3q8h: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
==Crystal structure of 2c-methyl-d-erythritol 2,4-cyclodiphosphate synthase from burkholderia pseudomallei in complex with cytidine derivative EBSI01028== | ==Crystal structure of 2c-methyl-d-erythritol 2,4-cyclodiphosphate synthase from burkholderia pseudomallei in complex with cytidine derivative EBSI01028== | ||
<StructureSection load='3q8h' size='340' side='right' caption='[[3q8h]], [[Resolution|resolution]] 1.75Å' scene=''> | <StructureSection load='3q8h' size='340' side='right'caption='[[3q8h]], [[Resolution|resolution]] 1.75Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3q8h]] is a 3 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3q8h]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_pseudomallei"_whitmore_1913 "bacillus pseudomallei" whitmore 1913]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3Q8H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3Q8H FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AO9:5-DEOXY-5-[(IMIDAZO[2,1-B][1,3]THIAZOL-5-YLCARBONYL)AMINO]CYTIDINE'>AO9</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AO9:5-DEOXY-5-[(IMIDAZO[2,1-B][1,3]THIAZOL-5-YLCARBONYL)AMINO]CYTIDINE'>AO9</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3f0d|3f0d]], [[3ikf|3ikf]], [[3ike|3ike]], [[3ieq|3ieq]], [[3ke1|3ke1]], [[3mbm|3mbm]], [[3p0z|3p0z]], [[3jvh|3jvh]], [[3k14|3k14]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3f0d|3f0d]], [[3ikf|3ikf]], [[3ike|3ike]], [[3ieq|3ieq]], [[3ke1|3ke1]], [[3mbm|3mbm]], [[3p0z|3p0z]], [[3jvh|3jvh]], [[3k14|3k14]]</div></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ispF, mecS, BPSL2098 ([ | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ispF, mecS, BPSL2098 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=28450 "Bacillus pseudomallei" Whitmore 1913])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/2-C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.6.1.12 4.6.1.12] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3q8h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q8h OCA], [https://pdbe.org/3q8h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3q8h RCSB], [https://www.ebi.ac.uk/pdbsum/3q8h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3q8h ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[[ | [[https://www.uniprot.org/uniprot/ISPF_BURPS ISPF_BURPS]] Involved in the biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), two major building blocks of isoprenoid compounds. Catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-CPP) with a corresponding release of cytidine 5-monophosphate (CMP) (By similarity).[HAMAP-Rule:MF_00107] | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
| Line 23: | Line 23: | ||
==See Also== | ==See Also== | ||
*[[MECDP synthase|MECDP synthase]] | *[[MECDP synthase 3D structures|MECDP synthase 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
| Line 30: | Line 30: | ||
[[Category: Bacillus pseudomallei whitmore 1913]] | [[Category: Bacillus pseudomallei whitmore 1913]] | ||
[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]] | [[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]] | ||
[[Category: Large Structures]] | |||
[[Category: Structural genomic]] | [[Category: Structural genomic]] | ||
[[Category: Isoprene biosynthesis]] | [[Category: Isoprene biosynthesis]] | ||
Revision as of 08:57, 8 June 2022
Crystal structure of 2c-methyl-d-erythritol 2,4-cyclodiphosphate synthase from burkholderia pseudomallei in complex with cytidine derivative EBSI01028Crystal structure of 2c-methyl-d-erythritol 2,4-cyclodiphosphate synthase from burkholderia pseudomallei in complex with cytidine derivative EBSI01028
Structural highlights
Function[ISPF_BURPS] Involved in the biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), two major building blocks of isoprenoid compounds. Catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-CPP) with a corresponding release of cytidine 5-monophosphate (CMP) (By similarity).[HAMAP-Rule:MF_00107] Publication Abstract from PubMedPublished biological data suggest that the methyl erythritol phosphate (MEP) pathway, a non-mevalonate isoprenoid biosynthetic pathway, is essential for certain bacteria and other infectious disease organisms. One highly conserved enzyme in the MEP pathway is 2C-methyl-d-erythritol 2,4-cyclodiphosphate synthase (IspF). Fragment-bound complexes of IspF from Burkholderia pseudomallei were used to design and synthesize a series of molecules linking the cytidine moiety to different zinc pocket fragment binders. Testing by surface plasmon resonance (SPR) found one molecule in the series to possess binding affinity equal to that of cytidine diphosphate, despite lacking any metal-coordinating phosphate groups. Close inspection of the SPR data suggest different binding stoichiometries between IspF and test compounds. Crystallographic analysis shows important variations between the binding mode of one synthesized compound and the pose of the bound fragment from which it was designed. The binding modes of these molecules add to our structural knowledge base for IspF and suggest future refinements in this compound series. Cytidine derivatives as IspF inhibitors of Burkolderia pseudomallei.,Zhang Z, Jakkaraju S, Blain J, Gogol K, Zhao L, Hartley RC, Karlsson CA, Staker BL, Edwards TE, Stewart LJ, Myler PJ, Clare M, Begley DW, Horn JR, Hagen TJ Bioorg Med Chem Lett. 2013 Dec 15;23(24):6860-3. doi: 10.1016/j.bmcl.2013.09.101., Epub 2013 Oct 8. PMID:24157367[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||||||||