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| | <StructureSection load='5mlx' size='340' side='right'caption='[[5mlx]], [[Resolution|resolution]] 1.60Å' scene=''> | | <StructureSection load='5mlx' size='340' side='right'caption='[[5mlx]], [[Resolution|resolution]] 1.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5mlx]] 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=5MLX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MLX FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5mlx]] 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=5MLX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MLX FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.6Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">phaZ7 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29443 ATCC 17989])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></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=5mlx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mlx OCA], [http://pdbe.org/5mlx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mlx RCSB], [http://www.ebi.ac.uk/pdbsum/5mlx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mlx 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=5mlx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mlx OCA], [https://pdbe.org/5mlx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5mlx RCSB], [https://www.ebi.ac.uk/pdbsum/5mlx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5mlx ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q939Q9_PAULE Q939Q9_PAULE] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 17989]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Jendrossek, D]] | + | [[Category: Paucimonas lemoignei]] |
| - | [[Category: Kellici, T]] | + | [[Category: Jendrossek D]] |
| - | [[Category: Mavromoustakos, T]] | + | [[Category: Kellici T]] |
| - | [[Category: Papageorgiou, A C]] | + | [[Category: Mavromoustakos T]] |
| - | [[Category: Biopolymer degradation]] | + | [[Category: Papageorgiou AC]] |
| - | [[Category: Conformational change]]
| + | |
| - | [[Category: Depolymerase]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| Structural highlights
Function
Q939Q9_PAULE
Publication Abstract from PubMed
An open and a closed conformation of a surface loop in PhaZ7 extracellular poly(3-hydroxybutyrate) depolymerase were identified in two high-resolution crystal structures of a PhaZ7 Y105E mutant. Molecular dynamics (MD) simulations revealed high root mean square fluctuations (RMSF) of the 281-295 loop, in particular at residue Asp289 (RMSF 7.62 A). Covalent docking between a 3-hydroxybutyric acid trimer and the catalytic residue Ser136 showed that the binding energy of the substrate is significantly more favorable in the open loop conformation compared to that in the closed loop conformation. MD simulations with the substrate covalently bound depicted 1 A RMSF higher values for the residues 281-295 in comparison to the apo (substrate-free) form. In addition, the presence of the substrate in the active site enhanced the ability of the loop to adopt a closed form. Taken together, the analysis suggests that the flexible loop 281-295 of PhaZ7 depolymerase can act as a lid domain to control substrate access to the active site of the enzyme. Proteins 2017;. (c) 2017 Wiley Periodicals, Inc.
Crystal structure analysis, covalent docking, and molecular dynamics calculations reveal a conformational switch in PhaZ7 PHB depolymerase.,Kellici TF, Mavromoustakos T, Jendrossek D, Papageorgiou AC Proteins. 2017 Apr 3. doi: 10.1002/prot.25296. PMID:28370478[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Kellici TF, Mavromoustakos T, Jendrossek D, Papageorgiou AC. Crystal structure analysis, covalent docking, and molecular dynamics calculations reveal a conformational switch in PhaZ7 PHB depolymerase. Proteins. 2017 Apr 3. doi: 10.1002/prot.25296. PMID:28370478 doi:http://dx.doi.org/10.1002/prot.25296
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