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==Crystal structure of an NAD kinase from Archaeoglobus fulgidus in complex with ATP==
==Crystal structure of an NAD kinase from Archaeoglobus fulgidus in complex with ATP==
<StructureSection load='1z0s' size='340' side='right' caption='[[1z0s]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
<StructureSection load='1z0s' size='340' side='right'caption='[[1z0s]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1z0s]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Arcfl Arcfl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z0S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Z0S FirstGlance]. <br>
<table><tr><td colspan='2'>[[1z0s]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z0S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Z0S FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ppnK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 ARCFL])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1z0s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z0s OCA], [https://pdbe.org/1z0s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1z0s RCSB], [https://www.ebi.ac.uk/pdbsum/1z0s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1z0s ProSAT], [https://www.topsan.org/Proteins/BSGC/1z0s TOPSAN]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1z0s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z0s OCA], [http://pdbe.org/1z0s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1z0s RCSB], [http://www.ebi.ac.uk/pdbsum/1z0s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1z0s ProSAT], [http://www.topsan.org/Proteins/BSGC/1z0s TOPSAN]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/NADK_ARCFU NADK_ARCFU]] 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.<ref>PMID:16242716</ref>
[https://www.uniprot.org/uniprot/NADK_ARCFU NADK_ARCFU] 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.<ref>PMID:16242716</ref>  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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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=1z0s ConSurf].
</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=1z0s ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
NAD kinase is a ubiquitous enzyme that catalyzes the phosphorylation of NAD to NADP using ATP or inorganic polyphosphate (poly(P)) as phosphate donor, and is regarded as the only enzyme responsible for the synthesis of NADP. We present here the crystal structures of an NAD kinase from the archaeal organism Archaeoglobus fulgidus in complex with its phosphate donor ATP at 1.7 A resolution, with its substrate NAD at 3.05 A resolution, and with the product NADP in two different crystal forms at 2.45 A and 2.0 A resolution, respectively. In the ATP bound structure, the AMP portion of the ATP molecule is found to use the same binding site as the nicotinamide ribose portion of NAD/NADP in the NAD/NADP bound structures. A magnesium ion is found to be coordinated to the phosphate tail of ATP as well as to a pyrophosphate group. The conserved GGDG loop forms hydrogen bonds with the pyrophosphate group in the ATP-bound structure and the 2' phosphate group of the NADP in the NADP-bound structures. A possible phosphate transfer mechanism is proposed on the basis of the structures presented.
Crystal structures of an NAD kinase from Archaeoglobus fulgidus in complex with ATP, NAD, or NADP.,Liu J, Lou Y, Yokota H, Adams PD, Kim R, Kim SH J Mol Biol. 2005 Nov 25;354(2):289-303. Epub 2005 Sep 30. PMID:16242716<ref>PMID:16242716</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1z0s" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Arcfl]]
[[Category: Archaeoglobus fulgidus]]
[[Category: Adams, P D]]
[[Category: Large Structures]]
[[Category: Structural genomic]]
[[Category: Adams PD]]
[[Category: Kim, R]]
[[Category: Kim R]]
[[Category: Kim, S H]]
[[Category: Kim SH]]
[[Category: Liu, J]]
[[Category: Liu J]]
[[Category: Lou, Y]]
[[Category: Lou Y]]
[[Category: Yokota, H]]
[[Category: Yokota H]]
[[Category: Atp]]
[[Category: Atp-binding]]
[[Category: Bsgc]]
[[Category: Nad]]
[[Category: Nad kinase]]
[[Category: Nadp]]
[[Category: PSI, Protein structure initiative]]
[[Category: Transferase]]

Latest revision as of 12:01, 14 February 2024

Crystal structure of an NAD kinase from Archaeoglobus fulgidus in complex with ATPCrystal structure of an NAD kinase from Archaeoglobus fulgidus in complex with ATP

Structural highlights

1z0s is a 4 chain structure with sequence from Archaeoglobus fulgidus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.7Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

NADK_ARCFU 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.[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ Liu J, Lou Y, Yokota H, Adams PD, Kim R, Kim SH. Crystal structures of an NAD kinase from Archaeoglobus fulgidus in complex with ATP, NAD, or NADP. J Mol Biol. 2005 Nov 25;354(2):289-303. Epub 2005 Sep 30. PMID:16242716 doi:10.1016/j.jmb.2005.09.026

1z0s, resolution 1.70Å

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