3qas: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
Line 3: Line 3:
<StructureSection load='3qas' size='340' side='right'caption='[[3qas]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
<StructureSection load='3qas' size='340' side='right'caption='[[3qas]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3qas]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QAS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QAS FirstGlance]. <br>
<table><tr><td colspan='2'>[[3qas]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QAS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QAS FirstGlance]. <br>
</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">uppS, ispU, rth, yaeS ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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]] 1.7&#8491;</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ditrans,polycis-undecaprenyl-diphosphate_synthase_((2E,6E)-farnesyl-_diphosphate_specific) Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl- diphosphate specific)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.31 2.5.1.31] </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=3qas FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qas OCA], [https://pdbe.org/3qas PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qas RCSB], [https://www.ebi.ac.uk/pdbsum/3qas PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qas 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=3qas FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qas OCA], [https://pdbe.org/3qas PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qas RCSB], [https://www.ebi.ac.uk/pdbsum/3qas PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qas ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/UPPS_ECOLI UPPS_ECOLI]] Generates ditrans,octacis-undecaprenyl pyrophosphate (UPP) from isopentenyl pyrophosphate (IPP) and farnesyl diphosphate (FPP). UPP is the precursor of glycosyl carrier lipid in the biosynthesis of bacterial cell wall polysaccharide components such as peptidoglycan and lipopolysaccharide.<ref>PMID:12756244</ref> 
[https://www.uniprot.org/uniprot/UPPS_ECOLI UPPS_ECOLI] Generates ditrans,octacis-undecaprenyl pyrophosphate (UPP) from isopentenyl pyrophosphate (IPP) and farnesyl diphosphate (FPP). UPP is the precursor of glycosyl carrier lipid in the biosynthesis of bacterial cell wall polysaccharide components such as peptidoglycan and lipopolysaccharide.<ref>PMID:12756244</ref>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Undecaprenyl pyrophosphate synthase (UPPS) is a cis-prenyltransferase enzyme, which is required for cell-wall biosynthesis in bacteria. UPPS is an attractive target for anti-microbial therapy. We performed long molecular dynamics (MD) simulations and docking studies on UPPS to investigate its dynamic behavior and the influence of protein flexibility on the design of UPPS inhibitors. We also describe the first x-ray crystallographic structure of E. coli apo-UPPS. The MD simulations indicate that UPPS is a highly flexible protein, with mobile binding pockets in the active site. By carrying out docking studies with experimentally validated UPPS inhibitors using high and low populated conformational states extracted from the MD simulations, we show that structurally dissimilar compounds can bind preferentially to different and rarely sampled conformational states. By performing structural analyses on the newly obtained apo-UPPS and other crystal structures previously published, we show that the changes observed during the MD simulation are very similar to those seen in the crystal structures obtained in the presence or absense of ligands. We believe that this is the first time that a rare "expanded pocket" state, a key to drug design and verified by crystallography, has been extracted from an MD simulation.
 
Applying Molecular Dynamics Simulations to Identify Rarely Sampled Ligand-bound Conformational States of Undecaprenyl Pyrophosphate Synthase, an Antibacterial Target.,Sinko W, de Oliveira C, Williams S, Van Wynsberghe A, Durrant JD, Cao R, Oldfield E, Andrew McCammon J Chem Biol Drug Des. 2011 Feb 5. doi: 10.1111/j.1747-0285.2011.01101.x. PMID:21294851<ref>PMID:21294851</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3qas" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Undecaprenyl pyrophosphate synthase|Undecaprenyl pyrophosphate synthase]]
*[[Undecaprenyl pyrophosphate synthase 3D structures|Undecaprenyl pyrophosphate synthase 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Ecoli]]
[[Category: Escherichia coli K-12]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Cao, R]]
[[Category: Cao R]]
[[Category: Oldfield, E]]
[[Category: Oldfield E]]
[[Category: Alpha-helix]]
[[Category: Isoprenoid biosynthesis]]
[[Category: Transferase]]

Latest revision as of 14:38, 14 March 2024

Structure of Undecaprenyl Diphosphate synthaseStructure of Undecaprenyl Diphosphate synthase

Structural highlights

3qas is a 2 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.7Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

UPPS_ECOLI Generates ditrans,octacis-undecaprenyl pyrophosphate (UPP) from isopentenyl pyrophosphate (IPP) and farnesyl diphosphate (FPP). UPP is the precursor of glycosyl carrier lipid in the biosynthesis of bacterial cell wall polysaccharide components such as peptidoglycan and lipopolysaccharide.[1]

See Also

References

  1. ↑ Chang SY, Ko TP, Liang PH, Wang AH. Catalytic mechanism revealed by the crystal structure of undecaprenyl pyrophosphate synthase in complex with sulfate, magnesium, and triton. J Biol Chem. 2003 Aug 1;278(31):29298-307. Epub 2003 May 19. PMID:12756244 doi:10.1074/jbc.M302687200

3qas, resolution 1.70Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=3qas&oldid=4095665"