4yza: Difference between revisions
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4yza]] 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=4YZA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YZA FirstGlance]. <br> | <table><tr><td colspan='2'>[[4yza]] 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=4YZA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YZA FirstGlance]. <br> | ||
</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=GTR:BETA-D-GALACTOPYRANURONIC+ACID'>GTR</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</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>, <scene name='pdbligand=X1X:ALPHA-D-TALOPYRANURONIC+ACID'>X1X</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]] 1.25Å</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=GTR:BETA-D-GALACTOPYRANURONIC+ACID'>GTR</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</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>, <scene name='pdbligand=X1X:ALPHA-D-TALOPYRANURONIC+ACID'>X1X</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=4yza FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yza OCA], [https://pdbe.org/4yza PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yza RCSB], [https://www.ebi.ac.uk/pdbsum/4yza PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yza 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=4yza FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yza OCA], [https://pdbe.org/4yza PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yza RCSB], [https://www.ebi.ac.uk/pdbsum/4yza PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yza ProSAT]</span></td></tr> | ||
</table> | </table> | ||
Latest revision as of 12:50, 25 December 2024
C. bescii Family 3 pectate lyase double mutant K108A/Q111A in complex with trigalacturonic acidC. bescii Family 3 pectate lyase double mutant K108A/Q111A in complex with trigalacturonic acid
Structural highlights
FunctionPublication Abstract from PubMedThe 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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