1iv4: Difference between revisions

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-[[Image:1iv4.gif|left|200px]]
- {{Structure
+==Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase (bound form Substrate)==
-|PDB= 1iv4 |SIZE=350|CAPTION= <scene name='initialview01'>1iv4</scene>, resolution 1.55&Aring;
+<StructureSection load='1iv4' size='340' side='right'caption='[[1iv4]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=C5P:CYTIDINE-5&#39;-MONOPHOSPHATE'>C5P</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>
+<table><tr><td colspan='2'>[[1iv4]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IV4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IV4 FirstGlance]. <br>
-|ACTIVITY= <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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.55&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C5P:CYTIDINE-5-MONOPHOSPHATE'>C5P</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1iv4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iv4 OCA], [https://pdbe.org/1iv4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1iv4 RCSB], [https://www.ebi.ac.uk/pdbsum/1iv4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1iv4 ProSAT], [https://www.topsan.org/Proteins/RSGI/1iv4 TOPSAN]</span></td></tr>
-|RELATEDENTRY=[[1iv1|1IV1]], [[1iv2|1IV2]], [[1iv3|1IV3]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1iv4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iv4 OCA], [http://www.ebi.ac.uk/pdbsum/1iv4 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1iv4 RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/ISPF_THET8 ISPF_THET8] 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).<ref>PMID:12499535</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/iv/1iv4_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=1iv4 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Precursors for isoprenoid synthesis are essential in all organisms. These compounds are synthesized by one of two known routes: the well characterized mevalonate pathway or a recently discovered non-mevalonate route which is used in many bacteria and human pathogens. Since the second pathway is both vital and unlike any found in humans, enzymes catalysing reactions along this synthetic route are possible drug targets. The structure of one such enzyme from the thermophilic bacterium Thermus thermophilus has been solved to high resolution in the presence of substrate and with a substrate analogue. Enzyme co-crystallized with substrate shows only one product, cytosine monophosphate (CMP), in the active site. At the high resolution of the refinement (1.6 A) the positions and coordination of the magnesium ions in the active site are clearly seen.
-'''Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase (bound form Substrate)'''
+Structure and catalytic mechanism of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MECDP) synthase, an enzyme in the non-mevalonate pathway of isoprenoid synthesis.,Kishida H, Wada T, Unzai S, Kuzuyama T, Takagi M, Terada T, Shirouzu M, Yokoyama S, Tame JR, Park SY Acta Crystallogr D Biol Crystallogr. 2003 Jan;59(Pt 1):23-31. Epub 2002, Dec 19. PMID:12499535<ref>PMID:12499535</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1iv4" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-Precursors for isoprenoid synthesis are essential in all organisms. These compounds are synthesized by one of two known routes: the well characterized mevalonate pathway or a recently discovered non-mevalonate route which is used in many bacteria and human pathogens. Since the second pathway is both vital and unlike any found in humans, enzymes catalysing reactions along this synthetic route are possible drug targets. The structure of one such enzyme from the thermophilic bacterium Thermus thermophilus has been solved to high resolution in the presence of substrate and with a substrate analogue. Enzyme co-crystallized with substrate shows only one product, cytosine monophosphate (CMP), in the active site. At the high resolution of the refinement (1.6 A) the positions and coordination of the magnesium ions in the active site are clearly seen.
+*[[MECDP synthase 3D structures|MECDP synthase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-IV4 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IV4 OCA].
+__TOC__
+</StructureSection>
-==Reference==
+[[Category: Large Structures]]
-Structure and catalytic mechanism of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MECDP) synthase, an enzyme in the non-mevalonate pathway of isoprenoid synthesis., Kishida H, Wada T, Unzai S, Kuzuyama T, Takagi M, Terada T, Shirouzu M, Yokoyama S, Tame JR, Park SY, Acta Crystallogr D Biol Crystallogr. 2003 Jan;59(Pt 1):23-31. Epub 2002, Dec 19. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12499535 12499535]
-[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]
-[[Category: Single protein]]
 [[Category: Thermus thermophilus]]
-[[Category: Kishida, H.]]
+[[Category: Kishida H]]
-[[Category: Kuzuyama, T.]]
+[[Category: Kuzuyama T]]
-[[Category: Park, S Y.]]
+[[Category: Park S-Y]]
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+[[Category: Sirouzu M]]
-[[Category: Sirouzu, M.]]
+[[Category: Tame JRH]]
-[[Category: Tame, J R.H.]]
+[[Category: Terada T]]
-[[Category: Terada, T.]]
+[[Category: Unzai S]]
-[[Category: Unzai, S.]]
+[[Category: Wada T]]
-[[Category: Wada, T.]]
+[[Category: Yokoyama S]]
-[[Category: Yokoyama, S.]]
-[[Category: isoprenoid]]
-[[Category: non-mevalonate]]
-[[Category: riken structural genomics/proteomics initiative]]
-[[Category: rsgi]]
-[[Category: structural genomic]]
-[[Category: synthase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:25:03 2008''