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| | <StructureSection load='3li3' size='340' side='right'caption='[[3li3]], [[Resolution|resolution]] 1.66Å' scene=''> | | <StructureSection load='3li3' size='340' side='right'caption='[[3li3]], [[Resolution|resolution]] 1.66Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3li3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Common_european_squid Common european squid]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LI3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LI3 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3li3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Loligo_vulgaris Loligo vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LI3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LI3 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 1.66Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3li4|3li4]], [[3li5|3li5]]</div></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Diisopropyl-fluorophosphatase Diisopropyl-fluorophosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.8.2 3.1.8.2] </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=3li3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3li3 OCA], [https://pdbe.org/3li3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3li3 RCSB], [https://www.ebi.ac.uk/pdbsum/3li3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3li3 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=3li3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3li3 OCA], [https://pdbe.org/3li3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3li3 RCSB], [https://www.ebi.ac.uk/pdbsum/3li3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3li3 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/DFPA_LOLVU DFPA_LOLVU]] Biological function and substrate unknown. However, it is capable of acting on phosphorus anhydride bonds (such as phosphorus-halide and phosphorus-cyanide) in organophosphorus compounds (including nerve gases).<ref>PMID:15966726</ref>
| + | [https://www.uniprot.org/uniprot/DFPA_LOLVU DFPA_LOLVU] Biological function and substrate unknown. However, it is capable of acting on phosphorus anhydride bonds (such as phosphorus-halide and phosphorus-cyanide) in organophosphorus compounds (including nerve gases).<ref>PMID:15966726</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Common european squid]] | |
| - | [[Category: Diisopropyl-fluorophosphatase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Chen, J C.H]] | + | [[Category: Loligo vulgaris]] |
| - | [[Category: Beta propeller]] | + | [[Category: Chen JC-H]] |
| - | [[Category: Calcium binding]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Phosphotriesterase]]
| + | |
| Structural highlights
Function
DFPA_LOLVU Biological function and substrate unknown. However, it is capable of acting on phosphorus anhydride bonds (such as phosphorus-halide and phosphorus-cyanide) in organophosphorus compounds (including nerve gases).[1]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
The calcium-dependent phosphotriesterase diisopropyl fluorophosphatase (DFPase) from the squid Loligo vulgaris efficiently hydrolyzes a wide range of organophosphorus nerve agents. The two calcium ions within DFPase play essential roles for its function. The lower affinity calcium ion located at the bottom of the active site participates in the reaction mechanism, while the high affinity calcium in the center of the protein maintains structural integrity of the enzyme. The activity and structures of three DFPase variants targeting the catalytic calcium-binding site are reported (D121E, N120D/N175D/D229N, and E21Q/N120D/N175D/D229N), and the effect of these mutations on the overall structural dynamics of DFPase is examined using molecular dynamics simulations. While D229 is crucial for enzymatic activity, E21 is essential for calcium binding. Although at least two negatively charged side chains are required for calcium binding, the addition of a third charge significantly lowers the activity. Furthermore, the arrangement of these charges in the binding site is important for enzymatic activity. These results, together with earlier mutational, structural, and kinetic studies, show a highly evolved calcium-binding environment, with a specific electrostatic topology crucial for activity. A number of structural homologues of DFPase have been recently identified, including a chimeric variant of Paraoxonase 1 (PON1), drug resistance protein 35 (Drp35) from Staphylococcus aureus and the gluconolactonase XC5397 from Xanthomonas campestris. Surprisingly, despite low sequence identity, these proteins share remarkably similar calcium-binding environments to DFPase.
Structural characterization of the catalytic calcium-binding site in diisopropyl fluorophosphatase (DFPase)--comparison with related beta-propeller enzymes.,Blum MM, Chen JC Chem Biol Interact. 2010 Sep 6;187(1-3):373-9. Epub 2010 Mar 3. PMID:20206152[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Katsemi V, Lucke C, Koepke J, Lohr F, Maurer S, Fritzsch G, Ruterjans H. Mutational and structural studies of the diisopropylfluorophosphatase from Loligo vulgaris shed new light on the catalytic mechanism of the enzyme. Biochemistry. 2005 Jun 28;44(25):9022-33. PMID:15966726 doi:10.1021/bi0500675
- ↑ Blum MM, Chen JC. Structural characterization of the catalytic calcium-binding site in diisopropyl fluorophosphatase (DFPase)--comparison with related beta-propeller enzymes. Chem Biol Interact. 2010 Sep 6;187(1-3):373-9. Epub 2010 Mar 3. PMID:20206152 doi:10.1016/j.cbi.2010.02.043
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