This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


3t1g

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (13:14, 14 March 2024) (edit) (undo)
 
Line 3: Line 3:
<StructureSection load='3t1g' size='340' side='right'caption='[[3t1g]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
<StructureSection load='3t1g' size='340' side='right'caption='[[3t1g]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3t1g]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T1G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3T1G FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[3t1g]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T1G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3T1G 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>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.35&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1a4l|1a4l]]</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>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Adenosine deaminase, ADA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</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=3t1g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t1g OCA], [https://pdbe.org/3t1g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3t1g RCSB], [https://www.ebi.ac.uk/pdbsum/3t1g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3t1g 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=3t1g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t1g OCA], [https://pdbe.org/3t1g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3t1g RCSB], [https://www.ebi.ac.uk/pdbsum/3t1g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3t1g ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
-
[[https://www.uniprot.org/uniprot/ADA_MOUSE ADA_MOUSE]] Catalyzes the hydrolytic deamination of adenosine and 2-deoxyadenosine. Plays an important role in purine metabolism and in adenosine homeostasis. Modulates signaling by extracellular adenosine, and so contributes indirectly to cellular signaling events. Acts as a positive regulator of T-cell coactivation, by binding DPP4. Its interaction with DPP4 regulates lymphocyte-epithelial cell adhesion (By similarity).
+
[https://www.uniprot.org/uniprot/ADA_MOUSE ADA_MOUSE] Catalyzes the hydrolytic deamination of adenosine and 2-deoxyadenosine. Plays an important role in purine metabolism and in adenosine homeostasis. Modulates signaling by extracellular adenosine, and so contributes indirectly to cellular signaling events. Acts as a positive regulator of T-cell coactivation, by binding DPP4. Its interaction with DPP4 regulates lymphocyte-epithelial cell adhesion (By similarity).
-
<div style="background-color:#fffaf0;">
+
-
== Publication Abstract from PubMed ==
+
-
The ability to redesign enzymes to catalyze noncognate chemical transformations would have wide-ranging applications. We developed a computational method for repurposing the reactivity of metalloenzyme active site functional groups to catalyze new reactions. Using this method, we engineered a zinc-containing mouse adenosine deaminase to catalyze the hydrolysis of a model organophosphate with a catalytic efficiency (k(cat)/K(m)) of approximately 10(4) M(-1) s(-1) after directed evolution. In the high-resolution crystal structure of the enzyme, all but one of the designed residues adopt the designed conformation. The designed enzyme efficiently catalyzes the hydrolysis of the R(P) isomer of a coumarinyl analog of the nerve agent cyclosarin, and it shows marked substrate selectivity for coumarinyl leaving groups. Computational redesign of native enzyme active sites complements directed evolution methods and offers a general approach for exploring their untapped catalytic potential for new reactivities.
+
-
 
+
-
Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis.,Khare SD, Kipnis Y, Greisen PJ, Takeuchi R, Ashani Y, Goldsmith M, Song Y, Gallaher JL, Silman I, Leader H, Sussman JL, Stoddard BL, Tawfik DS, Baker D Nat Chem Biol. 2012 Feb 5;8(3):294-300. doi: 10.1038/nchembio.777. PMID:22306579<ref>PMID:22306579</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 3t1g" style="background-color:#fffaf0;"></div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
-
[[Category: Lk3 transgenic mice]]
+
[[Category: Mus musculus]]
-
[[Category: Stoddard, B L]]
+
[[Category: Stoddard BL]]
-
[[Category: Takeuchi, R]]
+
[[Category: Takeuchi R]]
-
[[Category: Artificial enzyme]]
+
-
[[Category: Computational design]]
+
-
[[Category: Directed evolution]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: Hydrolysis]]
+
-
[[Category: Metallo-dependent hydrolase]]
+
-
[[Category: Organophosphate binding]]
+
-
[[Category: Tim beta/alpha-barrel]]
+

Current revision

Engineering of organophosphate hydrolase by computational design and directed evolution

PDB ID 3t1g

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3t1g"
Personal tools