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| | ==Structure of PhaZ7 PHB depolymerase in complex with 3HB trimer== | | ==Structure of PhaZ7 PHB depolymerase in complex with 3HB trimer== |
| - | <StructureSection load='4btv' size='340' side='right' caption='[[4btv]], [[Resolution|resolution]] 1.59Å' scene=''> | + | <StructureSection load='4btv' size='340' side='right'caption='[[4btv]], [[Resolution|resolution]] 1.59Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4btv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_17989 Atcc 17989]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BTV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4BTV FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4btv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Paucimonas_lemoignei Paucimonas lemoignei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BTV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4BTV FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=RB3:(1R)-3-{[(1R)-3-METHOXY-1-METHYL-3-OXOPROPYL]OXY}-1-METHYL-3-OXOPROPYL+(3R)-3-HYDROXYBUTANOATE'>RB3</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]] 1.594Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4bvj|4bvj]], [[4bvk|4bvk]], [[4bvl|4bvl]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=RB3:(1R)-3-{[(1R)-3-METHOXY-1-METHYL-3-OXOPROPYL]OXY}-1-METHYL-3-OXOPROPYL+(3R)-3-HYDROXYBUTANOATE'>RB3</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Poly(3-hydroxybutyrate)_depolymerase Poly(3-hydroxybutyrate) depolymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.75 3.1.1.75] </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=4btv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4btv OCA], [https://pdbe.org/4btv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4btv RCSB], [https://www.ebi.ac.uk/pdbsum/4btv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4btv ProSAT]</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=4btv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4btv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4btv RCSB], [http://www.ebi.ac.uk/pdbsum/4btv PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 4btv" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 17989]] | + | [[Category: Large Structures]] |
| - | [[Category: Hermawan, S]] | + | [[Category: Paucimonas lemoignei]] |
| - | [[Category: Jendrossek, D]] | + | [[Category: Hermawan S]] |
| - | [[Category: Papageorgiou, A C]] | + | [[Category: Jendrossek D]] |
| - | [[Category: Subedi, B]] | + | [[Category: Papageorgiou AC]] |
| - | [[Category: Catalytic triad]]
| + | [[Category: Subedi B]] |
| - | [[Category: Hydrolase]]
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| Structural highlights
Publication Abstract from PubMed
Five amino acids (Y105, Y176, Y189, Y189, W207) that constitute the substrate binding site of PHB depolymerase PhaZ7 were identified. All residues are located at a single surface-exposed location of PhaZ7. Exchange of these amino acids by less hydrophobic, hydrophilic or negatively charged residues reduced binding of PhaZ7 to PHB. Modifications of other residues at the PhaZ7 surface (F9, Y66, Y103, Y124, Y169, Y172, Y173, F198, Y203, Y204, F251, W252) had no effect on substrate binding. The PhaZ7 wild type protein, three muteins with single amino acid exchanges (Y105A, Y105E, Y190E), a PhaZ7 variant with deletion of residues 202-208, and PhaZ7 in which the active site serine had been replaced by alanine (S136A) were crystallized and their structures were determined at 1.6 to 2.0 A resolution. The structures were almost identical but revealed flexibility of some regions. Structural analysis of PhaZ7 (S136A) with bound 3-hydroxybutyrate tetramer showed that the substrate binds in a cleft that is composed of Y105, Y176, Y189 and Y190 and thus confirmed the data obtained by site-directed mutagenesis. To the best of our knowledge this is the first example in which the substrate binding site of a PHB depolymerase is documented at a molecular and structural level.
Biochemical Analysis and Structure Determination of Paucimonas lemoignei Poly(3-hydroxybutyrate) (PHB) Depolymerase PhaZ7 Muteins Reveal the PHB Binding Site and Details of Substrate-Enzyme Interactions.,Jendrossek D, Hermawan S, Subedi B, Papageorgiou AC Mol Microbiol. 2013 Sep 5. doi: 10.1111/mmi.12391. PMID:24007310[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Jendrossek D, Hermawan S, Subedi B, Papageorgiou AC. Biochemical Analysis and Structure Determination of Paucimonas lemoignei Poly(3-hydroxybutyrate) (PHB) Depolymerase PhaZ7 Muteins Reveal the PHB Binding Site and Details of Substrate-Enzyme Interactions. Mol Microbiol. 2013 Sep 5. doi: 10.1111/mmi.12391. PMID:24007310 doi:10.1111/mmi.12391
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