Structure of an Enzyme Required for Aminoglycoside Antibiotic Resistance Reveals Homology to Eukaryotic Protein Kinases

Bacterial resistance to aminoglycoside antibiotics is almost exclusively accomplished through either phosphorylation, adenylylation, or acetylation of the antibacterial agent. The aminoglycoside kinase, APH(3')-IIIa, catalyzes the phosphorylation of a broad spectrum of aminoglycoside antibiotics. The crystal structure of this enzyme complexed with ADP was determined at 2.2 A. resolution. The three-dimensional fold of APH(3')-IIIa reveals a striking similarity to eukaryotic protein kinases despite a virtually complete lack of sequence homology. Nearly half of the APH(3')-IIIa sequence adopts a conformation identical to that seen in these kinases. Substantial differences are found in the location and conformation of residues presumably responsible for second-substrate specificity. These results indicate that APH(3') enzymes and eukaryotic-type protein kinases share a common ancestor.

[1]  P. Kraulis.  A program to produce both detailed and schematic plots of protein structures , 1991 .

[2]  A. Brünger.  Free R value: a novel statistical quantity for assessing the accuracy of crystal structures , 1992, Nature.

[3]  G. Wright,et al.  Broad spectrum aminoglycoside phosphotransferase type III from Enterococcus: overexpression, purification, and substrate specificity. , 1994, Biochemistry.

[4]  M. Kjeldgaard,et al.  O: A Macromolecule Modeling Environment , 1990 .

[5]  W. Kabsch,et al.  Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.

[6]  E. Billings,et al.  Crystallographic structure of a phosphonate derivative of the Enterobacter cloacae P99 cephalosporinase: mechanistic interpretation of a beta-lactamase transition-state analog. , 1994, Biochemistry.

[7]  D. Koshland.  Frontiers in Biotechnology , 1991, Science.

[8]  Elizabeth J. Goldsmith,et al.  Atomic structure of the MAP kinase ERK2 at 2.3 Å resolution , 1994, Nature.

[9]  J. Zheng,et al.  Crystal structure of the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase. , 1991, Science.

[10]  P. Courvalin,et al.  Nucleotide sequence of Acinetobacter baumannii aphA‐6 gene: evolutionary and functional implications of sequence homologies with nucleotide‐binding proteins, kinases and other aminoglycoside‐modifying enzymes , 1988, Molecular microbiology.

[11]  F. Young.  Biochemistry , 1955, The Indian Medical Gazette.

[12]  Catalytic mechanism of enterococcal kanamycin kinase (APH(3')-IIIa): viscosity, thio, and solvent isotope effects support a Theorell-Chance mechanism. , 1996, Biochemistry.

[13]  P. Rather,et al.  Molecular genetics of aminoglycoside resistance genes and familial relationships of the aminoglycoside-modifying enzymes. , 1993, Microbiological reviews.

[14]  S. Mobashery,et al.  A structure-based analysis of the inhibition of class A beta-lactamases by sulbactam. , 1994, Biochemistry.

[15]  Z. Otwinowski,et al.  Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[16]  C. Walsh,et al.  The Role of the Catalytic Base in the Protein Tyrosine Kinase Csk (*) , 1995, The Journal of Biological Chemistry.

[17]  R. Read.  Improved Fourier Coefficients for Maps Using Phases from Partial Structures with Errors , 1986 .

[18]  P. Kennelly,et al.  Fancy meeting you here! A fresh look at "prokaryotic" protein phosphorylation , 1996, Journal of bacteriology.

[19]  L. Johnson,et al.  Active and Inactive Protein Kinases: Structural Basis for Regulation , 1996, Cell.

[20]  Cheng‐Cai Zhang,et al.  Bacterial signalling involving eukaryotic‐type protein kinases , 1996, Molecular microbiology.

[21]  S. Brenner,et al.  Phosphotransferase sequence homology , 1987, Nature.

[22]  T. Smith,et al.  Structural basis for the inactivation of the P54 mutant of beta-lactamase from Staphylococcus aureus PC1. , 1991, Biochemistry.

[23]  K. Walsh.  The Protein Kinase Family , 1987 .

[24]  E A Merritt,et al.  Raster3D Version 2.0. A program for photorealistic molecular graphics. , 1994, Acta crystallographica. Section D, Biological crystallography.

[25]  B. C. Wang.  Resolution of phase ambiguity in macromolecular crystallography. , 1985, Methods in enzymology.

[26]  G. Wright,et al.  Kinetic Mechanism of Aminoglycoside Phosphotransferase Type IIIa , 1995, The Journal of Biological Chemistry.

[27]  Mitchell L. Cohen.  Epidemiology of Drug Resistance: Implications for a Post—Antimicrobial Era , 1992, Science.

[28]  L. Pedersen,et al.  Structural investigation of the antibiotic and ATP-binding sites in kanamycin nucleotidyltransferase. , 1995, Biochemistry.

[29]  P. Heinzel,et al.  Antibiotic resistance by modification: Many resistance genes could be derived from cellular control genes in actinomycetes - a hypothesis , 1988 .

[30]  I. Rayment,et al.  Molecular structure of kanamycin nucleotidyltransferase determined to 3.0-A resolution. , 1993, Biochemistry.

[31]  T. Hunter,et al.  The eukaryotic protein kinase superfamily: kinase (catalytic) domain structure and classification 1 , 1995, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[32]  D A Meyers,et al.  Major Susceptibility Locus for Prostate Cancer on Chromosome 1 Suggested by a Genome-Wide Search , 1996, Science.

[33]  J. Thornton,et al.  PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .

[34]  J Davies,et al.  Aminoglycoside antibiotic-inactivating enzymes in actinomycetes similar to those present in clinical isolates of antibiotic-resistant bacteria. , 1973, Proceedings of the National Academy of Sciences of the United States of America.

[35]  R. Bonomo,et al.  beta-Lactamase mutations far from the active site influence inhibitor binding. , 1995, Biochimica et biophysica acta.

[36]  R F Doolittle,et al.  Convergent evolution: the need to be explicit. , 1994, Trends in biochemical sciences.

[37]  J. Zheng,et al.  Structural framework for the protein kinase family. , 1992, Annual review of cell biology.

[38]  L. Johnson,et al.  Two structures of the catalytic domain of phosphorylase kinase: an active protein kinase complexed with substrate analogue and product. , 1995, Structure.

[39]  F. Richards,et al.  1H-15N heteronuclear NMR studies of Escherichia coli thioredoxin in samples isotopically labeled by residue type. , 1985, Biochemistry.

[40]  G. Wright,et al.  Regiospecificity of aminoglycoside phosphotransferase from Enterococci and Staphylococci (APH(3')-IIIa). , 1996, Biochemistry.

[41]  G. Wright,et al.  Mechanism of aminoglycoside 3'-phosphotransferase type IIIa: His188 is not a phosphate-accepting residue. , 1996, Chemistry & biology.

[42]  C. Gibbs,et al.  Rational scanning mutagenesis of a protein kinase identifies functional regions involved in catalysis and substrate interactions. , 1991, The Journal of biological chemistry.

[43]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.

[44]  J. Travis,et al.  Reviving the antibiotic miracle? , 1994, Science.

[45]  R. Bott,et al.  Designing substrate specificity by protein engineering of electrostatic interactions. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[46]  Susan S. Taylor,et al.  cAMP‐dependent protein kinase: Crystallographic insights into substrate recognition and phosphotransfer , 1994, Protein science : a publication of the Protein Society.

[47]  A. Patchett,et al.  Antibacterial Agents That Inhibit Lipid A Biosynthesis , 1996, Science.

[48]  A. Brünger.  Assessment of phase accuracy by cross validation: the free R value. Methods and applications. , 1993, Acta crystallographica. Section D, Biological crystallography.

[49]  G. Sarkar,et al.  The "megaprimer" method of site-directed mutagenesis. , 1990, BioTechniques.

[50]  Hiroto Yamaguchi,et al.  Structural basis for activation of human lymphocyte kinase Lck upon tyrosine phosphorylation , 1996, Nature.

[51]  E. Goldsmith,et al.  Mutation of position 52 in ERK2 creates a nonproductive binding mode for adenosine 5'-triphosphate. , 1996, Biochemistry.

[52]  S. Hubbard,et al.  Crystal structure of the tyrosine kinase domain of the human insulin receptor , 1994, Nature.

[53]  M. J. Adams.  Preparation and Analysis of Protein Crystals , 1983 .

[54]  William Arbuthnot Sir Lane,et al.  Active-site labeling of an aminoglycoside antibiotic phosphotransferase (APH(3')-IIIa). , 1994, Biochemistry.

[55]  O. Herzberg,et al.  Structure of a phosphonate-inhibited beta-lactamase. An analog of the tetrahedral transition state/intermediate of beta-lactam hydrolysis. , 1993, Journal of molecular biology.

[56]  T. Hunter,et al.  The protein kinase family: conserved features and deduced phylogeny of the catalytic domains. , 1988, Science.

[57]  J. Kuret,et al.  Structural basis for selectivity of the isoquinoline sulfonamide family of protein kinase inhibitors. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[58]  J. Puglisi,et al.  Structure of the A Site of Escherichia coli 16S Ribosomal RNA Complexed with an Aminoglycoside Antibiotic , 1996, Science.