3w0r: Difference between revisions

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<StructureSection load='3w0r' size='340' side='right'caption='[[3w0r]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
<StructureSection load='3w0r' size='340' side='right'caption='[[3w0r]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3w0r]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W0R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3W0R FirstGlance]. <br>
<table><tr><td colspan='2'>[[3w0r]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W0R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3W0R FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=HY0:HYGROMYCIN+B+VARIANT'>HY0</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]] 2.3&#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;'>[[3w0m|3w0m]], [[3w0n|3w0n]], [[3w0o|3w0o]], [[3w0p|3w0p]], [[3w0q|3w0q]], [[3w0s|3w0s]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=HY0:HYGROMYCIN+B+VARIANT'>HY0</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">hph ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Hygromycin_B_4-O-kinase Hygromycin B 4-O-kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.163 2.7.1.163] </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=3w0r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w0r OCA], [https://pdbe.org/3w0r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3w0r RCSB], [https://www.ebi.ac.uk/pdbsum/3w0r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3w0r 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=3w0r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w0r OCA], [https://pdbe.org/3w0r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3w0r RCSB], [https://www.ebi.ac.uk/pdbsum/3w0r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3w0r ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/KHYB_ECOLX KHYB_ECOLX]] The aminoglycoside phosphotransferases achieve inactivation of their antibiotic substrates by phosphorylation. Only phosphorylates hygromycin and closely related compounds such as demethyl analogs and destomycin.  
[https://www.uniprot.org/uniprot/KHYB_ECOLX KHYB_ECOLX] The aminoglycoside phosphotransferases achieve inactivation of their antibiotic substrates by phosphorylation. Only phosphorylates hygromycin and closely related compounds such as demethyl analogs and destomycin.
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Aminoglycoside 4-phosphotransferase-Ia (APH(4)-Ia)/Hygromycin B phosphotransferase (Hph) inactivates the aminoglycoside antibiotic hygromycin B (hygB) via phosphorylation. The crystal structure of the binary complex of APH(4)-Ia with hygB was recently reported. To characterize substrate recognition by the enzyme, we determined the crystal structure of the ternary complex of non-hydrolyzable ATP analog AMP-PNP and hygB with wild-type, thermostable Hph mutant Hph5, and apo-mutant enzyme forms. The comparison between the ternary complex and apo structures revealed that Hph undergoes domain movement upon binding of AMP-PNP and hygB. This was about half amount of the case of APH(9)-Ia. We also determined the crystal structures of mutants in which the conserved, catalytically important residues Asp198 and Asn203, and the non-conserved Asn202, were converted to Ala, revealing the importance of Asn202 for catalysis. Hph5 contains five amino acid substitutions that alter its thermostability by 16 degrees C; its structure revealed that 4/5 mutations in Hph5 are located in the hydrophobic core and appear to increase thermostability by strengthening hydrophobic interactions.
 
Crystal structures of the ternary complex of APH(4)-Ia/Hph with hygromycin B and an ATP analog using a thermostable mutant.,Iino D, Takakura Y, Fukano K, Sasaki Y, Hoshino T, Ohsawa K, Nakamura A, Yajima S J Struct Biol. 2013 Jul;183(1):76-85. doi: 10.1016/j.jsb.2013.05.023. Epub 2013, Jun 7. PMID:23747390<ref>PMID:23747390</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3w0r" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacillus coli migula 1895]]
[[Category: Escherichia coli]]
[[Category: Hygromycin B 4-O-kinase]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Fukano, K]]
[[Category: Fukano K]]
[[Category: Hoshino, T]]
[[Category: Hoshino T]]
[[Category: Iino, D]]
[[Category: Iino D]]
[[Category: Nakamura, A]]
[[Category: Nakamura A]]
[[Category: Ohsawa, K]]
[[Category: Ohsawa K]]
[[Category: Sasaki, Y]]
[[Category: Sasaki Y]]
[[Category: Takakura, Y]]
[[Category: Takakura Y]]
[[Category: Yajima, S]]
[[Category: Yajima S]]
[[Category: Phosphotransferase]]
[[Category: Transferase-antibiotic complex]]

Latest revision as of 08:43, 20 March 2024

Crystal structure of a thermostable mutant of aminoglycoside phosphotransferase APH(4)-Ia (N202A), ternary complex with AMP-PNP and hygromycin B

3w0r, resolution 2.30Å

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