This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


3elc

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (15:21, 1 November 2023) (edit) (undo)
 
(6 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:3elc.png|left|200px]]
 
-
{{STRUCTURE_3elc| PDB=3elc | SCENE= }}
+
==Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase complexed with ligand==
 +
<StructureSection load='3elc' size='340' side='right'caption='[[3elc]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[3elc]] is a 3 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=3ELC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ELC 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]] 2.5&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=F01:4-AMINO-1-[(2R,3R,4S,5R)-3,4-DIHYDROXY-5-(HYDROXYMETHYL)OXOLAN-2-YL]-5-FLUORO-PYRIMIDIN-2-ONE'>F01</scene>, <scene name='pdbligand=GPP:GERANYL+DIPHOSPHATE'>GPP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=3elc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3elc OCA], [https://pdbe.org/3elc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3elc RCSB], [https://www.ebi.ac.uk/pdbsum/3elc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3elc ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/ISPF_ECOLI ISPF_ECOLI] 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). Also converts 4-diphosphocytidyl-2-C-methyl-D-erythritol into 2-C-methyl-D-erythritol 3,4-cyclophosphate and CMP.<ref>PMID:10694574</ref> <ref>PMID:22839733</ref>
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/el/3elc_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</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=3elc ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The nonmevalonate route to isoprenoid biosynthesis is essential in Gram-negative bacteria and apicomplexan parasites. The enzymes of this pathway are absent from mammals, contributing to their appeal as chemotherapeutic targets. One enzyme, 2C-methyl-d-erythritol-2,4-cyclodiphosphate synthase (IspF), has been validated as a target by genetic approaches in bacteria. Virtual screening against Escherichia coli IspF (EcIspF) was performed by combining a hierarchical filtering methodology with molecular docking. Docked compounds were inspected and 10 selected for experimental validation. A surface plasmon resonance assay was developed and two weak ligands identified. Crystal structures of EcIspF complexes were determined to support rational ligand development. Cytosine analogues and Zn(2+)-binding moieties were characterized. One of the putative Zn(2+)-binding compounds gave the lowest measured K(D) to date (1.92 +/- 0.18 muM). These data provide a framework for the development of IspF inhibitors to generate lead compounds of therapeutic potential against microbial pathogens.
-
===Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase complexed with ligand===
+
A structure-based approach to ligand discovery for 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase: a target for antimicrobial therapy.,Ramsden NL, Buetow L, Dawson A, Kemp LA, Ulaganathan V, Brenk R, Klebe G, Hunter WN J Med Chem. 2009 Apr 23;52(8):2531-42. PMID:19320487<ref>PMID:19320487</ref>
-
{{ABSTRACT_PUBMED_19320487}}
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
 
+
</div>
-
==About this Structure==
+
<div class="pdbe-citations 3elc" style="background-color:#fffaf0;"></div>
-
[[3elc]] is a 3 chain structure with sequence from [http://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=3ELC OCA].
+
==See Also==
==See Also==
-
*[[MECDP synthase|MECDP synthase]]
+
*[[MECDP synthase 3D structures|MECDP synthase 3D structures]]
-
 
+
== References ==
-
==Reference==
+
<references/>
-
<ref group="xtra">PMID:019320487</ref><references group="xtra"/>
+
__TOC__
-
[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]
+
</StructureSection>
-
[[Category: Escherichia coli k-12]]
+
[[Category: Escherichia coli K-12]]
-
[[Category: Hunter, W N.]]
+
[[Category: Large Structures]]
-
[[Category: Ramsden, N L.]]
+
[[Category: Hunter WN]]
-
[[Category: Ulaganathan, V.]]
+
[[Category: Ramsden NL]]
-
[[Category: Isoprene biosynthesis]]
+
[[Category: Ulaganathan V]]
-
[[Category: Lyase]]
+
-
[[Category: Magnesium]]
+
-
[[Category: Manganese]]
+
-
[[Category: Mecdp-synthase]]
+
-
[[Category: Metal-binding]]
+

Current revision

Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase complexed with ligand

PDB ID 3elc

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3elc"
Personal tools