3tyk: Difference between revisions

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-[[Image:3tyk.png|left|200px]]
-<!--
+==Crystal structure of aminoglycoside phosphotransferase APH(4)-Ia==
-The line below this paragraph, containing "STRUCTURE_3tyk", creates the "Structure Box" on the page.
+<StructureSection load='3tyk' size='340' side='right'caption='[[3tyk]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3tyk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3ovc 3ovc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TYK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TYK FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.95&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CSX:S-OXY+CYSTEINE'>CSX</scene>, <scene name='pdbligand=HY0:HYGROMYCIN+B+VARIANT'>HY0</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-{{STRUCTURE_3tyk|  PDB=3tyk  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3tyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tyk OCA], [https://pdbe.org/3tyk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tyk RCSB], [https://www.ebi.ac.uk/pdbsum/3tyk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tyk ProSAT]</span></td></tr>
+</table>
+== 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.
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The aminoglycoside phosphotransferase (APH) APH(4)-Ia is one of two enzymes responsible for bacterial resistance to the atypical aminoglycoside antibiotic hygromycin B (hygB). The crystal structure of APH(4)-Ia enzyme was solved in complex with hygB at 1.95 A resolution. The APH(4)-Ia structure adapts a general two-lobe architecture shared by other APH enzymes and eukaryotic kinases, with the active site located at the interdomain cavity. The enzyme forms an extended hydrogen bond network with hygB primarily through polar and acidic side chain groups. Individual alanine substitutions of seven residues involved in hygB binding did not have significant effect on APH(4)-Ia enzymatic activity, indicating that the binding affinity is spread across a distributed network. hygB appeared as the only substrate recognized by APH(4)-Ia among the panel of 14 aminoglycoside compounds. Analysis of the active site architecture and the interaction with the hygB molecule demonstrated several unique features supporting such restricted substrate specificity. Primarily the APH(4)-Ia substrate-binding site contains a cluster of hydrophobic residues that provides a complementary surface to the twisted structure of the substrate. Similar to APH(2'') enzymes, the APH(4)-Ia is able to utilize either ATP or GTP for phosphoryl transfer. The defined structural features of APH(4)-Ia interactions with hygB and the promiscuity in regard to ATP or GTP binding could be exploited for the design of novel aminoglycoside antibiotics or inhibitors of this enzyme.
-===Crystal structure of aminoglycoside phosphotransferase APH(4)-Ia===
+Structure and function of APH(4)-Ia, a hygromycin B resistance enzyme.,Stogios PJ, Shakya T, Evdokimova E, Savchenko A, Wright GD J Biol Chem. 2011 Jan 21;286(3):1966-75. Epub 2010 Nov 17. PMID:21084294<ref>PMID:21084294</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3tyk" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_21084294}}, adds the Publication Abstract to the page
+*[[Phosphotransferase 3D structures|Phosphotransferase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 21084294 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_21084294}}
+__TOC__
+</StructureSection>
-==About this Structure==
-[[3tyk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3ovc 3ovc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TYK OCA].
-==Reference==
-<ref group="xtra">PMID:021084294</ref><references group="xtra"/>
 [[Category: Escherichia coli]]
-[[Category: Hygromycin B 4-O-kinase]]
+[[Category: Large Structures]]
-[[Category: Anderson, W F.]]
+[[Category: Anderson WF]]
-[[Category: CSGID, Center for Structural Genomics of Infectious Diseases.]]
+[[Category: Chruszcz M]]
-[[Category: Chruszcz, M.]]
+[[Category: Evdokmova E]]
-[[Category: Evdokmova, E.]]
+[[Category: Fan Y]]
-[[Category: Fan, Y.]]
+[[Category: Minor W]]
-[[Category: Minor, W.]]
+[[Category: Savchenko A]]
-[[Category: Savchenko, A.]]
+[[Category: Shabalin IG]]
-[[Category: Shabalin, I G.]]
+[[Category: Shakya T]]
-[[Category: Shakya, T.]]
+[[Category: Stogios PJ]]
-[[Category: Stogios, P J.]]
+[[Category: Wright GD]]
-[[Category: Wright, G D.]]
-[[Category: Aminoglycoside binding]]
-[[Category: Aminoglycoside phosphotransferase]]
-[[Category: Antibiotic resistance]]
-[[Category: Center for structural genomics of infectious disease]]
-[[Category: Csgid]]
-[[Category: Cytoplasmic]]
-[[Category: Eukaryotic protein kinase-like fold]]
-[[Category: Phosphorylation]]
-[[Category: Phosphotransferase/kinase]]
-[[Category: Structural genomic]]
-[[Category: Transferase-antibiotic complex]]