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PDBsum entry 1kny

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protein ligands metals Protein-protein interface(s) links
Transferase PDB id
1kny
Jmol
Contents
Protein chains
253 a.a.
Ligands
APC ×2
KAN ×2
Metals
_MG ×2
Waters ×43
PDB id:
1kny
Name: Transferase
Title: Kanamycin nucleotidyltransferase
Structure: Kanamycin nucleotidyltransferase. Chain: a, b. Synonym: kntase. Engineered: yes. Mutation: yes
Source: Staphylococcus aureus. Organism_taxid: 1280. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.50Å     R-factor:   0.168    
Authors: L.C.Pedersen,M.M.Benning,H.M.Holden
Key ref:
L.C.Pedersen et al. (1995). Structural investigation of the antibiotic and ATP-binding sites in kanamycin nucleotidyltransferase. Biochemistry, 34, 13305-13311. PubMed id: 7577914 DOI: 10.1021/bi00041a005
Date:
07-Jul-95     Release date:   17-Aug-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P05057  (KANU_STAAU) -  Kanamycin nucleotidyltransferase
Seq:
Struc:
253 a.a.
253 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     transferase activity     2 terms  

 

 
DOI no: 10.1021/bi00041a005 Biochemistry 34:13305-13311 (1995)
PubMed id: 7577914  
 
 
Structural investigation of the antibiotic and ATP-binding sites in kanamycin nucleotidyltransferase.
L.C.Pedersen, M.M.Benning, H.M.Holden.
 
  ABSTRACT  
 
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)
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21256032 A.Itzen, W.Blankenfeldt, and R.S.Goody (2011).
Adenylylation: renaissance of a forgotten post-translational modification.
  Trends Biochem Sci, 36, 221-228.  
20564281 G.De Pascale, and G.D.Wright (2010).
Antibiotic resistance by enzyme inactivation: from mechanisms to solutions.
  Chembiochem, 11, 1325-1334.  
20397253 J.L.Houghton, K.D.Green, W.Chen, and S.Garneau-Tsodikova (2010).
The future of aminoglycosides: the end or renaissance?
  Chembiochem, 11, 880-902.  
20512827 J.Revuelta, F.Corzana, A.Bastida, and J.L.Asensio (2010).
The unusual nucleotide recognition properties of the resistance enzyme ANT(4'): inorganic tri/polyphosphate as a substrate for aminoglycoside inactivation.
  Chemistry, 16, 8635-8640.  
20822442 M.Morar, and G.D.Wright (2010).
The genomic enzymology of antibiotic resistance.
  Annu Rev Genet, 44, 25-51.  
20833577 M.S.Ramirez, and M.E.Tolmasky (2010).
Aminoglycoside modifying enzymes.
  Drug Resist Updat, 13, 151-171.  
20363937 Y.Zhang, E.L.Pohlmann, J.Serate, M.C.Conrad, and G.P.Roberts (2010).
Mutagenesis and functional characterization of the four domains of GlnD, a bifunctional nitrogen sensor protein.
  J Bacteriol, 192, 2711-2721.  
20004157 J.A.Sundlov, and A.M.Gulick (2009).
Insights into resistance against lincosamide antibiotics.
  Structure, 17, 1549-1550.  
19833706 K.Kuchta, L.Knizewski, L.S.Wyrwicz, L.Rychlewski, and K.Ginalski (2009).
Comprehensive classification of nucleotidyltransferase fold proteins: identification of novel families and their representatives in human.
  Nucleic Acids Res, 37, 7701-7714.  
20004168 M.Morar, K.Bhullar, D.W.Hughes, M.Junop, and G.D.Wright (2009).
Structure and mechanism of the lincosamide antibiotic adenylyltransferase LinB.
  Structure, 17, 1649-1659.
PDB codes: 3jyy 3jz0
17872511 G.Martin, and W.Keller (2007).
RNA-specific ribonucleotidyl transferases.
  RNA, 13, 1834-1849.  
17609790 M.Latorre, P.Peñalver, J.Revuelta, J.L.Asensio, E.García-Junceda, and A.Bastida (2007).
Rescue of the streptomycin antibiotic activity by using streptidine as a "decoy acceptor" for the aminoglycoside-inactivating enzyme adenyl transferase.
  Chem Commun (Camb), (), 2829-2831.  
17223131 P.B.Balbo, J.Toth, and A.Bohm (2007).
X-ray crystallographic and steady state fluorescence characterization of the protein dynamics of yeast polyadenylate polymerase.
  J Mol Biol, 366, 1401-1415.
PDB codes: 2hhp 2o1p
16391922 S.Jana, and J.K.Deb (2006).
Molecular understanding of aminoglycoside action and resistance.
  Appl Microbiol Biotechnol, 70, 140-150.  
16028221 C.Lehmann, S.Pullalarevu, W.Krajewski, M.A.Willis, A.Galkin, A.Howard, and O.Herzberg (2005).
Structure of HI0073 from Haemophilus influenzae, the nucleotide-binding domain of a two-protein nucleotidyl transferase.
  Proteins, 60, 807-811.
PDB code: 1no5
14997578 H.Erlandsen, J.M.Canaves, M.A.Elsliger, F.von Delft, L.S.Brinen, X.Dai, A.M.Deacon, R.Floyd, A.Godzik, C.Grittini, S.K.Grzechnik, L.Jaroszewski, H.E.Klock, E.Koesema, J.S.Kovarik, A.Kreusch, P.Kuhn, S.A.Lesley, D.McMullan, T.M.McPhillips, M.D.Miller, A.Morse, K.Moy, J.Ouyang, R.Page, A.Robb, K.Quijano, R.Schwarzenbacher, G.Spraggon, R.C.Stevens, H.van den Bedem, J.Velasquez, J.Vincent, X.Wang, B.West, G.Wolf, K.O.Hodgson, J.Wooley, and I.A.Wilson (2004).
Crystal structure of an HEPN domain protein (TM0613) from Thermotoga maritima at 1.75 A resolution.
  Proteins, 54, 806-809.
PDB code: 1o3u
15130478 Y.Xu, R.Zhang, A.Joachimiak, P.D.Carr, T.Huber, S.G.Vasudevan, and D.L.Ollis (2004).
Structure of the N-terminal domain of Escherichia coli glutamine synthetase adenylyltransferase.
  Structure, 12, 861-869.
PDB code: 1v4a
12486719 C.Lehmann, K.Lim, V.R.Chalamasetty, W.Krajewski, E.Melamud, A.Galkin, A.Howard, Z.Kelman, P.T.Reddy, A.G.Murzin, and O.Herzberg (2003).
The HI0073/HI0074 protein pair from Haemophilus influenzae is a member of a new nucleotidyltransferase family: structure, sequence analyses, and solution studies.
  Proteins, 50, 249-260.
PDB code: 1jog
14661958 J.Hoseki, A.Okamoto, N.Takada, A.Suenaga, N.Futatsugi, A.Konagaya, M.Taiji, T.Yano, S.Kuramitsu, and H.Kagamiyama (2003).
Increased rigidity of domain structures enhances the stability of a mutant enzyme created by directed evolution.
  Biochemistry, 42, 14469-14475.  
12765831 M.Grynberg, H.Erlandsen, and A.Godzik (2003).
HEPN: a common domain in bacterial drug resistance and human neurodegenerative proteins.
  Trends Biochem Sci, 28, 224-226.  
12925992 Q.Vicens, and E.Westhof (2003).
Molecular recognition of aminoglycoside antibiotics by ribosomal RNA and resistance enzymes: an analysis of x-ray crystal structures.
  Biopolymers, 70, 42-57.  
14636576 R.Hartmann, J.Justesen, S.N.Sarkar, G.C.Sen, and V.C.Yee (2003).
Crystal structure of the 2'-specific and double-stranded RNA-activated interferon-induced antiviral protein 2'-5'-oligoadenylate synthetase.
  Mol Cell, 12, 1173-1185.
PDB code: 1px5
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
11823435 M.Delarue, J.B.Boulé, J.Lescar, N.Expert-Bezançon, N.Jourdan, N.Sukumar, F.Rougeon, and C.Papanicolaou (2002).
Crystal structures of a template-independent DNA polymerase: murine terminal deoxynucleotidyltransferase.
  EMBO J, 21, 427-439.
PDB codes: 1jms 1kdh 1kej
12079787 Q.Vicens, and E.Westhof (2002).
Crystal structure of a complex between the aminoglycoside tobramycin and an oligonucleotide containing the ribosomal decoding a site.
  Chem Biol, 9, 747-755.
PDB code: 1lc4
11258909 B.Gerratana, P.A.Frey, and W.W.Cleland (2001).
Characterization of the transition-state structure of the reaction of kanamycin nucleotidyltransferase by heavy-atom kinetic isotope effects.
  Biochemistry, 40, 2972-2977.  
11258908 B.Gerratana, W.W.Cleland, and L.A.Reinhardt (2001).
Regiospecificity assignment for the reaction of kanamycin nucleotidyltransferase from Staphylococcus aureus.
  Biochemistry, 40, 2964-2971.  
11512519 E.Azucena, and S.Mobashery (2001).
Aminoglycoside-modifying enzymes: mechanisms of catalytic processes and inhibition.
  Drug Resist Updat, 4, 106-117.  
11685238 M.W.Maciejewski, R.Shin, B.Pan, A.Marintchev, A.Denninger, M.A.Mullen, K.Chen, M.R.Gryk, and G.P.Mullen (2001).
Solution structure of a viral DNA repair polymerase.
  Nat Struct Biol, 8, 936-941.
PDB code: 1jaj
10944102 G.Martin, W.Keller, and S.Doublié (2000).
Crystal structure of mammalian poly(A) polymerase in complex with an analog of ATP.
  EMBO J, 19, 4193-4203.
PDB code: 1f5a
10958780 J.Bard, A.M.Zhelkovsky, S.Helmling, T.N.Earnest, C.L.Moore, and A.Bohm (2000).
Structure of yeast poly(A) polymerase alone and in complex with 3'-dATP.
  Science, 289, 1346-1349.
PDB code: 1fa0
11083623 L.P.Kotra, J.Haddad, and S.Mobashery (2000).
Aminoglycosides: perspectives on mechanisms of action and resistance and strategies to counter resistance.
  Antimicrob Agents Chemother, 44, 3249-3256.  
11114506 M.F.Giraud, and J.H.Naismith (2000).
The rhamnose pathway.
  Curr Opin Struct Biol, 10, 687-696.  
11052676 S.Hoenke, M.Schmid, and P.Dimroth (2000).
Identification of the active site of phosphoribosyl-dephospho-coenzyme A transferase and relationship of the enzyme to an ancient class of nucleotidyltransferases.
  Biochemistry, 39, 13233-13240.  
11118200 W.Blankenfeldt, M.Asuncion, J.S.Lam, and J.H.Naismith (2000).
The structural basis of the catalytic mechanism and regulation of glucose-1-phosphate thymidylyltransferase (RmlA).
  EMBO J, 19, 6652-6663.
PDB codes: 1fxo 1fzw 1g0r 1g1l 1g23 1g2v 1g3l
10508782 C.H.Weber, Y.S.Park, S.Sanker, C.Kent, and M.L.Ludwig (1999).
A prototypical cytidylyltransferase: CTP:glycerol-3-phosphate cytidylyltransferase from bacillus subtilis.
  Structure, 7, 1113-1124.
PDB code: 1coz
10508725 G.D.Wright (1999).
Aminoglycoside-modifying enzymes.
  Curr Opin Microbiol, 2, 499-503.  
  10595540 G.Martin, P.Jenö, and W.Keller (1999).
Mapping of ATP binding regions in poly(A) polymerases by photoaffinity labeling and by mutational analysis identifies a domain conserved in many nucleotidyltransferases.
  Protein Sci, 8, 2380-2391.  
10047577 J.Jäger, and J.D.Pata (1999).
Getting a grip: polymerases and their substrate complexes.
  Curr Opin Struct Biol, 9, 21-28.  
10428949 K.Brown, F.Pompeo, S.Dixon, D.Mengin-Lecreulx, C.Cambillau, and Y.Bourne (1999).
Crystal structure of the bifunctional N-acetylglucosamine 1-phosphate uridyltransferase from Escherichia coli: a paradigm for the related pyrophosphorylase superfamily.
  EMBO J, 18, 4096-4107.
PDB codes: 1fwy 1fxj
10378269 L.E.Wybenga-Groot, K.Draker, G.D.Wright, and A.M.Berghuis (1999).
Crystal structure of an aminoglycoside 6'-N-acetyltransferase: defining the GCN5-related N-acetyltransferase superfamily fold.
  Structure, 7, 497-507.
PDB code: 1b87
  10103173 M.P.Mingeot-Leclercq, Y.Glupczynski, and P.M.Tulkens (1999).
Aminoglycosides: activity and resistance.
  Antimicrob Agents Chemother, 43, 727-737.  
10561594 M.Simitsopoulou, H.Avila, and F.Franceschi (1999).
Ribosomal gene disruption in the extreme thermophile Thermus thermophilus HB8. Generation of a mutant lacking ribosomal protein S17.
  Eur J Biochem, 266, 524-532.  
9188741 A.V.Efimov (1997).
Structural trees for protein superfamilies.
  Proteins, 28, 241-260.  
  9145851 G.D.Wright, and P.Ladak (1997).
Overexpression and characterization of the chromosomal aminoglycoside 6'-N-acetyltransferase from Enterococcus faecium.
  Antimicrob Agents Chemother, 41, 956-960.  
9211644 J.Davies, and G.D.Wright (1997).
Bacterial resistance to aminoglycoside antibiotics.
  Trends Microbiol, 5, 234-240.  
9070426 L.Jiang, A.K.Suri, R.Fiala, and D.J.Patel (1997).
Saccharide-RNA recognition in an aminoglycoside antibiotic-RNA aptamer complex.
  Chem Biol, 4, 35-50.
PDB code: 1tob
  8665867 G.Martin, and W.Keller (1996).
Mutational analysis of mammalian poly(A) polymerase identifies a region for primer binding and catalytic domain, homologous to the family X polymerases, and to other nucleotidyltransferases.
  EMBO J, 15, 2593-2603.  
8841119 H.Pelletier, M.R.Sawaya, W.Wolfle, S.H.Wilson, and J.Kraut (1996).
A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta.
  Biochemistry, 35, 12762-12777.
PDB codes: 1zqt 7ice 7icf 7icg 7ich 7ici 7icj 7ick 7icl 7icm 7icn 7ico 7icp 7icq 7icr 7ics 7ict 7icu 7icv 8icj 8ick 8icl 8icm 8icn 8ico 8icp 8icq 8icr 8ics 8ict 8icu 8icv 8icw 8icx 8icy 9icf 9ick 9icn 9ico 9icp 9icq 9icr 9ics 9ict 9icu 9icv
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 codes are shown on the right.