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5z8a

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Current revision (10:26, 27 March 2024) (edit) (undo)
 
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==Crystal structure of GenB1 from Micromonospora echinospora in complex with JI-20A and PLP (external aldimine)==
==Crystal structure of GenB1 from Micromonospora echinospora in complex with JI-20A and PLP (external aldimine)==
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<StructureSection load='5z8a' size='340' side='right' caption='[[5z8a]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
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<StructureSection load='5z8a' size='340' side='right'caption='[[5z8a]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5z8a]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_15837 Atcc 15837]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z8A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z8A FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5z8a]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Micromonospora_echinospora Micromonospora echinospora]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z8A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Z8A FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=JIA:(2~{R},3~{R},4~{R},5~{R})-2-[(1~{S},2~{S},3~{R},4~{S},6~{R})-3-[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-(aminomethyl)-3-azanyl-4,5-bis(oxidanyl)oxan-2-yl]oxy-4,6-bis(azanyl)-2-oxidanyl-cyclohexyl]oxy-5-methyl-4-(methylamino)oxane-3,5-diol'>JIA</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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]] 1.398&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">gacK, genB1, gntW ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1877 ATCC 15837])</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=JIA:(2~{R},3~{R},4~{R},5~{R})-2-[(1~{S},2~{S},3~{R},4~{S},6~{R})-3-[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-(aminomethyl)-3-azany+l-4,5-bis(oxidanyl)oxan-2-yl]oxy-4,6-bis(azanyl)-2-oxidanyl-cyclohexyl]oxy-5-methyl-4-(methylamino)oxane-3,5-diol'>JIA</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
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<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=5z8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z8a OCA], [http://pdbe.org/5z8a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z8a RCSB], [http://www.ebi.ac.uk/pdbsum/5z8a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z8a ProSAT]</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=5z8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z8a OCA], [https://pdbe.org/5z8a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5z8a RCSB], [https://www.ebi.ac.uk/pdbsum/5z8a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5z8a ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/Q70KD9_MICEC Q70KD9_MICEC]
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Gentamicin B (GB), a valuable starting material for the preparation of the semisynthetic aminoglycoside antibiotic isepamicin, is produced in trace amounts by the wild-type Micromonospora echinospora. Though the biosynthetic pathway to GB has remained obscure for decades, we have now identified three hidden pathways to GB production via seven hitherto unknown intermediates in M. echinospora. The narrow substrate specificity of a key glycosyltransferase and the C6'-amination enzymes, in combination with the weak and unsynchronized gene expression of the 2'-deamination enzymes, limits GB production in M. echinospora. The crystal structure of the aminotransferase involved in C6'-amination explains its substrate specificity. Some of the new intermediates displayed similar premature termination codon readthrough activity but with reduced toxicity compared to the natural aminoglycoside G418. This work not only led to the discovery of unknown biosynthetic routes to GB, but also demonstrated the potential to mine new aminoglycosides from nature for drug discovery.
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Complete reconstitution of the diverse pathways of gentamicin B biosynthesis.,Ban YH, Song MC, Hwang JY, Shin HL, Kim HJ, Hong SK, Lee NJ, Park JW, Cha SS, Liu HW, Yoon YJ Nat Chem Biol. 2019 Jan 14. pii: 10.1038/s41589-018-0203-4. doi:, 10.1038/s41589-018-0203-4. PMID:30643280<ref>PMID:30643280</ref>
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==See Also==
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*[[Aminotransferase 3D structures|Aminotransferase 3D structures]]
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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 5z8a" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Atcc 15837]]
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[[Category: Large Structures]]
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[[Category: Cha, S S]]
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[[Category: Micromonospora echinospora]]
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[[Category: Hong, S K]]
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[[Category: Cha SS]]
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[[Category: Aminotransferase]]
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[[Category: Hong SK]]
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[[Category: Plp-binding]]
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[[Category: Transferase]]
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Current revision

Crystal structure of GenB1 from Micromonospora echinospora in complex with JI-20A and PLP (external aldimine)

PDB ID 5z8a

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