3nm6: Difference between revisions

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-{{STRUCTURE_3nm6|  PDB=3nm6  |  SCENE=  }}
-===Helicobacter pylori MTAN complexed with adenine and tris===
-{{ABSTRACT_PUBMED_20954236}}
-==Function==
+==Helicobacter pylori MTAN complexed with adenine and tris==
-[[http://www.uniprot.org/uniprot/MTNN_HELPJ MTNN_HELPJ]] Responsible for cleavage of the glycosidic bond in both 5'-methylthioadenosine (MTA) and S-adenosylhomocysteine (SAH) (By similarity).
+<StructureSection load='3nm6' size='340' side='right'caption='[[3nm6]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3nm6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori_J99 Helicobacter pylori J99]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NM6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NM6 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.602&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADE:ADENINE'>ADE</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></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=3nm6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nm6 OCA], [https://pdbe.org/3nm6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nm6 RCSB], [https://www.ebi.ac.uk/pdbsum/3nm6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nm6 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MQMTN_HELPJ MQMTN_HELPJ] Catalyzes the direct conversion of aminodeoxyfutalosine (AFL) into dehypoxanthine futalosine (DHFL) and adenine via the hydrolysis of the N-glycosidic bond; this reaction seems to represent an essential step in the menaquinone biosynthesis pathway in Helicobacter species. Also catalyzes the hydrolysis of 5'-methylthioadenosine (MTA) to adenine and 5'-methylthioribose. Can also probably use S-adenosylhomocysteine (SAH) as substrate, leading to adenine and S-ribosylhomocysteine. These other activities highlight the tremendous versatility of the enzyme, which also plays key roles in S-adenosylmethionine recycling and in the biosynthesis of the quorum-sensing molecule autoinducer-2.<ref>PMID:20954236</ref> <ref>PMID:22891633</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The bacterial enzyme 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) plays a central role in three essential metabolic pathways in bacteria: methionine salvage, purine salvage, and polyamine biosynthesis. Recently, its role in the pathway that leads to the production of autoinducer II, an important component in quorum-sensing, has garnered much interest. Because of this variety of roles, MTAN is an attractive target for developing new classes of inhibitors that influence bacterial virulence and biofilm formation. To gain insight toward the development of new classes of MTAN inhibitors, the interactions between the Helicobacter pylori encoded MTAN and its substrates and substrate analogs were probed using X-ray crystallography. The structures of MTAN, an MTAN-Formycin A complex, and an adenine bound form were solved by molecular replacement and refined to 1.7, 1.8, and 1.6 A, respectively. The ribose binding site in the MTAN and MTAN-adenine co-crystal structures contain a tris[hydroxymethyl]aminomethane molecule, that stabilizes the closed form of the enzyme and displaces a nucleophilic water molecule necessary for catalysis. This research gives insight to the interactions between MTAN and bound ligands that promote closing of the enzyme active site and highlights the potential for designing new classes of MTAN inhibitors using a link/grow or ligand assembly development strategy based on the described H. pylori MTAN crystal structures.
-==About this Structure==
+Enzyme-ligand interactions that drive active site rearrangements in the Helicobacter pylori 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase.,Ronning DR, Iacopelli NM, Mishra V Protein Sci. 2010 Oct 15. PMID:20954236<ref>PMID:20954236</ref>
-[[3nm6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NM6 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<ref group="xtra">PMID:020954236</ref><references group="xtra"/><references/>
+</div>
-[[Category: Adenosylhomocysteine nucleosidase]]
+<div class="pdbe-citations 3nm6" style="background-color:#fffaf0;"></div>
-[[Category: Helicobacter pylori]]
+== References ==
-[[Category: Iacopelli, N M.]]
+<references/>
-[[Category: Ronning, D R.]]
+__TOC__
-[[Category: Hydrolase]]
+</StructureSection>
-[[Category: Nucleosidase]]
+[[Category: Helicobacter pylori J99]]
+[[Category: Large Structures]]
+[[Category: Iacopelli NM]]
+[[Category: Ronning DR]]