9ti2: Difference between revisions

Line 1:

~~'''Unreleased structure'''~~

The ~~entry 9ti2~~ is ~~ON HOLD~~

==Crystal structure of the zinc-containing Phosphotriesterase dPTE2-H55(pi)MH==

== Structural highlights ==

<table><tr><td colspan='2'>[[9ti2]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Brevundimonas_diminuta Brevundimonas diminuta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9TI2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9TI2 FirstGlance]. <br>

</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.69Å</td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=MHS:N1-METHYLATED+HISTIDINE'>MHS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=9ti2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9ti2 OCA], [https://pdbe.org/9ti2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9ti2 RCSB], [https://www.ebi.ac.uk/pdbsum/9ti2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9ti2 ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/OPD_BREDI OPD_BREDI] Has an unusual substrate specificity for synthetic organophosphate triesters and phosphorofluoridates. All of the phosphate triesters found to be substrates are synthetic compounds. The identity of any naturally occurring substrate for the enzyme is unknown. Has no detectable activity with phosphate monoesters or diesters and no activity as an esterase or protease. It catalyzes the hydrolysis of the insecticide paraoxon at a rate approaching the diffusion limit and thus appears to be optimally evolved for utilizing this synthetic substrate.

== Publication Abstract from PubMed ==

Hydrolytic metalloenzymes employ Lewis-acidic metal cofactors to activate water molecules, generating nucleophilic hydroxide species that facilitate catalysis. Their catalytic efficiency across a wide pH range is often governed by the protonation state of the metal-bound water, reflected in pK(a) values typically between 6.8 and 9. Modulating this parameter is key to expanding enzymatic activity for improved activity at neutral to acidic pH. Herein, we apply genetic code expansion to mutate the primary metal-coordination sphere of a model metallohydrolase: the dizinc phosphotriesterase from Pseudomonas diminuta. Substitution of the most catalytically indispensable coordinating histidine residue (H55) to N(pi)-methyl-l-histidine (piMH) resulted in substantial enzyme yields, efficient metal coordination for either Zn(2+) or Co(2+), and up to 5-fold improved tolerance to acidic conditions. Detailed mechanistic analysis revealed a systematic decrease in catalytic pK(a) and attenuation of several catalytic rate constants. These results add to the growing body of evidence demonstrating the power of ncAA-based engineering for refined tuning of enzyme properties.

~~Authors~~:

Catalytic pK(a) Attenuation in a Hydrolytic Metalloenzyme by Genetic Code Expansion.,Manser BP, Deliz Liang A Biochemistry. 2026 Feb 18. doi: 10.1021/acs.biochem.5c00768. PMID:41705832<ref>PMID:41705832</ref>

~~Description~~:

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

[[Category: ~~Unreleased~~ Structures]]

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Brevundimonas diminuta]]

[[Category: Large Structures]]

[[Category: Deliz Liang A]]

[[Category: Manser BP]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9ti2 is ON HOLD
+==Crystal structure of the zinc-containing Phosphotriesterase dPTE2-H55(pi)MH==
+<StructureSection load='9ti2' size='340' side='right'caption='[[9ti2]], [[Resolution|resolution]] 1.69&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9ti2]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Brevundimonas_diminuta Brevundimonas diminuta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9TI2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9TI2 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.69&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=MHS:N1-METHYLATED+HISTIDINE'>MHS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=9ti2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9ti2 OCA], [https://pdbe.org/9ti2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9ti2 RCSB], [https://www.ebi.ac.uk/pdbsum/9ti2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9ti2 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/OPD_BREDI OPD_BREDI] Has an unusual substrate specificity for synthetic organophosphate triesters and phosphorofluoridates. All of the phosphate triesters found to be substrates are synthetic compounds. The identity of any naturally occurring substrate for the enzyme is unknown. Has no detectable activity with phosphate monoesters or diesters and no activity as an esterase or protease. It catalyzes the hydrolysis of the insecticide paraoxon at a rate approaching the diffusion limit and thus appears to be optimally evolved for utilizing this synthetic substrate.
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Hydrolytic metalloenzymes employ Lewis-acidic metal cofactors to activate water molecules, generating nucleophilic hydroxide species that facilitate catalysis. Their catalytic efficiency across a wide pH range is often governed by the protonation state of the metal-bound water, reflected in pK(a) values typically between 6.8 and 9. Modulating this parameter is key to expanding enzymatic activity for improved activity at neutral to acidic pH. Herein, we apply genetic code expansion to mutate the primary metal-coordination sphere of a model metallohydrolase: the dizinc phosphotriesterase from Pseudomonas diminuta. Substitution of the most catalytically indispensable coordinating histidine residue (H55) to N(pi)-methyl-l-histidine (piMH) resulted in substantial enzyme yields, efficient metal coordination for either Zn(2+) or Co(2+), and up to 5-fold improved tolerance to acidic conditions. Detailed mechanistic analysis revealed a systematic decrease in catalytic pK(a) and attenuation of several catalytic rate constants. These results add to the growing body of evidence demonstrating the power of ncAA-based engineering for refined tuning of enzyme properties.
-Authors:
+Catalytic pK(a) Attenuation in a Hydrolytic Metalloenzyme by Genetic Code Expansion.,Manser BP, Deliz Liang A Biochemistry. 2026 Feb 18. doi: 10.1021/acs.biochem.5c00768. PMID:41705832<ref>PMID:41705832</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 9ti2" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Brevundimonas diminuta]]
+[[Category: Large Structures]]
+[[Category: Deliz Liang A]]
+[[Category: Manser BP]]