1u0r: Difference between revisions

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-[[Image:1u0r.gif|left|200px]]
- {{Structure
+==Crystal structure of Mycobacterium tuberculosis NAD kinase==
-|PDB= 1u0r |SIZE=350|CAPTION= <scene name='initialview01'>1u0r</scene>, resolution 2.80&Aring;
+<StructureSection load='1u0r' size='340' side='right'caption='[[1u0r]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND=
+<table><tr><td colspan='2'>[[1u0r]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U0R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1U0R FirstGlance]. <br>
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/NAD(+)_kinase NAD(+) kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.23 2.7.1.23] </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]] 2.8&#8491;</td></tr>
-|GENE= ppnK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis])
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1u0r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u0r OCA], [https://pdbe.org/1u0r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1u0r RCSB], [https://www.ebi.ac.uk/pdbsum/1u0r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1u0r ProSAT]</span></td></tr>
-|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PRK03372 ppnK]</span>
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1u0r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u0r OCA], [http://www.ebi.ac.uk/pdbsum/1u0r PDBsum], [http://www.fli-leibniz.de/cgi-bin/ImgLib.pl?CODE=1kfv JenaLib], [http://www.rcsb.org/pdb/explore.do?structureId=1u0r RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/NADK_MYCTU NADK_MYCTU] Involved in the regulation of the intracellular balance of NAD and NADP, and is a key enzyme in the biosynthesis of NADP. Catalyzes specifically the phosphorylation on 2'-hydroxyl of the adenosine moiety of NAD to yield NADP. It can use ATP and other nucleoside triphosphates as well as inorganic polyphosphate (poly(P)) as a source of phosphorus.[HAMAP-Rule:MF_00361]<ref>PMID:11006082</ref> <ref>PMID:15182203</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/u0/1u0r_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=1u0r ConSurf].
+<div style="clear:both"></div>
-'''Crystal structure of Mycobacterium tuberculosis NAD kinase'''
+==See Also==
+*[[NAD kinase|NAD kinase]]
+== References ==
-==Overview==
+<references/>
-NAD kinase catalyzes the magnesium-dependent phosphorylation of NAD, representing the sole source of freshly synthesized NADP in all organisms. The enzyme is essential for the growth of the deadly multidrug-resistant pathogen Mycobacterium tuberculosis and is an attractive target for novel antitubercular agents. The crystal structure of NAD kinase has been solved by multiwavelength anomalous dispersion at a resolution of 2.3 A in its T state. Two crystal forms have been obtained revealing either a dimer or a tetramer. The enzyme architecture discloses a novel molecular arrangement, with each subunit consisting of an alpha/beta N-terminal domain and a C-terminal 12-stranded beta sandwich domain, connected by swapped beta strands. The C-terminal domain shows a striking internal approximate 222 symmetry and an unprecedented topology, revealing a novel fold within the family of all beta structures. The catalytic site is located in the long crevice that defines the interface between the domains. The conserved GGDG structural fingerprint of the catalytic site is reminiscent of the related region in 6-phosphofructokinase, supporting the hypothesis that NAD kinase belongs to a newly reported superfamily of kinases.
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-U0R is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U0R OCA].
-==Reference==
-A novel fold revealed by Mycobacterium tuberculosis NAD kinase, a key allosteric enzyme in NADP biosynthesis., Garavaglia S, Raffaelli N, Finaurini L, Magni G, Rizzi M, J Biol Chem. 2004 Sep 24;279(39):40980-6. Epub 2004 Jul 21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15269221 15269221]
 [[Category: Mycobacterium tuberculosis]]
-[[Category: NAD(+) kinase]]
+[[Category: Finaurini L]]
-[[Category: Single protein]]
+[[Category: Garavaglia S]]
-[[Category: Finaurini, L.]]
+[[Category: Magni G]]
-[[Category: Garavaglia, S.]]
+[[Category: Raffaelli N]]
-[[Category: Magni, G.]]
+[[Category: Rizzi M]]
-[[Category: Raffaelli, N.]]
-[[Category: Rizzi, M.]]
-[[Category: TBSGC, TB Structural Genomics Consortium.]]
-[[Category: alpha-beta]]
-[[Category: beta sandwich]]
-[[Category: protein structure initiative]]
-[[Category: psi]]
-[[Category: structural genomic]]
-[[Category: tb structural genomics consortium]]
-[[Category: tbsgc]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 26 06:08:42 2008''