2vbu: Difference between revisions

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-{{Seed}}
-[[Image:2vbu.png|left|200px]]
-<!--
+==Riboflavin kinase Mj0056 from Methanocaldococcus jannaschii in complex with CDP==
-The line below this paragraph, containing "STRUCTURE_2vbu", creates the "Structure Box" on the page.
+<StructureSection load='2vbu' size='340' side='right'caption='[[2vbu]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2vbu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VBU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VBU FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CDP:CYTIDINE-5-DIPHOSPHATE'>CDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene></td></tr>
-{{STRUCTURE_2vbu|  PDB=2vbu  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vbu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vbu OCA], [https://pdbe.org/2vbu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vbu RCSB], [https://www.ebi.ac.uk/pdbsum/2vbu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vbu ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RIFK_METJA RIFK_METJA] Catalyzes the CTP-dependent phosphorylation of riboflavin (vitamin B2) to form flavin mononucleotide (FMN). Can also utilize UTP as the phosphate donor, although less efficiently, and it is unclear if ATP and GTP can also serve as substrates (PubMed:18245297) or not (PubMed:18073108).<ref>PMID:18073108</ref> <ref>PMID:18245297</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/vb/2vbu_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=2vbu ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Proteins of the cradle-loop barrel metafold are formed by duplication of a conserved betaalphabeta-element, suggesting a common evolutionary origin from an ancestral group of nucleic acid-binding proteins. The basal fold within this metafold, the RIFT barrel, is also found in a wide range of enzymes, whose homologous relationship with the nucleic acid-binding group is unclear. We have characterized a protein family that is intermediate in sequence and structure between the basal group of cradle-loop barrels and one family of RIFT-barrel enzymes, the riboflavin kinases. We report the structure, substrate-binding mode, and catalytic activity for one of these proteins, Methanocaldococcus jannaschii Mj0056, which is an archaeal riboflavin kinase. Mj0056 is unusual in utilizing CTP rather than ATP as the donor nucleotide, and sequence conservation in the relevant residues suggests that this is a general feature of archaeal riboflavin kinases.
-===RIBOFLAVIN KINASE MJ0056 FROM METHANOCALDOCOCCUS JANNASCHII IN COMPLEX WITH CDP===
+A CTP-dependent archaeal riboflavin kinase forms a bridge in the evolution of cradle-loop barrels.,Ammelburg M, Hartmann MD, Djuranovic S, Alva V, Koretke KK, Martin J, Sauer G, Truffault V, Zeth K, Lupas AN, Coles M Structure. 2007 Dec;15(12):1577-90. PMID:18073108<ref>PMID:18073108</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_18073108}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2vbu" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 18073108 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18073108}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-VBU is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VBU OCA].
-==Reference==
-A CTP-dependent archaeal riboflavin kinase forms a bridge in the evolution of cradle-loop barrels., Ammelburg M, Hartmann MD, Djuranovic S, Alva V, Koretke KK, Martin J, Sauer G, Truffault V, Zeth K, Lupas AN, Coles M, Structure. 2007 Dec;15(12):1577-90. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18073108 18073108]
 [[Category: Methanocaldococcus jannaschii]]
-[[Category: Single protein]]
+[[Category: Ammelburg M]]
-[[Category: Transferase]]
+[[Category: Djuranovic S]]
-[[Category: Ammelburg, M.]]
+[[Category: Hartmann MD]]
-[[Category: Djuranovic, S.]]
+[[Category: Lupas AN]]
-[[Category: Hartmann, M D.]]
+[[Category: Martin J]]
-[[Category: Lupas, A N.]]
+[[Category: Zeth K]]
-[[Category: Martin, J.]]
-[[Category: Zeth, K.]]
-[[Category: Cradle-loop barrel]]
-[[Category: Ctp-dependent kinase]]
-[[Category: Fmn]]
-[[Category: Transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 23:57:08 2008''