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Transferase PDB id
1j7l
Jmol
Contents
Protein chains
263 a.a. *
Ligands
ADP ×2
Metals
_MG ×4
Waters ×297
* Residue conservation analysis
PDB id:
1j7l
Name: Transferase
Title: Crystal structure of 3',5"-aminoglycoside phosphotransferase type iiia adp complex
Structure: Aminoglycoside 3'-phosphotransferase. Chain: a, b. Synonym: aph(3')iii. Engineered: yes
Source: Enterococcus faecalis. Organism_taxid: 1351. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
Resolution:
2.20Å     R-factor:   0.220     R-free:   0.279
Authors: D.L.Burk,W.C.Hon,A.K.-W.Leung,A.M.Berghuis
Key ref:
D.L.Burk et al. (2001). Structural analyses of nucleotide binding to an aminoglycoside phosphotransferase. Biochemistry, 40, 8756-8764. PubMed id: 11467935 DOI: 10.1021/bi010504p
Date:
17-May-01     Release date:   08-Aug-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A3Y5  (KKA3_ENTFA) -  Aminoglycoside 3'-phosphotransferase
Seq:
Struc: 		264 a.a.
263 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.1.95  - Kanamycin kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + kanamycin = ADP + kanamycin 3'-phosphate
ATP
 + kanamycin
 =
ADP
Bound ligand (Het Group name = ADP)
corresponds exactly 		+ kanamycin 3'-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     response to antibiotic   2 terms 
  Biochemical function     nucleotide binding     7 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi010504p Biochemistry 40:8756-8764 (2001)
PubMed id: 11467935  
 
 
Structural analyses of nucleotide binding to an aminoglycoside phosphotransferase.
D.L.Burk, W.C.Hon, A.K.Leung, A.M.Berghuis.
 
  ABSTRACT  
 
is a bacterial enzyme that confers resistance to a range of aminoglycoside antibiotics while exhibiting striking homology to eukaryotic protein kinases (ePK). The structures of APH(3')-IIIa in its apoenzyme form and in complex with the nonhydrolyzable ATP analogue AMPPNP were determined to 3.2 and 2.4 A resolution, respectively. Furthermore, refinement of the previously determined ADP complex was completed. The structure of the apoenzyme revealed alternate positioning of a flexible loop (analogous to the P-loop of ePK's), occupying part of the nucleotide-binding pocket of the enzyme. Despite structural similarity to protein kinases, there was no evidence of domain movement associated with nucleotide binding. This rigidity is due to the presence of more extensive interlobe interactions in the APH(3')-IIIa structure than in the ePK's. Differences between the ADP and AMPPNP complexes are confined to the area of the nucleotide-binding pocket. The position of conserved active site residues and magnesium ions remains unchanged, but there are differences in metal coordination between the two nucleotide complexes. Comparison of the di/triphosphate binding site of APH(3')-IIIa with that of ePK's suggests that the reaction mechanism of APH(3")-IIIa and related aminoglycoside kinases will closely resemble that of eukaryotic protein kinases. However, the orientation of the adenine ring in the binding pocket differs between APH(3')-IIIa and the ePK's by a rotation of approximately 40 degrees. This alternate binding mode is likely a conserved feature among aminoglycoside kinases and could be exploited for the structure-based drug design of compounds to combat antibiotic resistance.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20833577 M.S.Ramirez, and M.E.Tolmasky (2010).
Aminoglycoside modifying enzymes.
  Drug Resist Updat, 13, 151-171.  
  20057078 M.Toth, S.Vakulenko, and C.A.Smith (2010).
Purification, crystallization and preliminary X-ray analysis of Enterococcus casseliflavus aminoglycoside-2''-phosphotransferase-IVa.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 81-84.  
19433564 D.H.Fong, and A.M.Berghuis (2009).
Structural basis of APH(3')-IIIa-mediated resistance to N1-substituted aminoglycoside antibiotics.
  Antimicrob Agents Chemother, 53, 3049-3055.
PDB code: 3h8p
19437437 L.Wu, and E.H.Serpersu (2009).
Deciphering interactions of the aminoglycoside phosphotransferase(3')-IIIa with its ligands.
  Biopolymers, 91, 801-809.  
19429619 P.G.Young, R.Walanj, V.Lakshmi, L.J.Byrnes, P.Metcalf, E.N.Baker, S.B.Vakulenko, and C.A.Smith (2009).
The crystal structures of substrate and nucleotide complexes of Enterococcus faecium aminoglycoside-2''-phosphotransferase-IIa [APH(2'')-IIa] provide insights into substrate selectivity in the APH(2'') subfamily.
  J Bacteriol, 191, 4133-4143.
PDB codes: 3ham 3hav
18787129 A.P.Kornev, S.S.Taylor, and L.F.Ten Eyck (2008).
A helix scaffold for the assembly of active protein kinases.
  Proc Natl Acad Sci U S A, 105, 14377-14382.  
  18259066 L.J.Byrnes, A.Badarau, S.B.Vakulenko, and C.A.Smith (2008).
Purification, crystallization and preliminary X-ray analysis of aminoglycoside-2''-phosphotransferase-Ic [APH(2'')-Ic] from Enterococcus gallinarum.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 126-129.  
18174989 M.Hainrichson, I.Nudelman, and T.Baasov (2008).
Designer aminoglycosides: the race to develop improved antibiotics and compounds for the treatment of human genetic diseases.
  Org Biomol Chem, 6, 227-239.  
17657587 S.Shakil, R.Khan, R.Zarrilli, and A.U.Khan (2008).
Aminoglycosides versus bacteria--a description of the action, resistance mechanism, and nosocomial battleground.
  J Biomed Sci, 15, 5.  
  17671368 D.Iino, Y.Takakura, M.Kuroiwa, R.Kawakami, Y.Sasaki, T.Hoshino, K.Ohsawa, A.Nakamura, and S.Yajima (2007).
Crystallization and preliminary crystallographic analysis of hygromycin B phosphotransferase from Escherichia coli.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 685-688.  
17961230 S.Y.Ku, K.A.Cornell, and P.L.Howell (2007).
Structure of Arabidopsis thaliana 5-methylthioribose kinase reveals a more occluded active site than its bacterial homolog.
  BMC Struct Biol, 7, 70.
PDB code: 2pyw
17522047 S.Y.Ku, P.Yip, K.A.Cornell, M.K.Riscoe, J.B.Behr, G.Guillerm, and P.L.Howell (2007).
Structures of 5-methylthioribose kinase reveal substrate specificity and unusual mode of nucleotide binding.
  J Biol Chem, 282, 22195-22206.
PDB codes: 2pu8 2pui 2pul 2pun 2pup
17009359 L.Milanese, A.Espinosa, J.M.Campos, M.A.Gallo, and A.Entrena (2006).
Insight into the inhibition of human choline kinase: homology modeling and molecular dynamics simulations.
  ChemMedChem, 1, 1216-1228.  
16936061 O.V.Mavrodi, D.V.Mavrodi, D.M.Weller, and L.S.Thomashow (2006).
Role of ptsP, orfT, and sss recombinase genes in root colonization by Pseudomonas fluorescens Q8r1-96.
  Appl Environ Microbiol, 72, 7111-7122.  
16391922 S.Jana, and J.K.Deb (2006).
Molecular understanding of aminoglycoside action and resistance.
  Appl Microbiol Biotechnol, 70, 140-150.  
16084385 A.Kohl, P.Amstutz, P.Parizek, H.K.Binz, C.Briand, G.Capitani, P.Forrer, A.Plückthun, and M.G.Grütter (2005).
Allosteric inhibition of aminoglycoside phosphotransferase by a designed ankyrin repeat protein.
  Structure, 13, 1131-1141.
PDB code: 2bkk
  16511108 C.T.Lemke, J.Hwang, B.Xiong, N.P.Cianciotto, and A.M.Berghuis (2005).
Crystallization and preliminary crystallographic analysis of an aminoglycoside kinase from Legionella pneumophila.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 606-608.  
16262717 D.A.Wright, J.A.Townsend, R.J.Winfrey, P.A.Irwin, J.Rajagopal, P.M.Lonosky, B.D.Hall, M.D.Jondle, and D.F.Voytas (2005).
High-frequency homologous recombination in plants mediated by zinc-finger nucleases.
  Plant J, 44, 693-705.  
16244704 E.D.Scheeff, and P.E.Bourne (2005).
Structural evolution of the protein kinase-like superfamily.
  PLoS Comput Biol, 1, e49.  
  16511055 R.Walanj, P.Young, H.M.Baker, E.N.Baker, P.Metcalf, J.W.Chow, S.Lerner, S.Vakulenko, and C.A.Smith (2005).
Purification, crystallization and preliminary X-ray analysis of Enterococcus faecium aminoglycoside-2''-phosphotransferase-Ib [APH(2'')-Ib].
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 410-413.  
15152095 B.S.Nield, R.D.Willows, A.E.Torda, M.R.Gillings, A.J.Holmes, K.M.Nevalainen, H.W.Stokes, and B.C.Mabbutt (2004).
New enzymes from environmental cassette arrays: functional attributes of a phosphotransferase and an RNA-methyltransferase.
  Protein Sci, 13, 1651-1659.  
14960577 C.Yuan, and C.Kent (2004).
Identification of critical residues of choline kinase A2 from Caenorhabditis elegans.
  J Biol Chem, 279, 17801-17809.  
15388945 D.H.Fong, and A.M.Berghuis (2004).
Crystallization and preliminary crystallographic analysis of 3'-aminoglycoside kinase type IIIa complexed with a eukaryotic protein kinase inhibitor, CKI-7.
  Acta Crystallogr D Biol Crystallogr, 60, 1897-1899.  
15229886 N.Fernandez-Fuentes, A.Hermoso, J.Espadaler, E.Querol, F.X.Aviles, and B.Oliva (2004).
Classification of common functional loops of kinase super-families.
  Proteins, 56, 539-555.  
12566434 D.D.Boehr, S.I.Jenkins, and G.D.Wright (2003).
The molecular basis of the expansive substrate specificity of the antibiotic resistance enzyme aminoglycoside acetyltransferase-6'-aminoglycoside phosphotransferase-2". The role of ASP-99 as an active site base important for acetyl transfer.
  J Biol Chem, 278, 12873-12880.  
  12445771 D.D.Boehr, A.R.Farley, G.D.Wright, and J.R.Cox (2002).
Analysis of the pi-pi stacking interactions between the aminoglycoside antibiotic kinase APH(3')-IIIa and its nucleotide ligands.
  Chem Biol, 9, 1209-1217.  
12006485 D.H.Fong, and A.M.Berghuis (2002).
Substrate promiscuity of an aminoglycoside antibiotic resistance enzyme via target mimicry.
  EMBO J, 21, 2323-2331.
PDB codes: 1l8t 1l8u 2b0q
  12191620 D.L.Burk, and A.M.Berghuis (2002).
Protein kinase inhibitors and antibiotic resistance.
  Pharmacol Ther, 93, 283-292.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.