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1yt5

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[[Image:1yt5.gif|left|200px]]<br /><applet load="1yt5" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1yt5, resolution 2.3&Aring;" />
 
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'''Crystal structure of NAD kinase from Thermotoga maritima'''<br />
 
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==Overview==
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==Crystal structure of NAD kinase from Thermotoga maritima==
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NAD kinase is the only known enzyme that catalyzes the formation of NADP, a coenzyme involved in most anabolic reactions and in the antioxidant defense system. Despite its importance, very little is known regarding the mechanism of catalysis and only recently have several NAD kinase structures been deposited in the PDB. Here, an independent investigation of the crystal structure of inorganic polyphosphate/ATP-NAD kinase, PPNK_THEMA, a protein from Thermotoga maritima, is reported at a resolution of 2.3 A. The crystal structure was solved using single-wavelength anomalous diffraction (SAD) data collected at the Se absorption-peak wavelength in a state in which no cofactors or substrates were bound. It revealed that the 258-amino-acid protein is folded into two distinct domains, similar to recently reported NAD kinases. The N-terminal alpha/beta-domain spans the first 100 amino acids and the last 30 amino acids of the polypeptide and has several topological matches in the PDB, whereas the other domain, which spans the middle 130 residues, adopts a unique beta-sandwich architecture and only appreciably matches the recently deposited PDB structures of NAD kinases.
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<StructureSection load='1yt5' size='340' side='right'caption='[[1yt5]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1yt5]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YT5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YT5 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]] 2.3&#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=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=1yt5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yt5 OCA], [https://pdbe.org/1yt5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yt5 RCSB], [https://www.ebi.ac.uk/pdbsum/1yt5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yt5 ProSAT], [https://www.topsan.org/Proteins/BSGC/1yt5 TOPSAN]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/NADK_THEMA NADK_THEMA] Involved in the regulation of the intracellular balance between NAD(H) and NADP(H), 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 (By similarity).
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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/yt/1yt5_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=1yt5 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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1YT5 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima] with <scene name='pdbligand=SO4:'>SO4</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. 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://oca.weizmann.ac.il/oca-bin/ocashort?id=1YT5 OCA].
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*[[NAD kinase|NAD kinase]]
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__TOC__
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==Reference==
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</StructureSection>
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Structure of a NAD kinase from Thermotoga maritima at 2.3 A resolution., Oganesyan V, Huang C, Adams PD, Jancarik J, Yokota HA, Kim R, Kim SH, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 Jul 1;61(Pt, 7):640-6. Epub 2005 Jun 30. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16511117 16511117]
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[[Category: Large Structures]]
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[[Category: NAD(+) kinase]]
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[[Category: Single protein]]
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[[Category: Thermotoga maritima]]
[[Category: Thermotoga maritima]]
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[[Category: BSGC, Berkeley Structural Genomics Center.]]
 
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[[Category: SO4]]
 
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[[Category: berkeley structural genomics center]]
 
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[[Category: bsgc]]
 
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[[Category: domain 1: alpha/beta domain2: beta sandwich]]
 
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[[Category: protein structure initiative]]
 
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[[Category: psi]]
 
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[[Category: structural genomics]]
 
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:08:49 2008''
 

Current revision

Crystal structure of NAD kinase from Thermotoga maritima

PDB ID 1yt5

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