4z06: Difference between revisions

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 ==C. bescii Family 3 pectate lyase double mutant K108A/R133A in complex with ALPHA-D-GALACTOPYRANURONIC ACID==
-<StructureSection load='4z06' size='340' side='right' caption='[[4z06]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
+<StructureSection load='4z06' size='340' side='right'caption='[[4z06]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4z06]] 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=4Z06 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Z06 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4z06]] 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=4Z06 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Z06 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADA:ALPHA-D-GALACTOPYRANURONIC+ACID'>ADA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</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]] 1.55&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4yz0|4yz0]], [[4yza|4yza]], [[4yzq|4yzq]], [[4yzx|4yzx]], [[4z03|4z03]], [[4z05|4z05]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADA:ALPHA-D-GALACTOPYRANURONIC+ACID'>ADA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</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=4z06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4z06 OCA], [https://pdbe.org/4z06 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4z06 RCSB], [https://www.ebi.ac.uk/pdbsum/4z06 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4z06 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=4z06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4z06 OCA], [http://pdbe.org/4z06 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4z06 RCSB], [http://www.ebi.ac.uk/pdbsum/4z06 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4z06 ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/B9MKT4_CALBD B9MKT4_CALBD]
-The unique active site of the Caldicellulosiruptor bescii family 3 pectate lyase (PL3) enzyme has been thoroughly characterized using a series of point mutations, X-ray crystallography, pK(a) calculations and biochemical assays. The X-ray structures of seven PL3 active-site mutants, five of them in complex with intact trigalacturonic acid, were solved and characterized structurally, biochemically and computationally. The results confirmed that Lys108 is the catalytic base, but there is no clear candidate for the catalytic acid. However, the reaction mechanism can also be explained by an antiperiplanar trans-elimination reaction, in which Lys108 abstracts a proton from the C5 atom without the help of simultaneous proton donation by an acidic residue. An acidified water molecule completes the anti beta-elimination reaction by protonating the O4 atom of the substrate. Both the C5 hydrogen and C4 hydroxyl groups of the substrate must be orientated in axial configurations, as for galacturonic acid, for this to be possible. The wild-type C. bescii PL3 displays a pH optimum that is lower than that of Bacillus subtilis PL1 according to activity measurements, indicating that C. bescii PL3 has acquired a lower pH optimum by utilizing lysine instead of arginine as the catalytic base, as well as by lowering the pK(a) of the catalytic base in a unique active-site environment.
-The catalytic mechanism and unique low pH optimum of Caldicellulosiruptor bescii family 3 pectate lyase.,Alahuhta M, Taylor LE 2nd, Brunecky R, Sammond DW, Michener W, Adams MW, Himmel ME, Bomble YJ, Lunin V Acta Crystallogr D Biol Crystallogr. 2015 Sep;71(Pt 9):1946-54. doi:, 10.1107/S1399004715013760. Epub 2015 Aug 25. PMID:26327384<ref>PMID:26327384</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 4z06" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Anaerocellum thermophilum]]
+[[Category: Caldicellulosiruptor bescii DSM 6725]]
-[[Category: Pectate lyase]]
+[[Category: Large Structures]]
-[[Category: Alahuhta, P M]]
+[[Category: Alahuhta PM]]
-[[Category: Lunin, V V]]
+[[Category: Lunin VV]]
-[[Category: Lyase]]
-[[Category: Parallel beta-helix]]
-[[Category: Pl3]]