6ime: Difference between revisions

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OCA

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-'''Unreleased structure'''
-The entry 6ime is ON HOLD
+==Rv2361c complex with substrate analogues==
+<StructureSection load='6ime' size='340' side='right'caption='[[6ime]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6ime]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IME OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IME FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.55&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=GST:GERANYL+S-THIOLODIPHOSPHATE'>GST</scene>, <scene name='pdbligand=ISY:3-METHYLBUT-3-ENYLSULFANYL(PHOSPHONOOXY)PHOSPHINIC+ACID'>ISY</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=6ime FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ime OCA], [https://pdbe.org/6ime PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ime RCSB], [https://www.ebi.ac.uk/pdbsum/6ime PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ime ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DPDS_MYCTU DPDS_MYCTU] Catalyzes the sequential condensation of isopentenyl diphosphate (IPP) in the cis configuration with (2Z,6E)-farnesyl diphosphate (Z-FPP or EZ-FPP) generating the 50 carbon product trans,polycis-decaprenyl diphosphate. When (2E,6E)-farnesyl diphosphate (E-FPP or EE-FPP) is used in vitro, both primary products decaprenyl diphosphate and (2E,6E,10E)-geranylgeranyl diphosphate (EEE-GGPP) are synthesized. M.tuberculosis does not synthesize (2E,6E,10Z)-geranylgeranyl diphosphate (EEZ-GGPP) and heptaprenyl diphosphate. Can also accept many different allylic substrates, including E-geranyl diphosphate (E-GPP), neryl diphosphate (NPP), and all-trans-geranyl-geranyl diphosphate.<ref>PMID:11004176</ref> <ref>PMID:10816587</ref> <ref>PMID:15516568</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Decaprenyl diphosphate synthase from Mycobacterium tuberculosis (MtDPPS, also known as Rv2361c) catalyzes the consecutive elongation of omega,E,Z-farnesyl diphosphate (EZ-FPP) by seven isoprene units by forming new cis double bonds. The protein folds into a butterfly-like homodimer like most other cis-type prenyltransferases. The starting allylic substrate EZ-FPP is bound to the S1 site and the homoallylic substrate to be incorporated, isopentenyl diphosphate, is bound to the S2 site. Here, a 1.55 A resolution structure of MtDPPS in complex with the substrate analogues geranyl S-thiodiphosphate (GSPP) and isopentenyl S-thiodiphosphate bound to their respective sites in one subunit clearly shows the active-site configuration and the magnesium-coordinated geometry for catalysis. The ligand-binding mode of GSPP in the other subunit indicates a possible pathway of product translocation from the S2 site to the S1 site, as required for the next step of the reaction. The preferred binding of negatively charged effectors to the S1 site also suggests a promising direction for inhibitor design.
-Authors:
+Substrate-analogue complex structure of Mycobacterium tuberculosis decaprenyl diphosphate synthase.,Ko TP, Xiao X, Guo RT, Huang JW, Liu W, Chen CC Acta Crystallogr F Struct Biol Commun. 2019 Apr 1;75(Pt 4):212-216. doi: , 10.1107/S2053230X19001213. Epub 2019 Mar 13. PMID:30950820<ref>PMID:30950820</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 6ime" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Mycobacterium tuberculosis H37Rv]]
+[[Category: Chen C-C]]
+[[Category: Guo R-T]]
+[[Category: Ko T-P]]
+[[Category: Liu W]]