1kny

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[[Image:1kny.gif|left|200px]]
 
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{{Structure
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==KANAMYCIN NUCLEOTIDYLTRANSFERASE==
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|PDB= 1kny |SIZE=350|CAPTION= <scene name='initialview01'>1kny</scene>, resolution 2.5&Aring;
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<StructureSection load='1kny' size='340' side='right'caption='[[1kny]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene> and <scene name='pdbligand=KAN:KANAMYCIN A'>KAN</scene>
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<table><tr><td colspan='2'>[[1kny]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. The February 2012 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Aminoglycoside Antibiotics'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2012_2 10.2210/rcsb_pdb/mom_2012_2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KNY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KNY FirstGlance]. <br>
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|ACTIVITY=
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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]] 2.5&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=KAN:KANAMYCIN+A'>KAN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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}}
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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=1kny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kny OCA], [https://pdbe.org/1kny PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kny RCSB], [https://www.ebi.ac.uk/pdbsum/1kny PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kny ProSAT]</span></td></tr>
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</table>
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'''KANAMYCIN NUCLEOTIDYLTRANSFERASE'''
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== Function ==
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[https://www.uniprot.org/uniprot/KANU_STAAU KANU_STAAU] Inactivates the antibiotic kanamycin by catalyzing the transfer of a nucleotidyl group from nucleoside triphosphates such as ATP to the 4'-hydroxyl group of the aminoglycoside.
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__TOC__
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==Overview==
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</StructureSection>
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Kanamycin nucleotidyltransferase (KNTase) is a plasmid-coded enzyme responsible for some types of bacterial resistance to aminoglycosides. The enzyme deactivates various antibiotics by transferring a nucleoside monophosphate group from ATP to the 4'-hydroxyl group of the drug. Detailed knowledge of the interactions between the protein and the substrates may lead to the design of aminoglycosides less susceptible to bacterial deactivation. Here we describe the structure of KNTase complexed with both the nonhydrolyzable nucleotide analog AMPCPP and kanamycin. Crystals employed in the investigation were grown from poly(ethylene glycol) solutions and belonged to the space group P2(1)2(1)2(1) with unit cell dimensions of a = 57.3 A, b = 102.2 A, c = 101.8 A, and one dimer in the asymmetric unit. Least-squares refinement of the model at 2.5 A resolution reduced the crystallographic R factor to 16.8%. The binding pockets for both the nucleotide and the antibiotic are extensively exposed to the solvent and are composed of amino acid residues contributed by both subunits in the dimer. There are few specific interactions between the protein and the adenine ring of the nucleotide; rather the AMPCPP molecule is locked into position by extensive hydrogen bonding between the alpha-, beta-, and gamma-phosphates and protein side chains. This, in part, may explain the observation that the enzyme can utilize other nucleotides such as GTP and UTP. The 4'-hydroxyl group of the antibiotic is approximately 5 A from the alpha-phosphorus of the nucleotide and is in the proper orientation for a single in-line displacement attack at the phosphorus.(ABSTRACT TRUNCATED AT 250 WORDS)
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[[Category: Aminoglycoside Antibiotics]]
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[[Category: Large Structures]]
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==About this Structure==
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[[Category: RCSB PDB Molecule of the Month]]
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1KNY is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KNY OCA].
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==Reference==
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Structural investigation of the antibiotic and ATP-binding sites in kanamycin nucleotidyltransferase., Pedersen LC, Benning MM, Holden HM, Biochemistry. 1995 Oct 17;34(41):13305-11. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/7577914 7577914]
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[[Category: Single protein]]
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[[Category: Staphylococcus aureus]]
[[Category: Staphylococcus aureus]]
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[[Category: Benning, M M.]]
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[[Category: Benning MM]]
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[[Category: Holden, H M.]]
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[[Category: Holden HM]]
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[[Category: Pedersen, L C.]]
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[[Category: Pedersen LC]]
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[[Category: APC]]
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[[Category: KAN]]
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[[Category: MG]]
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[[Category: antibiotic resistance]]
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[[Category: plasmid]]
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[[Category: transferase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:19:53 2008''
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KANAMYCIN NUCLEOTIDYLTRANSFERASE

PDB ID 1kny

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