4dhd: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4dhd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrobaculum_calidifontis_JCM_11548 Pyrobaculum calidifontis JCM 11548]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DHD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DHD FirstGlance]. <br>
<table><tr><td colspan='2'>[[4dhd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrobaculum_calidifontis_JCM_11548 Pyrobaculum calidifontis JCM 11548]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DHD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DHD FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.65&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=4dhd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dhd OCA], [https://pdbe.org/4dhd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dhd RCSB], [https://www.ebi.ac.uk/pdbsum/4dhd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dhd 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=4dhd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dhd OCA], [https://pdbe.org/4dhd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dhd RCSB], [https://www.ebi.ac.uk/pdbsum/4dhd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dhd ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/A3MSH1_PYRCJ A3MSH1_PYRCJ]]
[https://www.uniprot.org/uniprot/A3MSH1_PYRCJ A3MSH1_PYRCJ]  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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>
<div class="pdbe-citations 4dhd" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>

Latest revision as of 17:35, 14 March 2024

Crystal structure of isoprenoid synthase A3MSH1 (TARGET EFI-501992) from Pyrobaculum calidifontisCrystal structure of isoprenoid synthase A3MSH1 (TARGET EFI-501992) from Pyrobaculum calidifontis

Structural highlights

4dhd is a 1 chain structure with sequence from Pyrobaculum calidifontis JCM 11548. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.65Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A3MSH1_PYRCJ

4dhd, resolution 1.65Å

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