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.


4f2v

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (15:14, 14 March 2024) (edit) (undo)
 
(2 intermediate revisions not shown.)
Line 3: Line 3:
<StructureSection load='4f2v' size='340' side='right'caption='[[4f2v]], [[Resolution|resolution]] 2.49&Aring;' scene=''>
<StructureSection load='4f2v' size='340' side='right'caption='[[4f2v]], [[Resolution|resolution]] 2.49&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[4f2v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4F2V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4F2V FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[4f2v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4F2V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4F2V FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LMU:DODECYL-ALPHA-D-MALTOSIDE'>LMU</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 2.493&#8491;</td></tr>
-
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CXM:N-CARBOXYMETHIONINE'>CXM</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CXM:N-CARBOXYMETHIONINE'>CXM</scene>, <scene name='pdbligand=LMU:DODECYL-ALPHA-D-MALTOSIDE'>LMU</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1bq2|1bq2]]</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=4f2v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4f2v OCA], [https://pdbe.org/4f2v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4f2v RCSB], [https://www.ebi.ac.uk/pdbsum/4f2v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4f2v ProSAT]</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=4f2v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4f2v OCA], [http://pdbe.org/4f2v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4f2v RCSB], [http://www.ebi.ac.uk/pdbsum/4f2v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4f2v ProSAT]</span></td></tr>
+
</table>
</table>
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[https://www.uniprot.org/uniprot/TYSY_ECOLI TYSY_ECOLI] Provides the sole de novo source of dTMP for DNA biosynthesis. This protein also binds to its mRNA thus repressing its own translation.
-
A challenge in the computational design of enzymes is that multiple properties, including substrate binding, transition state stabilization and product release, must be simultaneously optimized, and this has limited the absolute activity of successful designs. Here, we focus on a single critical property of many enzymes: the nucleophilicity of an active site residue that initiates catalysis. We design proteins with idealized serine-containing catalytic triads and assess their nucleophilicity directly in native biological systems using activity-based organophosphate probes. Crystal structures of the most successful designs show unprecedented agreement with computational models, including extensive hydrogen bonding networks between the catalytic triad (or quartet) residues, and mutagenesis experiments demonstrate that these networks are critical for serine activation and organophosphate reactivity. Following optimization by yeast display, the designs react with organophosphate probes at rates comparable to natural serine hydrolases. Co-crystal structures with diisopropyl fluorophosphate bound to the serine nucleophile suggest that the designs could provide the basis for a new class of organophosphate capture agents.
+
-
 
+
-
Design of activated serine-containing catalytic triads with atomic-level accuracy.,Rajagopalan S, Wang C, Yu K, Kuzin AP, Richter F, Lew S, Miklos AE, Matthews ML, Seetharaman J, Su M, Hunt JF, Cravatt BF, Baker D Nat Chem Biol. 2014 Apr 6. doi: 10.1038/nchembio.1498. PMID:24705591<ref>PMID:24705591</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 4f2v" style="background-color:#fffaf0;"></div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
-
[[Category: Synthetic construct sequences]]
+
[[Category: Synthetic construct]]
-
[[Category: Acton, T B]]
+
[[Category: Acton TB]]
-
[[Category: Everett, J K]]
+
[[Category: Everett JK]]
-
[[Category: Hunt, J F]]
+
[[Category: Hunt JF]]
-
[[Category: Kohan, E]]
+
[[Category: Kohan E]]
-
[[Category: Kuzin, A]]
+
[[Category: Kuzin A]]
-
[[Category: Lew, S]]
+
[[Category: Lew S]]
-
[[Category: Maglaqui, M]]
+
[[Category: Maglaqui M]]
-
[[Category: Montelione, G T]]
+
[[Category: Montelione GT]]
-
[[Category: Structural genomic]]
+
[[Category: Rajagopalan S]]
-
[[Category: Rajagopalan, S]]
+
[[Category: Seetharaman J]]
-
[[Category: Seetharaman, J]]
+
[[Category: Tong L]]
-
[[Category: Tong, L]]
+
[[Category: Xiao R]]
-
[[Category: Xiao, R]]
+
-
[[Category: De novo design]]
+
-
[[Category: De novo protein]]
+
-
[[Category: Nesg]]
+
-
[[Category: PSI, Protein structure initiative]]
+
-
[[Category: Psi-biology]]
+

Current revision

Crystal Structure of de novo designed serine hydrolase, Northeast Structural Genomics Consortium (NESG) Target OR165

PDB ID 4f2v

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/4f2v"
Personal tools