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3tm0

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Current revision (13:33, 14 March 2024) (edit) (undo)
 
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<StructureSection load='3tm0' size='340' side='right'caption='[[3tm0]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
<StructureSection load='3tm0' size='340' side='right'caption='[[3tm0]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3tm0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"enterococcus_proteiformis"_thiercelin_and_jouhaud_1903 "enterococcus proteiformis" thiercelin and jouhaud 1903]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3h8p 3h8p]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TM0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TM0 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3tm0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterococcus_faecalis Enterococcus faecalis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3h8p 3h8p]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TM0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TM0 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=B31:(2S)-4-AMINO-N-[(1R,2S,3R,4R,5S)-5-AMINO-4-[(2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]-2-HYDROXY-3-(BETA-D-XYLOFURANOSYLOXY)CYCLOHEXYL]-2-HYDROXYBUTANAMIDE'>B31</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1j7i|1j7i]], [[1j7l|1j7l]], [[1j7u|1j7u]], [[1l8t|1l8t]], [[2b0q|2b0q]], [[3tl7|3tl7]]</div></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=B31:(2S)-4-AMINO-N-[(1R,2S,3R,4R,5S)-5-AMINO-4-[(2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]-2-HYDROXY-3-(BETA-D-XYLOFURANOSYLOXY)CYCLOHEXYL]-2-HYDROXYBUTANAMIDE'>B31</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">aph(3')-iiia, aphA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1351 "Enterococcus proteiformis" Thiercelin and Jouhaud 1903])</td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Kanamycin_kinase Kanamycin kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.95 2.7.1.95] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3tm0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tm0 OCA], [https://pdbe.org/3tm0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tm0 RCSB], [https://www.ebi.ac.uk/pdbsum/3tm0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tm0 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=3tm0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tm0 OCA], [https://pdbe.org/3tm0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tm0 RCSB], [https://www.ebi.ac.uk/pdbsum/3tm0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tm0 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[https://www.uniprot.org/uniprot/KKA3_ENTFL KKA3_ENTFL]] Resistance to kanamycin and structurally-related aminoglycosides, including amikacin.
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[https://www.uniprot.org/uniprot/KKA3_ENTFL KKA3_ENTFL] Resistance to kanamycin and structurally-related aminoglycosides, including amikacin.
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Butirosin is unique among the naturally occurring aminoglycosides, having a substituted amino group at position 1 (N1) of the 2-deoxystreptamine ring with an (S)-4-amino-2-hydroxybutyrate (AHB) group. While bacterial resistance to aminoglycosides can be ascribed chiefly to drug inactivation by plasmid-encoded aminoglycoside-modifying enzymes, the presence of an AHB group protects the aminoglycoside from binding to many resistance enzymes, and hence, the antibiotic retains its bactericidal properties. Consequently, several semisynthetic N1-substituted aminoglycosides, such as amikacin, isepamicin, and netilmicin, were developed. Unfortunately, butirosin, amikacin, and isepamicin are not resistant to inactivation by 3'-aminoglycoside O-phosphotransferase type IIIa [APH(3')-IIIa]. We report here the crystal structure of APH(3')-IIIa in complex with an ATP analog, AMPPNP [adenosine 5'-(beta,gamma-imido)triphosphate], and butirosin A to 2.4-A resolution. The structure shows that butirosin A binds to the enzyme in a manner analogous to other 4,5-disubstituted aminoglycosides, and the flexible antibiotic-binding loop is key to the accommodation of structurally diverse substrates. Based on the crystal structure, we have also constructed a model of APH(3')-IIIa in complex with amikacin, a commonly used semisynthetic N1-substituted 4,6-disubstituted aminoglycoside. Together, these results suggest a strategy to further derivatize the AHB group in order to generate new aminoglycoside derivatives that can elude inactivation by resistance enzymes while maintaining their ability to bind to the ribosomal A site.
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Structural basis of APH(3')-IIIa-mediated resistance to N1-substituted aminoglycoside antibiotics.,Fong DH, Berghuis AM Antimicrob Agents Chemother. 2009 Jul;53(7):3049-55. Epub 2009 May 11. PMID:19433564<ref>PMID:19433564</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3tm0" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[Phosphotransferase 3D structures|Phosphotransferase 3D structures]]
*[[Phosphotransferase 3D structures|Phosphotransferase 3D structures]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Enterococcus proteiformis thiercelin and jouhaud 1903]]
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[[Category: Enterococcus faecalis]]
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[[Category: Kanamycin kinase]]
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[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Berghuis, A M]]
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[[Category: Berghuis AM]]
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[[Category: Fong, D H]]
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[[Category: Fong DH]]
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[[Category: Phosphorylation]]
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[[Category: Protein kinase]]
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[[Category: Transferase-antibiotic complex]]
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Current revision

Crystal Structure of 3',5"-Aminoglycoside Phosphotransferase Type IIIa AMPPNP Butirosin A Complex

PDB ID 3tm0

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