4mv5: Difference between revisions
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==IspH in complex with 6-chloropyridin-3-ylmethyl diphosphate== | ==IspH in complex with 6-chloropyridin-3-ylmethyl diphosphate== | ||
<StructureSection load='4mv5' size='340' side='right' caption='[[4mv5]], [[Resolution|resolution]] 1.90Å' scene=''> | <StructureSection load='4mv5' size='340' side='right'caption='[[4mv5]], [[Resolution|resolution]] 1.90Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4mv5]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MV5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4MV5 FirstGlance]. <br> | <table><tr><td colspan='2'>[[4mv5]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MV5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4MV5 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2E7:(6-CHLOROPYRIDIN-3-YL)METHYL+TRIHYDROGEN+DIPHOSPHATE'>2E7</scene>, <scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2E7:(6-CHLOROPYRIDIN-3-YL)METHYL+TRIHYDROGEN+DIPHOSPHATE'>2E7</scene>, <scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ke8|3ke8]], [[3dnf|3dnf]], [[3f7t|3f7t]], [[4mux|4mux]], [[4muy|4muy]], [[4mv0|4mv0]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ke8|3ke8]], [[3dnf|3dnf]], [[3f7t|3f7t]], [[4mux|4mux]], [[4muy|4muy]], [[4mv0|4mv0]]</td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ECDH1ME8569_0026, ispH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxy-3-methylbut-2-enyl_diphosphate_reductase 4-hydroxy-3-methylbut-2-enyl diphosphate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.1.2 1.17.1.2] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxy-3-methylbut-2-enyl_diphosphate_reductase 4-hydroxy-3-methylbut-2-enyl diphosphate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.1.2 1.17.1.2] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4mv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mv5 OCA], [http://pdbe.org/4mv5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4mv5 RCSB], [http://www.ebi.ac.uk/pdbsum/4mv5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4mv5 ProSAT]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4mv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mv5 OCA], [http://pdbe.org/4mv5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4mv5 RCSB], [http://www.ebi.ac.uk/pdbsum/4mv5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4mv5 ProSAT]</span></td></tr> | ||
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==See Also== | ==See Also== | ||
*[[4-hydroxy-3-methylbut-2-enyl diphosphate reductase|4-hydroxy-3-methylbut-2-enyl diphosphate reductase]] | *[[4-hydroxy-3-methylbut-2-enyl diphosphate reductase 3D structures|4-hydroxy-3-methylbut-2-enyl diphosphate reductase 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase]] | [[Category: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase]] | ||
[[Category: Ecoli]] | |||
[[Category: Large Structures]] | |||
[[Category: Bacher, A]] | [[Category: Bacher, A]] | ||
[[Category: Eisenreich, W]] | [[Category: Eisenreich, W]] | ||
Revision as of 11:24, 10 April 2019
IspH in complex with 6-chloropyridin-3-ylmethyl diphosphateIspH in complex with 6-chloropyridin-3-ylmethyl diphosphate
Structural highlights
Function[C9QSC3_ECOD1] Converts 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate into isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) (By similarity).[SAAS:SAAS003451_004_011514][HAMAP-Rule:MF_00191] Publication Abstract from PubMed(E)-1-Hydroxy-2-methylbut-2-enyl 4-diphosphate reductase (IspH) is a [Fe4S4] cluster-containing enzyme involved in isoprenoid biosynthesis in many bacteria as well as in malaria parasites and is an important drug target. Several inhibitors including amino and thiol substrate analogues, as well as acetylene and pyridine diphosphates, have been reported. Here, we investigate the mode of binding of four pyridine diphosphates to Escherichia coli IspH by using X-ray crystallography. In three cases, one of the iron atoms in the cluster is absent, but in the structure with (pyridin-3-yl)methyl diphosphate, the most potent pyridine-analogue inhibitor reported previously, the fourth iron of the [Fe4S4] cluster is present and interacts with the pyridine ring of the ligand. Based on the results of quantum chemical calculations together with the crystallographic results we propose a side-on eta2 coordination of the nitrogen and the carbon in the 2-position of the pyridine ring to the unique fourth iron in the cluster, which is in the reduced state. The X-ray structure enables excellent predictions using density functional theory of the 14N hyperfine coupling and quadrupole coupling constants reported previously using HYSCORE spectroscopy, as well as providing a further example of the ability of such [Fe4S4]-containing proteins to form organometallic complexes. Insights into the Binding of Pyridines to the Iron-Sulfur Enzyme IspH.,Span I, Wang K, Eisenreich W, Bacher A, Zhang Y, Oldfield E, Groll M J Am Chem Soc. 2014 May 22. PMID:24813236[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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