1oj4: Difference between revisions

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-[[Image:1oj4.gif|left|200px]]<br />
-<applet load="1oj4" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1oj4, resolution 2.01&Aring;" />
-'''TERNARY COMPLEX OF 4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL KINASE'''<br />
-==Overview==
+==Ternary complex of 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase==
--Diphosphocytidyl-2C-methyl-d-erythritol kinase, an essential enzyme in, the nonmevalonate pathway of isopentenyl diphosphate and dimethylallyl, diphosphate biosynthesis, catalyzes the single ATP-dependent, phosphorylation stage affording, 4-diphosphocytidyl-2C-methyl-d-erythritol-2-phosphate. The 2-A resolution, crystal structure of the Escherichia coli enzyme in a ternary complex with, substrate and a nonhydrolyzable ATP analogue reveals the molecular, determinants of specificity and catalysis. The enzyme subunit displays the, alpha/beta fold characteristic of the galactose kinase/homoserine, kinase/mevalonate kinase/phosphomevalonate kinase superfamily, arranged, into cofactor and substrate-binding domains with the catalytic center, positioned in a deep cleft between domains. Comparisons with related, members of this superfamily indicate that the core regions of each domain, are conserved, whereas there are significant differences in the, substrate-binding pockets. The nonmevalonate pathway is essential in many, microbial pathogens and distinct from the mevalonate pathway used by, mammals. The high degree of sequence conservation of the enzyme across, bacterial species suggests similarities in structure, specificity, and, mechanism. Our model therefore provides an accurate template to facilitate, the structure-based design of broad-spectrum antimicrobial agents.
+<StructureSection load='1oj4' size='340' side='right'caption='[[1oj4]], [[Resolution|resolution]] 2.01&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1oj4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_O6 Escherichia coli O6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OJ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OJ4 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]] 2.01&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=CDM:4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL'>CDM</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=1oj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oj4 OCA], [https://pdbe.org/1oj4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oj4 RCSB], [https://www.ebi.ac.uk/pdbsum/1oj4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oj4 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ISPE_ECOL6 ISPE_ECOL6] Catalyzes the phosphorylation of the position 2 hydroxy group of 4-diphosphocytidyl-2C-methyl-D-erythritol (By similarity).[HAMAP-Rule:MF_00061]
+== 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/oj/1oj4_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1oj4 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+-Diphosphocytidyl-2C-methyl-d-erythritol kinase, an essential enzyme in the nonmevalonate pathway of isopentenyl diphosphate and dimethylallyl diphosphate biosynthesis, catalyzes the single ATP-dependent phosphorylation stage affording 4-diphosphocytidyl-2C-methyl-d-erythritol-2-phosphate. The 2-A resolution crystal structure of the Escherichia coli enzyme in a ternary complex with substrate and a nonhydrolyzable ATP analogue reveals the molecular determinants of specificity and catalysis. The enzyme subunit displays the alpha/beta fold characteristic of the galactose kinase/homoserine kinase/mevalonate kinase/phosphomevalonate kinase superfamily, arranged into cofactor and substrate-binding domains with the catalytic center positioned in a deep cleft between domains. Comparisons with related members of this superfamily indicate that the core regions of each domain are conserved, whereas there are significant differences in the substrate-binding pockets. The nonmevalonate pathway is essential in many microbial pathogens and distinct from the mevalonate pathway used by mammals. The high degree of sequence conservation of the enzyme across bacterial species suggests similarities in structure, specificity, and mechanism. Our model therefore provides an accurate template to facilitate the structure-based design of broad-spectrum antimicrobial agents.
-==About this Structure==
+Biosynthesis of isoprenoids: crystal structure of 4-diphosphocytidyl-2C-methyl-D-erythritol kinase.,Miallau L, Alphey MS, Kemp LE, Leonard GA, McSweeney SM, Hecht S, Bacher A, Eisenreich W, Rohdich F, Hunter WN Proc Natl Acad Sci U S A. 2003 Aug 5;100(16):9173-8. Epub 2003 Jul 23. PMID:12878729<ref>PMID:12878729</ref>
-OJ4 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with CL, CDM and ANP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/4-(cytidine_5'-diphospho)-2-C-methyl-D-erythritol_kinase 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.148 2.7.1.148] Structure known Active Site: AC1. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1OJ4 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Biosynthesis of isoprenoids: crystal structure of 4-diphosphocytidyl-2C-methyl-D-erythritol kinase., Miallau L, Alphey MS, Kemp LE, Leonard GA, McSweeney SM, Hecht S, Bacher A, Eisenreich W, Rohdich F, Hunter WN, Proc Natl Acad Sci U S A. 2003 Aug 5;100(16):9173-8. Epub 2003 Jul 23. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12878729 12878729]
+</div>
-[[Category: 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase]]
+<div class="pdbe-citations 1oj4" style="background-color:#fffaf0;"></div>
-[[Category: Escherichia coli]]
+== References ==
-[[Category: Single protein]]
+<references/>
-[[Category: Alphey, M.S.]]
+__TOC__
-[[Category: Hunter, W.N.]]
+</StructureSection>
-[[Category: Miallau, L.]]
+[[Category: Escherichia coli O6]]
-[[Category: ANP]]
+[[Category: Large Structures]]
-[[Category: CDM]]
+[[Category: Alphey MS]]
-[[Category: CL]]
+[[Category: Hunter WN]]
-[[Category: ghmp kinase superfamily transferase]]
+[[Category: Miallau L]]
-[[Category: isoprenoids biosynthesis]]
-[[Category: kinase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov  5 13:58:03 2007''