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| | ==Structure of diol dehydratase complexed with glycerol== | | ==Structure of diol dehydratase complexed with glycerol== |
| - | <StructureSection load='3auj' size='340' side='right' caption='[[3auj]], [[Resolution|resolution]] 2.10Å' scene=''> | + | <StructureSection load='3auj' size='340' side='right'caption='[[3auj]], [[Resolution|resolution]] 2.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3auj]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_oxytocus_perniciosus"_flugge_1886 "bacillus oxytocus perniciosus" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AUJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3AUJ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3auj]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_oxytocus_perniciosus"_flugge_1886 "bacillus oxytocus perniciosus" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AUJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AUJ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1dio|1dio]], [[1egm|1egm]], [[1egv|1egv]], [[1eex|1eex]], [[1iwb|1iwb]], [[1uc4|1uc4]], [[1uc5|1uc5]]</td></tr> | + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1dio|1dio]], [[1egm|1egm]], [[1egv|1egv]], [[1eex|1eex]], [[1iwb|1iwb]], [[1uc4|1uc4]], [[1uc5|1uc5]]</div></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pddA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=571 "Bacillus oxytocus perniciosus" Flugge 1886]), pddB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=571 "Bacillus oxytocus perniciosus" Flugge 1886]), pddC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=571 "Bacillus oxytocus perniciosus" Flugge 1886])</td></tr> | + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pddA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=571 "Bacillus oxytocus perniciosus" Flugge 1886]), pddB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=571 "Bacillus oxytocus perniciosus" Flugge 1886]), pddC ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=571 "Bacillus oxytocus perniciosus" Flugge 1886])</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Propanediol_dehydratase Propanediol dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.28 4.2.1.28] </span></td></tr> | + | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Propanediol_dehydratase Propanediol dehydratase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.28 4.2.1.28] </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=3auj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3auj OCA], [http://pdbe.org/3auj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3auj RCSB], [http://www.ebi.ac.uk/pdbsum/3auj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3auj 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=3auj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3auj OCA], [https://pdbe.org/3auj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3auj RCSB], [https://www.ebi.ac.uk/pdbsum/3auj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3auj ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Bacillus oxytocus perniciosus flugge 1886]] | | [[Category: Bacillus oxytocus perniciosus flugge 1886]] |
| | + | [[Category: Large Structures]] |
| | [[Category: Propanediol dehydratase]] | | [[Category: Propanediol dehydratase]] |
| | [[Category: Fukuoka, M]] | | [[Category: Fukuoka, M]] |
| Structural highlights
3auj is a 6 chain structure with sequence from "bacillus_oxytocus_perniciosus"_flugge_1886 "bacillus oxytocus perniciosus" flugge 1886. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Ligands: | , , , |
| Related: | |
| Gene: | pddA ("Bacillus oxytocus perniciosus" Flugge 1886), pddB ("Bacillus oxytocus perniciosus" Flugge 1886), pddC ("Bacillus oxytocus perniciosus" Flugge 1886) |
| Activity: | Propanediol dehydratase, with EC number 4.2.1.28 |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Publication Abstract from PubMed
Coenzyme B(12) dependent diol dehydratase undergoes mechanism-based inactivation by glycerol, accompanying the irreversible cleavage of the coenzyme Co-C bond. Bachovchin et al. [Biochemistry16, 1082-1092 (1977)] reported that glycerol bound in the G(S) conformation, in which the pro-S-CH(2) OH group is oriented to the hydrogen-abstracting site, primarily contributes to the inactivation reaction. To understand the mechanism of inactivation by glycerol, we analyzed the X-ray structure of diol dehydratase complexed with cyanocobalamin and glycerol. Glycerol is bound to the active site preferentially in the same conformation as that of (S)-1,2-propanediol, i.e. in the G(S) conformation, with its 3-OH group hydrogen bonded to Seralpha301, but not to nearby Glnalpha336. k(inact) of the Salpha301A, Qalpha336A and Salpha301A/Qalpha336A mutants with glycerol was much smaller than that of the wild-type enzyme. k(cat) /k(inact) showed that the Salpha301A and Qalpha336A mutants are substantially more resistant to glycerol inactivation than the wild-type enzyme, suggesting that Seralpha301 and Glnalpha336 are directly or indirectly involved in the inactivation. The degree of preference for (S)-1,2-propanediol decreased on these mutations. The substrate activities towards longer chain 1,2-diols significantly increased on the Salpha301A/Qalpha336A double mutation, probably because these amino acid substitutions yield more space for accommodating a longer alkyl group on C3 of 1,2-diols. Database Structural data are available in the Protein Data Bank under the accession number 3AUJ. Structured digital abstract * Diol dehydrase gamma subunit, Diol dehydrase beta subunit and Diol dehydrase alpha subunit physically interact by X-ray crystallography (View interaction).
Redesign of coenzyme B(12) dependent diol dehydratase to be resistant to the mechanism-based inactivation by glycerol and act on longer chain 1,2-diols.,Yamanishi M, Kinoshita K, Fukuoka M, Saito T, Tanokuchi A, Ikeda Y, Obayashi H, Mori K, Shibata N, Tobimatsu T, Toraya T FEBS J. 2012 Mar;279(5):793-804. doi: 10.1111/j.1742-4658.2012.08470.x. Epub 2012, Jan 30. PMID:22221669[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Yamanishi M, Kinoshita K, Fukuoka M, Saito T, Tanokuchi A, Ikeda Y, Obayashi H, Mori K, Shibata N, Tobimatsu T, Toraya T. Redesign of coenzyme B(12) dependent diol dehydratase to be resistant to the mechanism-based inactivation by glycerol and act on longer chain 1,2-diols. FEBS J. 2012 Mar;279(5):793-804. doi: 10.1111/j.1742-4658.2012.08470.x. Epub 2012, Jan 30. PMID:22221669 doi:http://dx.doi.org/10.1111/j.1742-4658.2012.08470.x
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