3vex

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Current revision (14:26, 14 March 2024) (edit) (undo)
 
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<StructureSection load='3vex' size='340' side='right'caption='[[3vex]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
<StructureSection load='3vex' size='340' side='right'caption='[[3vex]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3vex]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"streptomyces_tenebrarius"_higgins_and_kastner_(1968) "streptomyces tenebrarius" higgins and kastner (1968)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VEX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VEX FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3vex]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptoalloteichus_tenebrarius Streptoalloteichus tenebrarius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VEX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VEX 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=CA0:5-O-[(S)-(CARBAMOYLOXY)(HYDROXY)PHOSPHORYL]ADENOSINE'>CA0</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.9&#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;'>[[3ven|3ven]], [[3veo|3veo]], [[3ver|3ver]], [[3ves|3ves]], [[3vet|3vet]], [[3vew|3vew]], [[3vez|3vez]], [[3vf2|3vf2]], [[3vf4|3vf4]]</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=CA0:5-O-[(S)-(CARBAMOYLOXY)(HYDROXY)PHOSPHORYL]ADENOSINE'>CA0</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">tacA, tobZ ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1933 "Streptomyces tenebrarius" Higgins and Kastner (1968)])</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=3vex FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vex OCA], [https://pdbe.org/3vex PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vex RCSB], [https://www.ebi.ac.uk/pdbsum/3vex PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vex 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=3vex FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vex OCA], [https://pdbe.org/3vex PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vex RCSB], [https://www.ebi.ac.uk/pdbsum/3vex PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vex ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[https://www.uniprot.org/uniprot/TOBZ_STRSD TOBZ_STRSD]] TobZ is involved in the biosynthesis of the 2-deoxystreptamine-containing aminoglycoside antibiotics such as nebramycin 5 and 6-O-carbamoylkanamycin. Catalyzes the hydrolysis of carbamoyl phosphate and its subsequent adenylation by ATP to yield O-carbamoyladenylate. Then it catalyzes the transfer of the carbamoyl moiety from O-carbamoyladenylate to the tobramycin 6-hydroxy group to yield nebramycin 5. It catalyzes the same reaction with kanamycin A. These reactions are considerably slower in the presence of deoxy-ATP.<ref>PMID:20936279</ref> <ref>PMID:22383337</ref>
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[https://www.uniprot.org/uniprot/TOBZ_STRSD TOBZ_STRSD] TobZ is involved in the biosynthesis of the 2-deoxystreptamine-containing aminoglycoside antibiotics such as nebramycin 5 and 6-O-carbamoylkanamycin. Catalyzes the hydrolysis of carbamoyl phosphate and its subsequent adenylation by ATP to yield O-carbamoyladenylate. Then it catalyzes the transfer of the carbamoyl moiety from O-carbamoyladenylate to the tobramycin 6-hydroxy group to yield nebramycin 5. It catalyzes the same reaction with kanamycin A. These reactions are considerably slower in the presence of deoxy-ATP.<ref>PMID:20936279</ref> <ref>PMID:22383337</ref>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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An ancient reaction vessel: TobZ carbamoylates the antibiotic tobramycin to form nebramycin 5'. The YrdC-like domain (blue) catalyzes the formation of the novel intermediate carbamoyladenylate, which is channeled through a common "reaction chamber" to the Kae1-like domain (brown), site of carbamoyl transfer.
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The O-Carbamoyltransferase TobZ Catalyzes an Ancient Enzymatic Reaction.,Parthier C, Gorlich S, Jaenecke F, Breithaupt C, Brauer U, Fandrich U, Clausnitzer D, Wehmeier UF, Bottcher C, Scheel D, Stubbs MT Angew Chem Int Ed Engl. 2012 Mar 1. doi: 10.1002/anie.201108896. PMID:22383337<ref>PMID:22383337</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 3vex" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
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</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Goerlich, S]]
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[[Category: Streptoalloteichus tenebrarius]]
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[[Category: Jaenecke, F]]
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[[Category: Goerlich S]]
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[[Category: Parthier, C]]
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[[Category: Jaenecke F]]
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[[Category: Stubbs, M T]]
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[[Category: Parthier C]]
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[[Category: Adenylation]]
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[[Category: Stubbs MT]]
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[[Category: Antibiotic biosynthesis]]
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[[Category: Enzyme evolution]]
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[[Category: Structural enzymology]]
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[[Category: Substrate assisted catalysis]]
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[[Category: Substrate channeling]]
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[[Category: Transferase]]
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Current revision

Crystal structure of the O-carbamoyltransferase TobZ H14N variant in complex with carbamoyl adenylate intermediate

PDB ID 3vex

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Proteopedia Page Contributors and Editors (what is this?)

OCA

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