3ven: Difference between revisions

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<StructureSection load='3ven' size='340' side='right'caption='[[3ven]], [[Resolution|resolution]] 1.57&Aring;' scene=''>
<StructureSection load='3ven' size='340' side='right'caption='[[3ven]], [[Resolution|resolution]] 1.57&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3ven]] 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=3VEN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VEN FirstGlance]. <br>
<table><tr><td colspan='2'>[[3ven]] 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=3VEN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VEN FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.57&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3veo|3veo]], [[3ver|3ver]], [[3ves|3ves]], [[3vet|3vet]], [[3vew|3vew]], [[3vex|3vex]], [[3vez|3vez]], [[3vf2|3vf2]], [[3vf4|3vf4]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
<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>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ven FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ven OCA], [https://pdbe.org/3ven PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ven RCSB], [https://www.ebi.ac.uk/pdbsum/3ven PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ven 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=3ven FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ven OCA], [https://pdbe.org/3ven PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ven RCSB], [https://www.ebi.ac.uk/pdbsum/3ven PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ven ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[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> 
[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>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
 
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>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3ven" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
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</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Goerlich, S]]
[[Category: Streptoalloteichus tenebrarius]]
[[Category: Jaenecke, F]]
[[Category: Goerlich S]]
[[Category: Parthier, C]]
[[Category: Jaenecke F]]
[[Category: Stubbs, M T]]
[[Category: Parthier C]]
[[Category: Adenylation]]
[[Category: Stubbs MT]]
[[Category: Antibiotic biosynthesis]]
[[Category: Enzyme evolution]]
[[Category: Structural enzymology]]
[[Category: Substrate assisted catalysis]]
[[Category: Substrate channeling]]
[[Category: Transferase]]

Latest revision as of 13:35, 1 March 2024

Crystal structure of the O-carbamoyltransferase TobZCrystal structure of the O-carbamoyltransferase TobZ

Structural highlights

3ven is a 1 chain structure with sequence from Streptoalloteichus tenebrarius. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.57Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.[1] [2]

References

  1. ↑ Ni X, Li D, Yang L, Huang T, Li H, Xia H. Construction of kanamycin B overproducing strain by genetic engineering of Streptomyces tenebrarius. Appl Microbiol Biotechnol. 2011 Feb;89(3):723-31. doi: 10.1007/s00253-010-2908-5., Epub 2010 Oct 9. PMID:20936279 doi:http://dx.doi.org/10.1007/s00253-010-2908-5
  2. ↑ Parthier C, Gorlich S, Jaenecke F, Breithaupt C, Brauer U, Fandrich U, Clausnitzer D, Wehmeier UF, Bottcher C, Scheel D, Stubbs MT. The O-Carbamoyltransferase TobZ Catalyzes an Ancient Enzymatic Reaction. Angew Chem Int Ed Engl. 2012 Mar 1. doi: 10.1002/anie.201108896. PMID:22383337 doi:10.1002/anie.201108896

3ven, resolution 1.57Å

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