1nd4: Difference between revisions
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|PDB= 1nd4 |SIZE=350|CAPTION= <scene name='initialview01'>1nd4</scene>, resolution 2.1Å | |PDB= 1nd4 |SIZE=350|CAPTION= <scene name='initialview01'>1nd4</scene>, resolution 2.1Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand= | |LIGAND= <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> | ||
|ACTIVITY= [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] | |ACTIVITY= <span class='plainlinks'>[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] </span> | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY= | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1nd4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nd4 OCA], [http://www.ebi.ac.uk/pdbsum/1nd4 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1nd4 RCSB]</span> | |||
}} | }} | ||
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[[Category: Shewry, S C.]] | [[Category: Shewry, S C.]] | ||
[[Category: Smith, C A.]] | [[Category: Smith, C A.]] | ||
[[Category: atpase]] | [[Category: atpase]] | ||
[[Category: kanamycin]] | [[Category: kanamycin]] | ||
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[[Category: protein kinase]] | [[Category: protein kinase]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:28:43 2008'' | ||
Revision as of 22:28, 30 March 2008
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| , resolution 2.1Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , | ||||||
| Activity: | Kanamycin kinase, with EC number 2.7.1.95 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of aminoglycoside-3'-phosphotransferase-IIa
OverviewOverview
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.
About this StructureAbout this Structure
1ND4 is a Single protein structure of sequence from Klebsiella pneumoniae. Full crystallographic information is available from OCA.
ReferenceReference
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:12628253
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