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.

3p0z

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with cytidine and FOL955, 4-(1H-imidazol)-1-yl)phenol

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3p0z"

Categories: Burkholderia pseudomallei 1710b | Large Structures

@@ Line 1: / Line 1: @@
 ==Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with cytidine and FOL955, 4-(1H-imidazol)-1-yl)phenol==
-<StructureSection load='3p0z' size='340' side='right' caption='[[3p0z]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
+<StructureSection load='3p0z' size='340' side='right'caption='[[3p0z]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3p0z]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Burp1 Burp1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3P0Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3P0Z FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3p0z]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_pseudomallei_1710b Burkholderia pseudomallei 1710b]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3P0Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3P0Z FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CTN:4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE'>CTN</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MSR:4-(1H-IMIDAZOL-1-YL)PHENOL'>MSR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.95&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3f0d|3f0d]], [[3jvh|3jvh]], [[3ike|3ike]], [[3ieq|3ieq]], [[3ikf|3ikf]], [[3mbm|3mbm]], [[3k14|3k14]], [[3ke1|3ke1]], [[3p10|3p10]]</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=CTN:4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE'>CTN</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MSR:4-(1H-IMIDAZOL-1-YL)PHENOL'>MSR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ispF, BURPS1710b_2511 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320372 BURP1])</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=3p0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3p0z OCA], [https://pdbe.org/3p0z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3p0z RCSB], [https://www.ebi.ac.uk/pdbsum/3p0z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3p0z ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://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 [http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3p0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3p0z OCA], [http://pdbe.org/3p0z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3p0z RCSB], [http://www.ebi.ac.uk/pdbsum/3p0z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3p0z ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/ISPF_BURP1 ISPF_BURP1]] 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]
+[https://www.uniprot.org/uniprot/ISPF_BURP1 ISPF_BURP1] 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;">
-== Publication Abstract from PubMed ==
-As part of the Seattle Structural Genomics Center for Infectious Disease, we seek to enhance structural genomics with ligand-bound structure data which can serve as a blueprint for structure-based drug design. We have adapted fragment-based screening methods to our structural genomics pipeline to generate multiple ligand-bound structures of high priority drug targets from pathogenic organisms. In this study, we report fragment screening methods and structure determination results for 2C-methyl-D-erythritol-2,4-cyclo-diphosphate (MECP) synthase from Burkholderia pseudomallei, the gram-negative bacterium which causes melioidosis. Screening by nuclear magnetic resonance spectroscopy as well as crystal soaking followed by X-ray diffraction led to the identification of several small molecules which bind this enzyme in a critical metabolic pathway. A series of complex structures obtained with screening hits reveal distinct binding pockets and a range of small molecules which form complexes with the target. Additional soaks with these compounds further demonstrate a subset of fragments to only bind the protein when present in specific combinations. This ensemble of fragment-bound complexes illuminates several characteristics of MECP synthase, including a previously unknown binding surface external to the catalytic active site. These ligand-bound structures now serve to guide medicinal chemists and structural biologists in rational design of novel inhibitors for this enzyme.
-Leveraging structure determination with fragment screening for infectious disease drug targets: MECP synthase from Burkholderia pseudomallei.,Begley DW, Hartley RC, Davies DR, Edwards TE, Leonard JT, Abendroth J, Burris CA, Bhandari J, Myler PJ, Staker BL, Stewart LJ J Struct Funct Genomics. 2011 Jul;12(2):63-76. Epub 2011 Feb 26. PMID:21359640<ref>PMID:21359640</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3p0z" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[MECDP synthase|MECDP synthase]]
+*[[MECDP synthase 3D structures|MECDP synthase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]
+[[Category: Burkholderia pseudomallei 1710b]]
-[[Category: Burp1]]
+[[Category: Large Structures]]
-[[Category: Structural genomic]]
-[[Category: Cytidine]]
-[[Category: Fol955]]
-[[Category: Isoprene biosynthesis]]
-[[Category: Ispf]]
-[[Category: Lyase]]
-[[Category: Mep pathway]]
-[[Category: Metal-binding]]
-[[Category: Msr]]
-[[Category: Ssgcid]]

3p0z

From Proteopedia

Current revision

Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with cytidine and FOL955, 4-(1H-imidazol)-1-yl)phenol

Structural highlights

Function

See Also

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox