1u0r: Difference between revisions

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<StructureSection load='1u0r' size='340' side='right'caption='[[1u0r]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
<StructureSection load='1u0r' size='340' side='right'caption='[[1u0r]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1u0r]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. 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 [http://proteopedia.org/fgij/fg.htm?mol=1U0R FirstGlance]. <br>
<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>
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1u0t|1u0t]]</div></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]] 2.8&#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=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</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=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>
<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'>[http://proteopedia.org/fgij/fg.htm?mol=1u0r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u0r OCA], [http://pdbe.org/1u0r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1u0r RCSB], [http://www.ebi.ac.uk/pdbsum/1u0r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1u0r ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://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>
[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 ==
== 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=1u0r 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=1u0r ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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:15269221<ref>PMID:15269221</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1u0r" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
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</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Finaurini, L]]
[[Category: Mycobacterium tuberculosis]]
[[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: Structural genomic]]
[[Category: Rizzi M]]
[[Category: Alpha-beta]]
[[Category: Beta sandwich]]
[[Category: PSI, Protein structure initiative]]
[[Category: Signaling protein]]
[[Category: Tbsgc]]
[[Category: Transferase]]

Latest revision as of 11:43, 14 February 2024

Crystal structure of Mycobacterium tuberculosis NAD kinaseCrystal structure of Mycobacterium tuberculosis NAD kinase

Structural highlights

1u0r is a 4 chain structure with sequence from Mycobacterium tuberculosis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.8Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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][1] [2]

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. ↑ Kawai S, Mori S, Mukai T, Suzuki S, Yamada T, Hashimoto W, Murata K. Inorganic Polyphosphate/ATP-NAD kinase of Micrococcus flavus and Mycobacterium tuberculosis H37Rv. Biochem Biophys Res Commun. 2000 Sep 16;276(1):57-63. PMID:11006082 doi:http://dx.doi.org/10.1006/bbrc.2000.3433
  2. ↑ Raffaelli N, Finaurini L, Mazzola F, Pucci L, Sorci L, Amici A, Magni G. Characterization of Mycobacterium tuberculosis NAD kinase: functional analysis of the full-length enzyme by site-directed mutagenesis. Biochemistry. 2004 Jun 15;43(23):7610-7. PMID:15182203 doi:http://dx.doi.org/10.1021/bi049650w

1u0r, resolution 2.80Å

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