3vf2

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Current revision (14:26, 14 March 2024) (edit) (undo)
 
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<StructureSection load='3vf2' size='340' side='right'caption='[[3vf2]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
<StructureSection load='3vf2' size='340' side='right'caption='[[3vf2]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3vf2]] 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=3VF2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VF2 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3vf2]] 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=3VF2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VF2 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=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CP:PHOSPHORIC+ACID+MONO(FORMAMIDE)ESTER'>CP</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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]] 2.9&#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]], [[3vex|3vex]], [[3vez|3vez]], [[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=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CP:PHOSPHORIC+ACID+MONO(FORMAMIDE)ESTER'>CP</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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=3vf2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vf2 OCA], [https://pdbe.org/3vf2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vf2 RCSB], [https://www.ebi.ac.uk/pdbsum/3vf2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vf2 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=3vf2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vf2 OCA], [https://pdbe.org/3vf2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vf2 RCSB], [https://www.ebi.ac.uk/pdbsum/3vf2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vf2 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 3vf2" 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 M473I variant in complex with carbamoyl phosphate and ADP

PDB ID 3vf2

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Proteopedia Page Contributors and Editors (what is this?)

OCA

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