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.


3p8r

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (10:39, 21 February 2024) (edit) (undo)
 
(2 intermediate revisions not shown.)
Line 1: Line 1:
 +
==CRYSTAL STRUCTURE OF POLYPRENYL SYNTHASE FROM Vibrio cholerae==
==CRYSTAL STRUCTURE OF POLYPRENYL SYNTHASE FROM Vibrio cholerae==
-
<StructureSection load='3p8r' size='340' side='right' caption='[[3p8r]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+
<StructureSection load='3p8r' size='340' side='right'caption='[[3p8r]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3p8r]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Vibrio_cholerae Vibrio cholerae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3P8R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3P8R FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[3p8r]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_cholerae Vibrio cholerae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3P8R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3P8R FirstGlance]. <br>
-
</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">VC_0890 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=666 Vibrio cholerae])</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]] 2.5&#8491;</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=3p8r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3p8r OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3p8r RCSB], [http://www.ebi.ac.uk/pdbsum/3p8r PDBsum]</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=3p8r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3p8r OCA], [https://pdbe.org/3p8r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3p8r RCSB], [https://www.ebi.ac.uk/pdbsum/3p8r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3p8r ProSAT]</span></td></tr>
</table>
</table>
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[https://www.uniprot.org/uniprot/Q9KTL2_VIBCH Q9KTL2_VIBCH]
-
The number of available protein sequences has increased exponentially with the advent of high-throughput genomic sequencing, creating a significant challenge for functional annotation. Here, we describe a large-scale study on assigning function to unknown members of the trans-polyprenyl transferase (E-PTS) subgroup in the isoprenoid synthase superfamily, which provides substrates for the biosynthesis of the more than 55,000 isoprenoid metabolites. Although the mechanism for determining the product chain length for these enzymes is known, there is no simple relationship between function and primary sequence, so that assigning function is challenging. We addressed this challenge through large-scale bioinformatics analysis of &gt;5,000 putative polyprenyl transferases; experimental characterization of the chain-length specificity of 79 diverse members of this group; determination of 27 structures of 19 of these enzymes, including seven cocrystallized with substrate analogs or products; and the development and successful application of a computational approach to predict function that leverages available structural data through homology modeling and docking of possible products into the active site. The crystallographic structures and computational structural models of the enzyme-ligand complexes elucidate the structural basis of specificity. As a result of this study, the percentage of E-PTS sequences similar to functionally annotated ones (BLAST e-value &lt;/= 1e-70) increased from 40.6 to 68.8%, and the percentage of sequences similar to available crystal structures increased from 28.9 to 47.4%. The high accuracy of our blind prediction of newly characterized enzymes indicates the potential to predict function to the complete polyprenyl transferase subgroup of the isoprenoid synthase superfamily computationally.
+
-
 
+
-
Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily.,Wallrapp FH, Pan JJ, Ramamoorthy G, Almonacid DE, Hillerich BS, Seidel R, Patskovsky Y, Babbitt PC, Almo SC, Jacobson MP, Poulter CD Proc Natl Acad Sci U S A. 2013 Mar 14. PMID:23493556<ref>PMID:23493556</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
 +
[[Category: Large Structures]]
[[Category: Vibrio cholerae]]
[[Category: Vibrio cholerae]]
-
[[Category: Almo, S C]]
+
[[Category: Almo SC]]
-
[[Category: Burley, S K]]
+
[[Category: Burley SK]]
-
[[Category: Dickey, M]]
+
[[Category: Dickey M]]
-
[[Category: Gerlt, J A]]
+
[[Category: Gerlt JA]]
-
[[Category: Structural genomic]]
+
[[Category: Patskovsky Y]]
-
[[Category: Patskovsky, Y]]
+
[[Category: Poulter CD]]
-
[[Category: Poulter, C D]]
+
[[Category: Sauder JM]]
-
[[Category: Sauder, J M]]
+
[[Category: Toro R]]
-
[[Category: Toro, R]]
+
-
[[Category: Isoprenyl synthase]]
+
-
[[Category: NYSGXRC, New York SGX Research Center for Structural Genomics]]
+
-
[[Category: Nysgrc]]
+
-
[[Category: PSI, Protein structure initiative]]
+
-
[[Category: Transferase]]
+

Current revision

CRYSTAL STRUCTURE OF POLYPRENYL SYNTHASE FROM Vibrio cholerae

PDB ID 3p8r

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/3p8r"
Personal tools