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| | <StructureSection load='6iy9' size='340' side='right'caption='[[6iy9]], [[Resolution|resolution]] 2.40Å' scene=''> | | <StructureSection load='6iy9' size='340' side='right'caption='[[6iy9]], [[Resolution|resolution]] 2.40Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6iy9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"actinomyces_hygroscopicus"_jensen_1931 "actinomyces hygroscopicus" jensen 1931]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IY9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IY9 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6iy9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_hygroscopicus Streptomyces hygroscopicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IY9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IY9 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=HY0:HYGROMYCIN+B+VARIANT'>HY0</scene>, <scene name='pdbligand=NHE:2-[N-CYCLOHEXYLAMINO]ETHANE+SULFONIC+ACID'>NHE</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]] 2.4Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=HY0:HYGROMYCIN+B+VARIANT'>HY0</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NHE:2-[N-CYCLOHEXYLAMINO]ETHANE+SULFONIC+ACID'>NHE</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">hyg ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1912 "Actinomyces hygroscopicus" Jensen 1931])</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=6iy9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iy9 OCA], [https://pdbe.org/6iy9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6iy9 RCSB], [https://www.ebi.ac.uk/pdbsum/6iy9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6iy9 ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Hygromycin-B_7''-O-kinase Hygromycin-B 7''-O-kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.119 2.7.1.119] </span></td></tr>
| + | |
| - | <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=6iy9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iy9 OCA], [http://pdbe.org/6iy9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6iy9 RCSB], [http://www.ebi.ac.uk/pdbsum/6iy9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6iy9 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/KHYB_STRHY KHYB_STRHY]] The aminoglycoside phosphotransferases achieve inactivation of their antibiotic substrates by phosphorylation. | + | [https://www.uniprot.org/uniprot/KHYB_STRHY KHYB_STRHY] The aminoglycoside phosphotransferases achieve inactivation of their antibiotic substrates by phosphorylation. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Actinomyces hygroscopicus jensen 1931]] | |
| - | [[Category: Hygromycin-B 7''-O-kinase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Adachi, Y]] | + | [[Category: Streptomyces hygroscopicus]] |
| - | [[Category: Ito, S]] | + | [[Category: Adachi Y]] |
| - | [[Category: Nakamura, A]] | + | [[Category: Ito S]] |
| - | [[Category: Sasaki, Y]] | + | [[Category: Nakamura A]] |
| - | [[Category: Shimamura, T]] | + | [[Category: Sasaki Y]] |
| - | [[Category: Takenoya, M]] | + | [[Category: Shimamura T]] |
| - | [[Category: Yajima, S]] | + | [[Category: Takenoya M]] |
| - | [[Category: Yamanaka, R]] | + | [[Category: Yajima S]] |
| - | [[Category: Complex]]
| + | [[Category: Yamanaka R]] |
| - | [[Category: Kinase]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
KHYB_STRHY The aminoglycoside phosphotransferases achieve inactivation of their antibiotic substrates by phosphorylation.
Publication Abstract from PubMed
Hygromycin B (HygB) is one of the aminoglycoside antibiotics, and it is widely used as a reagent in molecular-biology experiments. Two kinases are known to inactivate HygB through phosphorylation: aminoglycoside 7-phosphotransferase-Ia [APH(7)-Ia] from Streptomyces hygroscopicus and aminoglycoside 4-phosphotransferase-Ia [APH(4)-Ia] from Escherichia coli. They phosphorylate the hydroxyl groups at positions 7 and 4 of the HygB molecule, respectively. Previously, the crystal structure of APH(4)-Ia was reported as a ternary complex with HygB and 5'-adenylyl-beta,gamma-imidodiphosphate (AMP-PNP). To investigate the differences in the substrate-recognition mechanism between APH(7)-Ia and APH(4)-Ia, the crystal structure of APH(7)-Ia complexed with HygB is reported. The overall structure of APH(7)-Ia is similar to those of other aminoglycoside phosphotransferases, including APH(4)-Ia, and consists of an N-terminal lobe (N-lobe) and a C-terminal lobe (C-lobe). The latter also comprises a core and a helical domain. Accordingly, the APH(7)-Ia and APH(4)-Ia structures fit globally when the structures are superposed at three catalytically important conserved residues, His, Asp and Asn, in the Brenner motif, which is conserved in aminoglycoside phosphotransferases as well as in eukaryotic protein kinases. On the other hand, the phosphorylated hydroxyl groups of HygB in both structures come close to the Asp residue, and the HygB molecules in each structure lie in opposite directions. These molecules were held by the helical domain in the C-lobe, which exhibited structural differences between the two kinases. Furthermore, based on the crystal structures of APH(7)-Ia and APH(4)-Ia, some mutated residues in their thermostable mutants reported previously were located at the same positions in the two enzymes.
Structural basis for the substrate recognition of aminoglycoside 7-phosphotransferase-Ia from Streptomyces hygroscopicus.,Takenoya M, Shimamura T, Yamanaka R, Adachi Y, Ito S, Sasaki Y, Nakamura A, Yajima S Acta Crystallogr F Struct Biol Commun. 2019 Sep 1;75(Pt 9):599-607. doi:, 10.1107/S2053230X19011105. Epub 2019 Aug 28. PMID:31475927[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Takenoya M, Shimamura T, Yamanaka R, Adachi Y, Ito S, Sasaki Y, Nakamura A, Yajima S. Structural basis for the substrate recognition of aminoglycoside 7-phosphotransferase-Ia from Streptomyces hygroscopicus. Acta Crystallogr F Struct Biol Commun. 2019 Sep 1;75(Pt 9):599-607. doi:, 10.1107/S2053230X19011105. Epub 2019 Aug 28. PMID:31475927 doi:http://dx.doi.org/10.1107/S2053230X19011105
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