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[[Image:1nd4.jpg|left|200px]]<br /><applet load="1nd4" size="350" color="white" frame="true" align="right" spinBox="true"
caption="1nd4, resolution 2.1&Aring;" />
'''Crystal structure of aminoglycoside-3'-phosphotransferase-IIa'''<br />


==Overview==
==Crystal structure of aminoglycoside-3'-phosphotransferase-IIa==
A major factor in the emergence of antibiotic resistance is the existence of enzymes that chemically modify common antibiotics. The genes for these enzymes are commonly carried on mobile genetic elements, facilitating their spread. One such class of enzymes is the aminoglycoside phosphotransferase (APH) family, which uses ATP-mediated phosphate transfer to chemically modify and inactivate aminoglycoside antibiotics such as streptomycin and kanamycin. As part of a program to define the molecular basis for aminoglycoside recognition and inactivation by such enzymes, we have determined the high resolution (2.1A) crystal structure of aminoglycoside-3'-phosphotransferase-IIa (APH(3')-IIa) in complex with kanamycin. The structure was solved by molecular replacement using multiple models derived from the related aminoglycoside-3'-phosphotransferase-III enzyme (APH(3')-III), and refined to an R factor of 0.206 (R(free) 0.238). The bound kanamycin molecule is very well defined and occupies a highly negatively charged cleft formed by the C-terminal domain of the enzyme. Adjacent to this is the binding site for ATP, which can be modeled on the basis of nucleotide complexes of APH(3')-III; only one change is apparent with a loop, residues 28-34, in a position where it could fold over an incoming nucleotide. The three rings of the kanamycin occupy distinct sub-pockets in which a highly acidic loop, residues 151-166, and the C-terminal residues 260-264 play important parts in recognition. The A ring, the site of phosphoryl transfer, is adjacent to the catalytic base Asp190. These results give new information on the basis of aminoglycoside recognition, and on the relationship between this phosphotransferase family and the protein kinases.
<StructureSection load='1nd4' size='340' side='right'caption='[[1nd4]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1nd4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Klebsiella_pneumoniae Klebsiella pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ND4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ND4 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=KAN:KANAMYCIN+A'>KAN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></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=1nd4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nd4 OCA], [https://pdbe.org/1nd4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nd4 RCSB], [https://www.ebi.ac.uk/pdbsum/1nd4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nd4 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/KKA2_KLEPN KKA2_KLEPN] Resistance to kanamycin, neomycin, paromomycin, ribostamycin, butirosin and gentamicin B.
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nd/1nd4_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1nd4 ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1ND4 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Klebsiella_pneumoniae Klebsiella pneumoniae] with <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=ACT:'>ACT</scene>, <scene name='pdbligand=NA:'>NA</scene> and <scene name='pdbligand=KAN:'>KAN</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Kanamycin_kinase Kanamycin kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.95 2.7.1.95] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ND4 OCA].
*[[Phosphotransferase 3D structures|Phosphotransferase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
The crystal structure of aminoglycoside-3'-phosphotransferase-IIa, an enzyme responsible for antibiotic resistance., Nurizzo D, Shewry SC, Perlin MH, Brown SA, Dholakia JN, Fuchs RL, Deva T, Baker EN, Smith CA, J Mol Biol. 2003 Mar 21;327(2):491-506. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12628253 12628253]
[[Category: Kanamycin kinase]]
[[Category: Klebsiella pneumoniae]]
[[Category: Klebsiella pneumoniae]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Baker, E N.]]
[[Category: Baker EN]]
[[Category: Nurizzo, D.]]
[[Category: Nurizzo D]]
[[Category: Shewry, S C.]]
[[Category: Shewry SC]]
[[Category: Smith, C A.]]
[[Category: Smith CA]]
[[Category: ACT]]
[[Category: KAN]]
[[Category: MG]]
[[Category: NA]]
[[Category: atpase]]
[[Category: kanamycin]]
[[Category: phosphotransferase]]
[[Category: protein kinase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:04:47 2008''

Latest revision as of 16:27, 13 March 2024

Crystal structure of aminoglycoside-3'-phosphotransferase-IIaCrystal structure of aminoglycoside-3'-phosphotransferase-IIa

Structural highlights

1nd4 is a 2 chain structure with sequence from Klebsiella pneumoniae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.1Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

KKA2_KLEPN Resistance to kanamycin, neomycin, paromomycin, ribostamycin, butirosin and gentamicin B.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1nd4, resolution 2.10Å

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