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2r5w
From Proteopedia
(Difference between revisions)
(New page: 200px<br /><applet load="2r5w" size="350" color="white" frame="true" align="right" spinBox="true" caption="2r5w, resolution 2.30Å" /> '''Crystal structure of...) |
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| - | [[Image:2r5w.jpg|left|200px]]<br /><applet load="2r5w" size="350" color="white" frame="true" align="right" spinBox="true" | ||
| - | caption="2r5w, resolution 2.30Å" /> | ||
| - | '''Crystal structure of a bifunctional NMN adenylyltransferase/ADP ribose pyrophosphatase from Francisella tularensis'''<br /> | ||
| - | == | + | ==Crystal structure of a bifunctional NMN adenylyltransferase/ADP ribose pyrophosphatase from Francisella tularensis== |
| - | Bacterial NadM-Nudix is a bifunctional enzyme containing a nicotinamide mononucleotide (NMN) adenylyltransferase and an ADP-ribose (ADPR) pyrophosphatase domain. While most members of this enzyme family, such as that from a model cyanobacterium Synechocystis sp., are involved primarily in nicotinamide adenine dinucleotide (NAD) salvage/recycling pathways, its close homolog in a category-A biodefense pathogen, Francisella tularensis, likely plays a central role in a recently discovered novel pathway of NAD de novo synthesis. The crystal structures of NadM-Nudix from both species, including their complexes with various ligands and catalytic metal ions, revealed detailed configurations of the substrate binding and catalytic sites in both domains. The structure of the N-terminal NadM domain may be exploited for designing new antitularemia therapeutics. The ADPR binding site in the C-terminal Nudix domain is substantially different from that of Escherichia coli ADPR pyrophosphatase, and is more similar to human NUDT9. The latter observation provided new insights into the ligand binding mode of ADPR-gated | + | <StructureSection load='2r5w' size='340' side='right'caption='[[2r5w]], [[Resolution|resolution]] 2.30Å' scene=''> |
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[2r5w]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"francisella_tularensis_subsp._nearctica"_olsufjev_1970 "francisella tularensis subsp. nearctica" olsufjev 1970]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R5W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R5W FirstGlance]. <br> | ||
| + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | ||
| + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2qjt|2qjt]]</div></td></tr> | ||
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nadM ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=119856 "Francisella tularensis subsp. nearctica" Olsufjev 1970])</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=2r5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r5w OCA], [https://pdbe.org/2r5w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r5w RCSB], [https://www.ebi.ac.uk/pdbsum/2r5w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r5w ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Evolutionary Conservation == | ||
| + | [[Image:Consurf_key_small.gif|200px|right]] | ||
| + | Check<jmol> | ||
| + | <jmolCheckbox> | ||
| + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r5/2r5w_consurf.spt"</scriptWhenChecked> | ||
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
| + | <text>to colour the structure by Evolutionary Conservation</text> | ||
| + | </jmolCheckbox> | ||
| + | </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=2r5w ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Bacterial NadM-Nudix is a bifunctional enzyme containing a nicotinamide mononucleotide (NMN) adenylyltransferase and an ADP-ribose (ADPR) pyrophosphatase domain. While most members of this enzyme family, such as that from a model cyanobacterium Synechocystis sp., are involved primarily in nicotinamide adenine dinucleotide (NAD) salvage/recycling pathways, its close homolog in a category-A biodefense pathogen, Francisella tularensis, likely plays a central role in a recently discovered novel pathway of NAD de novo synthesis. The crystal structures of NadM-Nudix from both species, including their complexes with various ligands and catalytic metal ions, revealed detailed configurations of the substrate binding and catalytic sites in both domains. The structure of the N-terminal NadM domain may be exploited for designing new antitularemia therapeutics. The ADPR binding site in the C-terminal Nudix domain is substantially different from that of Escherichia coli ADPR pyrophosphatase, and is more similar to human NUDT9. The latter observation provided new insights into the ligand binding mode of ADPR-gated Ca2+ channel TRPM2. | ||
| - | + | Bifunctional NMN adenylyltransferase/ADP-ribose pyrophosphatase: structure and function in bacterial NAD metabolism.,Huang N, Sorci L, Zhang X, Brautigam CA, Li X, Raffaelli N, Magni G, Grishin NV, Osterman AL, Zhang H Structure. 2008 Feb;16(2):196-209. PMID:18275811<ref>PMID:18275811</ref> | |
| - | + | ||
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | [[Category: Francisella tularensis subsp. | + | <div class="pdbe-citations 2r5w" style="background-color:#fffaf0;"></div> |
| - | [[Category: | + | == References == |
| - | [[Category: Brautigan, C | + | <references/> |
| - | [[Category: Grishin, N | + | __TOC__ |
| - | [[Category: Huang, N | + | </StructureSection> |
| - | [[Category: Li, X | + | [[Category: Francisella tularensis subsp. nearctica olsufjev 1970]] |
| - | [[Category: Osterman, A | + | [[Category: Large Structures]] |
| - | [[Category: Raffaelli, N | + | [[Category: Brautigan, C]] |
| - | [[Category: Sorci, L | + | [[Category: Grishin, N]] |
| - | [[Category: Zhang, H | + | [[Category: Huang, N]] |
| - | [[Category: Zhang, X | + | [[Category: Li, X]] |
| - | [[Category: | + | [[Category: Osterman, A]] |
| - | [[Category: | + | [[Category: Raffaelli, N]] |
| - | [[Category: | + | [[Category: Sorci, L]] |
| - | [[Category: | + | [[Category: Zhang, H]] |
| - | + | [[Category: Zhang, X]] | |
| - | + | [[Category: Hydrolase]] | |
| - | + | [[Category: Nucleotidyltransferase]] | |
| - | + | [[Category: Transferase]] | |
| + | [[Category: Two domain protein]] | ||
Current revision
Crystal structure of a bifunctional NMN adenylyltransferase/ADP ribose pyrophosphatase from Francisella tularensis
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