3gz5: Difference between revisions

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<StructureSection load='3gz5' size='340' side='right'caption='[[3gz5]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
<StructureSection load='3gz5' size='340' side='right'caption='[[3gz5]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3gz5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_700550 Atcc 700550]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GZ5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GZ5 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3gz5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Shewanella_oneidensis Shewanella oneidensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GZ5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GZ5 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2.2&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3gz6|3gz6]], [[3gz8|3gz8]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NrtR, SO_1979 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70863 ATCC 700550])</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=3gz5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gz5 OCA], [https://pdbe.org/3gz5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gz5 RCSB], [https://www.ebi.ac.uk/pdbsum/3gz5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gz5 ProSAT]</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=3gz5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gz5 OCA], [https://pdbe.org/3gz5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gz5 RCSB], [https://www.ebi.ac.uk/pdbsum/3gz5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gz5 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q8EFJ3_SHEON Q8EFJ3_SHEON]
== 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=3gz5 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=3gz5 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Besides its function as an essential redox cofactor, nicotinamide adenine dinucleotide (NAD) also serves as a consumable substrate for several reactions with broad impact on many cellular processes. NAD homeostasis appears to be tightly controlled, but the mechanism of its regulation is little understood. Here we demonstrate that a previously predicted bacterial transcriptional regulator, NrtR, represses the transcription of NAD biosynthetic genes in vitro. The NAD metabolite ADP-ribose functions as an activator suppressing NrtR repressor activity. The presence of high ADP-ribose levels in the cell is indicative of active NAD turnover in bacteria, which could signal the activation of NAD biosynthetic gene expression via inhibiting the repressor function of NrtR. By comparing the crystal structures of NrtR in complex with DNA and with ADP-ribose, we identified a "Nudix switch" element that likely plays a critical role in the allosteric regulation of DNA binding and repressor function of NrtR.
Structure and function of an ADP-ribose-dependent transcriptional regulator of NAD metabolism.,Huang N, De Ingeniis J, Galeazzi L, Mancini C, Korostelev YD, Rakhmaninova AB, Gelfand MS, Rodionov DA, Raffaelli N, Zhang H Structure. 2009 Jul 15;17(7):939-51. PMID:19604474<ref>PMID:19604474</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3gz5" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[7%2C8-dihydro-8-oxoguanine triphosphatase 3D structures|7%2C8-dihydro-8-oxoguanine triphosphatase 3D structures]]
*[[7%2C8-dihydro-8-oxoguanine triphosphatase 3D structures|7%2C8-dihydro-8-oxoguanine triphosphatase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Atcc 700550]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Huang, N]]
[[Category: Shewanella oneidensis]]
[[Category: Zhang, H]]
[[Category: Huang N]]
[[Category: Dna binding protein]]
[[Category: Zhang H]]
[[Category: Nudix domain]]
[[Category: Whth domain]]

Latest revision as of 09:57, 21 February 2024

Crystal structure of Shewanella oneidensis NrtR

3gz5, resolution 2.20Å

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