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 [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_choleraesuis_str._a50 Salmonella enterica subsp. enterica serovar choleraesuis str. a50]. 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>
</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='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>
<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='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='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='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. A50])</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='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>
<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://pdbe.org/4f3c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4f3c RCSB], [http://www.ebi.ac.uk/pdbsum/4f3c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4f3c ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
</div>
<div class="pdbe-citations 4f3c" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
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</StructureSection>
</StructureSection>
[[Category: Adenosylhomocysteine nucleosidase]]
[[Category: Adenosylhomocysteine nucleosidase]]
[[Category: Salmonella enterica subsp. enterica serovar choleraesuis str. scsa50]]
[[Category: Salmonella enterica subsp. enterica serovar choleraesuis str. a50]]
[[Category: Almo, S C]]
[[Category: Almo, S C]]
[[Category: Bonanno, J B]]
[[Category: Bonanno, J B]]

Revision as of 10:24, 5 August 2016

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. a50. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:,
Gene:EMBL EFZ04802.1, mtnN, pfs, SCA50_0219 (Salmonella enterica subsp. enterica serovar Choleraesuis str. A50)
Activity:Adenosylhomocysteine nucleosidase, with EC number 3.2.2.9
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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]

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[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

  1. ↑ Haapalainen AM, Thomas K, Tyler PC, Evans GB, Almo SC, Schramm VL. Salmonella enterica MTAN at 1.36 A Resolution: A Structure-Based Design of Tailored Transition State Analogs. Structure. 2013 May 14. pii: S0969-2126(13)00121-4. doi:, 10.1016/j.str.2013.04.009. PMID:23685211 doi:10.1016/j.str.2013.04.009

4f3c, resolution 1.93Å

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