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1y3i

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(New page: 200px<br /><applet load="1y3i" size="450" color="white" frame="true" align="right" spinBox="true" caption="1y3i, resolution 2.60&Aring;" /> '''Crystal Structure of...)
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[[Image:1y3i.gif|left|200px]]<br /><applet load="1y3i" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1y3i, resolution 2.60&Aring;" />
 
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'''Crystal Structure of Mycobacterium tuberculosis NAD kinase-NAD complex'''<br />
 
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==Overview==
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==Crystal Structure of Mycobacterium tuberculosis NAD kinase-NAD complex==
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NAD kinase is a key enzyme in NADP biosynthesis. We solved the crystal, structure of polyphosphate/ATP-NAD kinase from Mycobacterium tuberculosis, (Ppnk) complexed with NAD (Ppnk-NAD) at 2.6A resolution using apo-Ppnk, structure solved in this work, and revealed the details of the structure, and NAD-binding site. Superimposition of tertiary structures of apo-Ppnk, and Ppnk-NAD demonstrated a substantial conformational difference in a, loop (Ppnk-flexible loop). As a quaternary structure, these Ppnk, structures exhibited tetramer as in solution condition. Notably, the, Ppnk-flexible loop was involved in the intersubunit contact and probably, related to the NAD-binding of the other subunit. Furthermore, the two, residues (Asp189, His226) substantially contributed to creating, NAD-binding site on the other subunit. The two residues and the residues, involved in NAD-binding were conserved. However, residues corresponding to, the Ppnk-flexible loop were not conserved, making us to speculate that the, Ppnk-flexible loop may be Ppnk-specific.
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<StructureSection load='1y3i' size='340' side='right'caption='[[1y3i]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1y3i]] is a 2 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=1Y3I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y3I FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
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<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=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1y3i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y3i OCA], [https://pdbe.org/1y3i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y3i RCSB], [https://www.ebi.ac.uk/pdbsum/1y3i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y3i ProSAT], [https://www.topsan.org/Proteins/TBSGC/1y3i TOPSAN]</span></td></tr>
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</table>
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== Function ==
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[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>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/y3/1y3i_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1y3i ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1Y3I is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis] with SO4, NAD and GOL as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1Y3I OCA].
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*[[NAD kinase|NAD kinase]]
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== References ==
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==Reference==
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<references/>
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NAD-binding mode and the significance of intersubunit contact revealed by the crystal structure of Mycobacterium tuberculosis NAD kinase-NAD complex., Mori S, Yamasaki M, Maruyama Y, Momma K, Kawai S, Hashimoto W, Mikami B, Murata K, Biochem Biophys Res Commun. 2005 Feb 11;327(2):500-8. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15629142 15629142]
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Mycobacterium tuberculosis]]
[[Category: Mycobacterium tuberculosis]]
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[[Category: NAD(+) kinase]]
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[[Category: Hashimoto W]]
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[[Category: Single protein]]
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[[Category: Kawai S]]
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[[Category: Hashimoto, W.]]
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[[Category: Maruyama Y]]
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[[Category: Kawai, S.]]
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[[Category: Mikami B]]
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[[Category: Maruyama, Y.]]
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[[Category: Momma K]]
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[[Category: Mikami, B.]]
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[[Category: Mori S]]
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[[Category: Momma, K.]]
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[[Category: Murata K]]
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[[Category: Mori, S.]]
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[[Category: Yamasaki M]]
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[[Category: Murata, K.]]
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[[Category: Yamasaki, M.]]
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[[Category: GOL]]
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[[Category: NAD]]
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[[Category: SO4]]
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[[Category: atp]]
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[[Category: mycobacterium tuberculosis]]
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[[Category: nad]]
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[[Category: nad kinase]]
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[[Category: polyphosphate]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 06:32:38 2007''
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Current revision

Crystal Structure of Mycobacterium tuberculosis NAD kinase-NAD complex

PDB ID 1y3i

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