2bne: Difference between revisions

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-{{Seed}}
-[[Image:2bne.png|left|200px]]
-<!--
+==The structure of E. coli UMP kinase in complex with UMP==
-The line below this paragraph, containing "STRUCTURE_2bne", creates the "Structure Box" on the page.
+<StructureSection load='2bne' size='340' side='right'caption='[[2bne]], [[Resolution|resolution]] 2.30&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'>[[2bne]] is a 2 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=2BNE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BNE 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]] 2.3&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=U5P:URIDINE-5-MONOPHOSPHATE'>U5P</scene></td></tr>
-{{STRUCTURE_2bne|  PDB=2bne  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2bne FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bne OCA], [https://pdbe.org/2bne PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bne RCSB], [https://www.ebi.ac.uk/pdbsum/2bne PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bne ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PYRH_ECOLI PYRH_ECOLI] Catalyzes the reversible phosphorylation of UMP to UDP, with ATP as the most efficient phosphate donor.<ref>PMID:7711027</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/bn/2bne_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=2bne ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Bacterial UMP kinases are essential enzymes involved in the multistep synthesis of nucleoside triphosphates. They are hexamers regulated by the allosteric activator GTP and inhibited by UTP. We solved the crystal structure of Escherichia coli UMP kinase bound to the UMP substrate (2.3 A resolution), the UDP product (2.6 A), or UTP (2.45 A). The monomer fold, unrelated to that of other nucleoside monophosphate kinases, belongs to the carbamate kinase-like superfamily. However, the phosphate acceptor binding cleft and subunit assembly are characteristic of UMP kinase. Interactions with UMP explain the high specificity for this natural substrate. UTP, previously described as an allosteric inhibitor, was unexpectedly found in the phosphate acceptor site, suggesting that it acts as a competitive inhibitor. Site-directed mutagenesis of residues Thr-138 and Asn-140, involved in both uracil recognition and active site interaction within the hexamer, decreased the activation by GTP and inhibition by UTP. These experiments suggest a cross-talk mechanism between enzyme subunits involved in cooperative binding at the phosphate acceptor site and in allosteric regulation by GTP. As bacterial UMP kinases have no counterpart in eukaryotes, the information provided here could help the design of new antibiotics.
-===THE STRUCTURE OF E. COLI UMP KINASE IN COMPLEX WITH UMP===
+Structure of Escherichia coli UMP kinase differs from that of other nucleoside monophosphate kinases and sheds new light on enzyme regulation.,Briozzo P, Evrin C, Meyer P, Assairi L, Joly N, Barzu O, Gilles AM J Biol Chem. 2005 Jul 8;280(27):25533-40. Epub 2005 Apr 27. PMID:15857829<ref>PMID:15857829</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2bne" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_15857829}}, adds the Publication Abstract to the page
+*[[Uridylate kinase|Uridylate kinase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 15857829 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15857829}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Escherichia coli K-12]]
-BNE is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BNE OCA].
+[[Category: Large Structures]]
+[[Category: Assairi L]]
-==Reference==
+[[Category: Barzu O]]
-<ref group="xtra">PMID:15857829</ref><references group="xtra"/>
+[[Category: Briozzo P]]
-[[Category: Escherichia coli]]
+[[Category: Evrin C]]
-[[Category: Nucleoside-phosphate kinase]]
+[[Category: Gilles AM]]
-[[Category: Assairi, L.]]
+[[Category: Joly N]]
-[[Category: Barzu, O.]]
+[[Category: Meyer P]]
-[[Category: Briozzo, P.]]
-[[Category: Evrin, C.]]
-[[Category: Gilles, A M.]]
-[[Category: Joly, N.]]
-[[Category: Meyer, P.]]
-[[Category: Nucleoside monophosphate kinase]]
-[[Category: Pyrimidine biosynthesis]]
-[[Category: Transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 18:16:17 2009''