3o4p

From Proteopedia

(Difference between revisions)

Revision as of 08:10, 4 November 2020

DFPase at 0.85 Angstrom resolution (H atoms included)

Structural highlights

3o4p is a 1 chain structure with sequence from Common european squid. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , , , , , , ,
Related:	1pjx
Activity:	Diisopropyl-fluorophosphatase, with EC number 3.1.8.2
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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]

Publication Abstract from PubMed

BACKGROUND: Hydrogen atoms represent about half of the total number of atoms in proteins and are often involved in substrate recognition and catalysis. Unfortunately, X-ray protein crystallography at usual resolution fails to access directly their positioning, mainly because light atoms display weak contributions to diffraction. However, sub-Angstrom diffraction data, careful modeling and a proper refinement strategy can allow the positioning of a significant part of hydrogen atoms. RESULTS: A comprehensive study on the X-ray structure of the diisopropyl-fluorophosphatase (DFPase) was performed, and the hydrogen atoms were modeled, including those of solvent molecules. This model was compared to the available neutron structure of DFPase, and differences in the protein and the active site solvation were noticed. CONCLUSIONS: A further examination of the DFPase X-ray structure provides substantial evidence about the presence of an activated water molecule that may constitute an interesting piece of information as regard to the enzymatic hydrolysis mechanism.

Hydrogen atoms in protein structures: high-resolution X-ray diffraction structure of the DFPase.,Elias M, Liebschner D, Koepke J, Lecomte C, Guillot B, Jelsch C, Chabriere E BMC Res Notes. 2013 Aug 2;6:308. doi: 10.1186/1756-0500-6-308. PMID:23915572^[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
↑ Elias M, Liebschner D, Koepke J, Lecomte C, Guillot B, Jelsch C, Chabriere E. Hydrogen atoms in protein structures: high-resolution X-ray diffraction structure of the DFPase. BMC Res Notes. 2013 Aug 2;6:308. doi: 10.1186/1756-0500-6-308. PMID:23915572 doi:10.1186/1756-0500-6-308

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3o4p"

@@ Line 1: / Line 1: @@
 ==DFPase at 0.85 Angstrom resolution (H atoms included)==
-<StructureSection load='3o4p' size='340' side='right' caption='[[3o4p]], [[Resolution|resolution]] 0.85&Aring;' scene=''>
+<StructureSection load='3o4p' size='340' side='right'caption='[[3o4p]], [[Resolution|resolution]] 0.85&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3o4p]] is a 1 chain structure with sequence from [http://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=3O4P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3O4P FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3o4p]] is a 1 chain structure with sequence from [http://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=3O4P OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3O4P FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DXE:1,2-DIMETHOXYETHANE'>DXE</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ME2:1-ETHOXY-2-(2-METHOXYETHOXY)ETHANE'>ME2</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MXE:2-METHOXYETHANOL'>MXE</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
+</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>, <scene name='pdbligand=DXE:1,2-DIMETHOXYETHANE'>DXE</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ME2:1-ETHOXY-2-(2-METHOXYETHOXY)ETHANE'>ME2</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MXE:2-METHOXYETHANOL'>MXE</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1pjx|1pjx]]</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diisopropyl-fluorophosphatase Diisopropyl-fluorophosphatase], with EC number [http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3o4p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o4p OCA], [http://pdbe.org/3o4p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3o4p RCSB], [http://www.ebi.ac.uk/pdbsum/3o4p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3o4p ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3o4p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o4p OCA], [http://pdbe.org/3o4p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3o4p RCSB], [http://www.ebi.ac.uk/pdbsum/3o4p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3o4p ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 26: / Line 26: @@
 [[Category: Common european squid]]
 [[Category: Diisopropyl-fluorophosphatase]]
+[[Category: Large Structures]]
 [[Category: Chabriere, E]]
 [[Category: Elias, M]]

3o4p

From Proteopedia

Revision as of 08:10, 4 November 2020

DFPase at 0.85 Angstrom resolution (H atoms included)

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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