2va1: Difference between revisions

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-{{Seed}}
-[[Image:2va1.png|left|200px]]
-<!--
+==Crystal structure of UMP kinase from Ureaplasma parvum==
-The line below this paragraph, containing "STRUCTURE_2va1", creates the "Structure Box" on the page.
+<StructureSection load='2va1' size='340' side='right'caption='[[2va1]], [[Resolution|resolution]] 2.50&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'>[[2va1]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Ureaplasma_parvum Ureaplasma parvum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VA1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VA1 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]] 2.5&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-{{STRUCTURE_2va1|  PDB=2va1  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2va1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2va1 OCA], [https://pdbe.org/2va1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2va1 RCSB], [https://www.ebi.ac.uk/pdbsum/2va1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2va1 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PYRH_UREPA PYRH_UREPA] Catalyzes the reversible phosphorylation of UMP to UDP, with ATP as the most efficient phosphate donor. Is also able to phosphorylate dUMP.<ref>PMID:17355283</ref> <ref>PMID:18021254</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/va/2va1_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=2va1 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The crystal structure of uridine monophosphate kinase (UMP kinase, UMPK) from the opportunistic pathogen Ureaplasma parvum was determined and showed similar three-dimensional fold as other bacterial and archaeal UMPKs that all belong to the amino acid kinase family. Recombinant UpUMPK exhibited Michaelis-Menten kinetics with UMP, with K(m) and V(max) values of 214 +/- 4 microm and 262 +/- 24 micromol.min(-1).mg(-1), respectively, but with ATP as variable substrate the kinetic analysis showed positive cooperativity, with an n value of 1.5 +/- 0.1. The end-product UTP was a competitive inhibitor against UMP and a noncompetitive inhibitor towards ATP. Unlike UMPKs from other bacteria, which are activated by GTP, GTP had no detectable effect on UpUMPK activity. An attempt to create a GTP-activated enzyme was made using site-directed mutagenesis. The mutant enzyme F133N (F133 corresponds to the residue in Escherichia coli that is involved in GTP activation), with F133A as a control, were expressed, purified and characterized. Both enzymes exhibited negative cooperativity with UMP, and GTP had no effect on enzyme activity, demonstrating that F133 is involved in subunit interactions but apparently not in GTP activation. The physiological role of UpUMPK in bacterial nucleic acid synthesis and its potential as target for development of antimicrobial agents are discussed.
-===CRYSTAL STRUCTURE OF UMP KINASE FROM UREAPLASMA PARVUM===
+Structural and functional investigations of Ureaplasma parvum UMP kinase--a potential antibacterial drug target.,Egeblad-Welin L, Welin M, Wang L, Eriksson S FEBS J. 2007 Dec;274(24):6403-14. Epub 2007 Nov 15. PMID:18021254<ref>PMID:18021254</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2va1" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18021254}}, adds the Publication Abstract to the page
+*[[Uridylate kinase|Uridylate kinase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18021254 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18021254}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-VA1 is a 6 chains structure of sequences from [http://en.wikipedia.org/wiki/Ureaplasma_parvum Ureaplasma parvum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VA1 OCA].
-==Reference==
-<ref group="xtra">PMID:18021254</ref><references group="xtra"/>
 [[Category: Ureaplasma parvum]]
-[[Category: Egeblad-Welin, L.]]
+[[Category: Egeblad-Welin L]]
-[[Category: Eriksson, S.]]
+[[Category: Eriksson S]]
-[[Category: Wang, L.]]
+[[Category: Wang L]]
-[[Category: Welin, M.]]
+[[Category: Welin M]]
-[[Category: Amino acid kinase family]]
-[[Category: Kinase]]
-[[Category: Pyrimidine biosynthesis]]
-[[Category: Transferase]]
-[[Category: Umpk]]
-[[Category: Uridylate kinase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 13:43:02 2009''