - | </td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pectin_lyase Pectin lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.10 4.2.2.10] </span></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]] 1.7Å</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=1qcx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qcx OCA], [http://pdbe.org/1qcx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qcx RCSB], [http://www.ebi.ac.uk/pdbsum/1qcx PDBsum]</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=1qcx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qcx OCA], [https://pdbe.org/1qcx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qcx RCSB], [https://www.ebi.ac.uk/pdbsum/1qcx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qcx ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PELB_ASPNG PELB_ASPNG]] Pectinolytic enzymes consist of four classes of enzymes: pectin lyase, polygalacturonase, pectin methylesterase and rhamnogalacturonase. Among pectinolytic enzymes, pectin lyase is the most important in depolymerization of pectin, since it cleaves internal glycosidic bonds of highly methylated pectins (By similarity). | + | [https://www.uniprot.org/uniprot/PELB_ASPNG PELB_ASPNG] Pectinolytic enzymes consist of four classes of enzymes: pectin lyase, polygalacturonase, pectin methylesterase and rhamnogalacturonase. Among pectinolytic enzymes, pectin lyase is the most important in depolymerization of pectin, since it cleaves internal glycosidic bonds of highly methylated pectins (By similarity). |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qc/1qcx_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qc/1qcx_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Aspergillus niger]] | | [[Category: Aspergillus niger]] |
| - | [[Category: Pectin lyase]] | + | [[Category: Large Structures]] |
| - | [[Category: Jurnak, F]] | + | [[Category: Jurnak F]] |
| - | [[Category: Vitali, J]] | + | [[Category: Vitali J]] |
| - | [[Category: Beta-helix protein]]
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| - | [[Category: Lyase]]
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| - | [[Category: Pectin]]
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| - | [[Category: Plant cell wall]]
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| Structural highlights
Function
PELB_ASPNG Pectinolytic enzymes consist of four classes of enzymes: pectin lyase, polygalacturonase, pectin methylesterase and rhamnogalacturonase. Among pectinolytic enzymes, pectin lyase is the most important in depolymerization of pectin, since it cleaves internal glycosidic bonds of highly methylated pectins (By similarity).
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
The three-dimensional structure of Aspergillus niger pectin lyase B (PLB) has been determined by crystallographic techniques at a resolution of 1.7 A. The model, with all 359 amino acids and 339 water molecules, refines to a final crystallographic R factor of 16.5%. The polypeptide backbone folds into a large right-handed cylinder, termed a parallel beta helix. Loops of various sizes and conformations protrude from the central helix and probably confer function. The largest loop of 53 residues folds into a small domain consisting of three antiparallel beta strands, one turn of an alpha helix, and one turn of a 3(10) helix. By comparison with the structure of Erwinia chrysanthemi pectate lyase C (PelC), the primary sequence alignment between the pectate and pectin lyase subfamilies has been corrected and the active site region for the pectin lyases deduced. The substrate-binding site in PLB is considerably less hydrophilic than the comparable PelC region and consists of an extensive network of highly conserved Trp and His residues. The PLB structure provides an atomic explanation for the lack of a catalytic requirement for Ca2+ in the pectin lyase family, in contrast to that found in the pectate lyase enzymes. Surprisingly, however, the PLB site analogous to the Ca2+ site in PelC is filled with a positive charge provided by a conserved Arg in the pectin lyases. The significance of the finding with regard to the enzymatic mechanism is discussed.
The tree-dimensional structure of aspergillus niger pectin lyase B at 1.7-A resolution.,Vitali J, Schick B, Kester HC, Visser J, Jurnak F Plant Physiol. 1998 Jan;116(1):69-80. PMID:9449837[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Vitali J, Schick B, Kester HC, Visser J, Jurnak F. The tree-dimensional structure of aspergillus niger pectin lyase B at 1.7-A resolution. Plant Physiol. 1998 Jan;116(1):69-80. PMID:9449837
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