1jp3: Difference between revisions

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<StructureSection load='1jp3' size='340' side='right'caption='[[1jp3]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
<StructureSection load='1jp3' size='340' side='right'caption='[[1jp3]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1jp3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JP3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JP3 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1jp3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JP3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JP3 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EGC:2-(2-{2-[2-(2-{2-[2-(2-{2-[4-(1,1,3,3-TETRAMETHYL-BUTYL)-PHENOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL'>EGC</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]] 1.8&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><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=EGC:2-(2-{2-[2-(2-{2-[2-(2-{2-[4-(1,1,3,3-TETRAMETHYL-BUTYL)-PHENOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL'>EGC</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=1jp3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jp3 OCA], [https://pdbe.org/1jp3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jp3 RCSB], [https://www.ebi.ac.uk/pdbsum/1jp3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jp3 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=1jp3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jp3 OCA], [https://pdbe.org/1jp3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jp3 RCSB], [https://www.ebi.ac.uk/pdbsum/1jp3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jp3 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>  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1jp3 ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1jp3 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The Escherichia coli undecaprayl-pyrophosphate synthase (UPPs) structure has been solved using the single wavelength anomalous diffraction method. The putative substrate-binding site is located near the end of the betaA-strand with Asp-26 playing a critical catalytic role. In both subunits, an elongated hydrophobic tunnel is found, surrounded by four beta-strands (betaA-betaB-betaD-betaC) and two helices (alpha2 and alpha3) and lined at the bottom with large residues Ile-62, Leu-137, Val-105, and His-103. The product distributions formed by the use of the I62A, V105A, and H103A mutants are similar to those observed for wild-type UPPs. Catalysis by the L137A UPPs, on the other hand, results in predominantly the formation of the C(70) polymer rather than the C(55) polymer. Ala-69 and Ala-143 are located near the top of the tunnel. In contrast to the A143V reaction, the C(30) intermediate is formed to a greater extent and is longer lived in the process catalyzed by the A69L mutant. These findings suggest that the small side chain of Ala-69 is required for rapid elongation to the C(55) product, whereas the large hydrophobic side chain of Leu-137 is required to limit the elongation to the C(55) product. The roles of residues located on a flexible loop were investigated. The S71A, N74A, or R77A mutants displayed 25-200-fold decrease in k(cat) values. W75A showed an 8-fold increase of the FPP K(m) value, and 22-33-fold increases in the IPP K(m) values were observed for E81A and S71A. The loop may function to bridge the interaction of IPP with FPP, needed to initiate the condensation reaction and serve as a hinge to control the substrate binding and product release.
Mechanism of product chain length determination and the role of a flexible loop in Escherichia coli undecaprenyl-pyrophosphate synthase catalysis.,Ko TP, Chen YK, Robinson H, Tsai PC, Gao YG, Chen AP, Wang AH, Liang PH J Biol Chem. 2001 Dec 14;276(50):47474-82. Epub 2001 Oct 1. PMID:11581264<ref>PMID:11581264</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1jp3" 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: Bacillus coli migula 1895]]
[[Category: Escherichia coli]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Chen, A P.C]]
[[Category: Chen APC]]
[[Category: Chen, Y K]]
[[Category: Chen YK]]
[[Category: Gao, Y G]]
[[Category: Gao YG]]
[[Category: Ko, T P]]
[[Category: Ko TP]]
[[Category: Liang, P H]]
[[Category: Liang PH]]
[[Category: Robinson, H]]
[[Category: Robinson H]]
[[Category: Tsai, P C]]
[[Category: Tsai PC]]
[[Category: Wang, A H.J]]
[[Category: Wang AHJ]]
[[Category: Flexible loop]]
[[Category: Hydrophobic tunnel]]
[[Category: Product chain length]]
[[Category: Rossmann fold]]
[[Category: Transferase]]
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