4f3c: Difference between revisions

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==Crystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Salmonella enterica with butyl-thio-DADMe-Immucillin-A==
==Crystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Salmonella enterica with butyl-thio-DADMe-Immucillin-A==
<StructureSection load='4f3c' size='340' side='right' caption='[[4f3c]], [[Resolution|resolution]] 1.93&Aring;' scene=''>
<StructureSection load='4f3c' size='340' side='right'caption='[[4f3c]], [[Resolution|resolution]] 1.93&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4f3c]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_choleraesuis_str._scsa50 Salmonella enterica subsp. enterica serovar choleraesuis str. scsa50]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4F3C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4F3C FirstGlance]. <br>
<table><tr><td colspan='2'>[[4f3c]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Choleraesuis_str._SCSA50 Salmonella enterica subsp. enterica serovar Choleraesuis str. SCSA50]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4F3C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4F3C FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BIG:(3R,4S)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-4-[(BUTYLSULFANYL)METHYL]PYRROLIDIN-3-OL'>BIG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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]] 1.93&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4f1w|4f1w]], [[4f2p|4f2p]], [[4f2w|4f2w]], [[4f3k|4f3k]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BIG:(3R,4S)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-4-[(BUTYLSULFANYL)METHYL]PYRROLIDIN-3-OL'>BIG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">EMBL EFZ04802.1, mtnN, pfs, SCA50_0219 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=904139 Salmonella enterica subsp. enterica serovar Choleraesuis str. SCSA50])</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=4f3c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4f3c OCA], [https://pdbe.org/4f3c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4f3c RCSB], [https://www.ebi.ac.uk/pdbsum/4f3c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4f3c 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/Adenosylhomocysteine_nucleosidase Adenosylhomocysteine nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.9 3.2.2.9] </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=4f3c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4f3c OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4f3c RCSB], [http://www.ebi.ac.uk/pdbsum/4f3c PDBsum]</span></td></tr>
</table>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/E8NLP5_SALET E8NLP5_SALET]] Catalyzes the irreversible cleavage of the glycosidic bond in both 5'-methylthioadenosine (MTA) and S-adenosylhomocysteine (SAH/AdoHcy) to adenine and the corresponding thioribose, 5'-methylthioribose and S-ribosylhomocysteine, respectively (By similarity).[HAMAP-Rule:MF_01684]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Accumulation of 5'-methylthioadenosine (MTA) and S-adenosylhomocysteine (SAH) in bacteria disrupts the S-adenosylmethionine pool to alter biological methylations, synthesis of polyamines, and production of quorum-sensing molecules. Bacterial metabolism of MTA and SAH depends on MTA/SAH nucleosidase (MTAN), an enzyme not present in humans and a target for quorum sensing because MTAN activity is essential for synthesis of autoinducer-2 molecules. Crystals of Salmonella enterica MTAN with product and transition state analogs of MTA and SAH explain the structural contacts causing pM binding affinity for the inhibitor and reveal a "water-wire" channel for the catalytic nucleophile. The crystal structure shows an extension of the binding pocket filled with polyethylene glycol. We exploited this discovery by the design and synthesis of tailored modifications of the currently existing transition state analogs to fill this site. This site was not anticipated in MTAN structures. Tailored inhibitors with dissociation constants of 5 to 15 pM are characterized.
Salmonella enterica MTAN at 1.36 A Resolution: A Structure-Based Design of Tailored Transition State Analogs.,Haapalainen AM, Thomas K, Tyler PC, Evans GB, Almo SC, Schramm VL Structure. 2013 May 14. pii: S0969-2126(13)00121-4. doi:, 10.1016/j.str.2013.04.009. PMID:23685211<ref>PMID:23685211</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Adenosylhomocysteine nucleosidase]]
[[Category: Large Structures]]
[[Category: Salmonella enterica subsp. enterica serovar choleraesuis str. scsa50]]
[[Category: Salmonella enterica subsp. enterica serovar Choleraesuis str. SCSA50]]
[[Category: Almo, S C]]
[[Category: Almo SC]]
[[Category: Bonanno, J B]]
[[Category: Bonanno JB]]
[[Category: Haapalainen, A M]]
[[Category: Haapalainen AM]]
[[Category: Schramm, V L]]
[[Category: Schramm VL]]
[[Category: Thomas, K]]
[[Category: Thomas K]]
[[Category: 5'-methylthioadenosine/s-adenosylhomocysteine nucleosidase]]
[[Category: Acting on glycosyl bond]]
[[Category: Adenosylhomocysteine nucleosidase activity]]
[[Category: Hydrolase-hydrolase inhibitor complex]]
[[Category: L-methionine biosynthetic process from s-adenosylmethionine]]
[[Category: L-methionine salvage from methylthioadenosine]]
[[Category: Methylthioadenosine nucleosidase activity]]

Latest revision as of 14:09, 1 March 2024

Crystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Salmonella enterica with butyl-thio-DADMe-Immucillin-ACrystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Salmonella enterica with butyl-thio-DADMe-Immucillin-A

Structural highlights

4f3c is a 2 chain structure with sequence from Salmonella enterica subsp. enterica serovar Choleraesuis str. SCSA50. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.93Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

4f3c, resolution 1.93Å

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