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(-) Description

Title :  CRYSTAL STRUCTURE OF AMINOGLYCOSIDE-3'-PHOSPHOTRANSFERASE-IIA
 
Authors :  D. Nurizzo, S. C. Shewry, E. N. Baker, C. A. Smith
Date :  06 Dec 02  (Deposition) - 16 Sep 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Phosphotransferase, Protein Kinase, Atpase, Kanamycin (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Nurizzo, S. C. Shewry, M. H. Perlin, S. A. Brown, J. N. Dholakia, R. L. Fuchs, T. Deva, E. N. Baker, C. A. Smith
The Crystal Structure Of Aminoglycoside-3'-Phosphotransferase-Iia, An Enzyme Responsible For Antibiotic Resistance
J. Mol. Biol. V. 327 491 2003
PubMed-ID: 12628253  |  Reference-DOI: 10.1016/S0022-2836(03)00121-9
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AMINOGLYCOSIDE 3'-PHOSPHOTRANSFERASE
    ChainsA, B
    EC Number2.7.1.95
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificKLEBSIELLA PNEUMONIAE
    Organism Taxid573
    SynonymAMINOGLYCOSIDE-3'-PHOSPHOTRANSFERASE-IIA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2KAN2Ligand/IonKANAMYCIN A
3MG2Ligand/IonMAGNESIUM ION
4NA2Ligand/IonSODIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:195 , ASP A:208 , HOH A:1615 , HOH A:1637 , HOH A:1688BINDING SITE FOR RESIDUE MG A 400
2AC2SOFTWAREPHE A:48 , GLU A:96 , VAL A:97BINDING SITE FOR RESIDUE ACT A 1500
3AC3SOFTWAREASP A:190 , CYS A:192 , KAN A:1300 , HOH A:1637BINDING SITE FOR RESIDUE NA A 1600
4AC4SOFTWAREASN B:195 , ASP B:208 , HOH B:2612 , HOH B:2697 , HOH B:2734 , HOH B:2744BINDING SITE FOR RESIDUE MG B 400
5AC5SOFTWAREPHE B:48 , VAL B:97 , MET B:197BINDING SITE FOR RESIDUE ACT B 2500
6AC6SOFTWAREASP B:190 , CYS B:192 , ASN B:195 , KAN B:2300BINDING SITE FOR RESIDUE NA B 2600
7AC7SOFTWAREASP A:157 , LEU A:158 , ASP A:159 , GLU A:160 , ASP A:190 , ARG A:211 , ARG A:226 , ASP A:227 , GLU A:230 , ASP A:261 , GLU A:262 , PHE A:264 , NA A:1600 , HOH A:1608 , HOH A:1645 , HOH A:1678 , HOH A:1688 , HOH A:1735 , HOH A:1777 , HOH A:1808BINDING SITE FOR RESIDUE KAN A 1300
8AC8SOFTWAREASP B:157 , LEU B:158 , ASP B:159 , ASP B:190 , ARG B:211 , ARG B:226 , ASP B:227 , GLU B:230 , ASP B:261 , GLU B:262 , PHE B:264 , NA B:2600 , HOH B:2609 , HOH B:2612 , HOH B:2670 , HOH B:2720BINDING SITE FOR RESIDUE KAN B 2300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ND4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1ND4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ND4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1ND4)

(-) Exons   (0, 0)

(no "Exon" information available for 1ND4)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:255
 aligned with KKA2_KLEPN | P00552 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:255
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259     
           KKA2_KLEPN    10 GSPAAWVERLFGYDWAQQTIGCSDAAVFRLSAQGRPVLFVKTDLSGALNELQDEAARLSWLATTGVPCAAVLDVVTEAGRDWLLLGEVPGQDLLSSHLAPAEKVSIMADAMRRLHTLDPATCPFDHQAKHRIERARTRMEAGLVDQDDLDEEHQGLAPAELFARLKARMPDGEDLVVTHGDACLPNIMVENGRFSGFIDCGRLGVADRYQDIALATRDIAEELGGEWADRFLVLYGIAAPDSQRIAFYRLLDEFF 264
               SCOP domains d1nd4a_ A: Aminoglycoside 3'-phosphotransferase IIa (Kanamycin kinase)                                                                                                                                                                                          SCOP domains
               CATH domains 1nd4A01 A:10-95 Phosphorylase Kinase; domain 1                                        1nd4A02 A:96-264  [code=3.90.1200.10, no name defined]                                                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh......eeee........eeeeee......eeeeee......hhhhhhhhhhhhhh.......eeeeee....eeeeee....ee......hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh........hhhhh..hhhhhhhhhhhh......eeee....hhh.eeee..eeeee......eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nd4 A  10 GSPAAWVERLFGYDWAQQTIGCSDAAVFRLSAQGRPVLFVKTDLSGALNELQDEAARLSWLATTGVPCAAVLDVVTEAGRDWLLLGEVPGQDLLSSHLAPAEKVSIMADAMRRLHTLDPATCPFDHQAKHRIERARTRMEAGLVDQDDLDEEHQGLAPAELFARLKARMPDGEDLVVTHGDACLPNIMVENGRFSGFIDCGRLGVADRYQDIALATRDIAEELGGEWADRFLVLYGIAAPDSQRIAFYRLLDEFF 264
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259     

Chain B from PDB  Type:PROTEIN  Length:255
 aligned with KKA2_KLEPN | P00552 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:255
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259     
           KKA2_KLEPN    10 GSPAAWVERLFGYDWAQQTIGCSDAAVFRLSAQGRPVLFVKTDLSGALNELQDEAARLSWLATTGVPCAAVLDVVTEAGRDWLLLGEVPGQDLLSSHLAPAEKVSIMADAMRRLHTLDPATCPFDHQAKHRIERARTRMEAGLVDQDDLDEEHQGLAPAELFARLKARMPDGEDLVVTHGDACLPNIMVENGRFSGFIDCGRLGVADRYQDIALATRDIAEELGGEWADRFLVLYGIAAPDSQRIAFYRLLDEFF 264
               SCOP domains d1nd4b_ B: Aminoglycoside 3'-phosphotransferase IIa (Kanamycin kinase)                                                                                                                                                                                          SCOP domains
               CATH domains 1nd4B01 B:10-95 Phosphorylase Kinase; domain 1                                        1nd4B02 B:96-264  [code=3.90.1200.10, no name defined]                                                                                                                    CATH domains
           Pfam domains (1) --------------APH-1nd4B01 B:24-257                                                                                                                                                                                                                      ------- Pfam domains (1)
           Pfam domains (2) --------------APH-1nd4B02 B:24-257                                                                                                                                                                                                                      ------- Pfam domains (2)
         Sec.struct. author ..hhhhh......eeee........eeeeee......eeeeeee.....hhhhhhhhhhhhhhh......eeeeee...eeeeeee....ee......hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh........hhhhh..hhhhhhhhhhhh......eeee....hhh.eeee..eeeee......eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nd4 B  10 GSPAAWVERLFGYDWAQQTIGCSDAAVFRLSAQGRPVLFVKTDLSGALNELQDEAARLSWLATTGVPCAAVLDVVTEAGRDWLLLGEVPGQDLLSSHLAPAEKVSIMADAMRRLHTLDPATCPFDHQAKHRIERARTRMEAGLVDQDDLDEEHQGLAPAELFARLKARMPDGEDLVVTHGDACLPNIMVENGRFSGFIDCGRLGVADRYQDIALATRDIAEELGGEWADRFLVLYGIAAPDSQRIAFYRLLDEFF 264
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259     

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: PKinase (934)
(-)
Family: APH (15)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (KKA2_KLEPN | P00552)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008910    kanamycin kinase activity    Catalysis of the reaction: ATP + kanamycin = ADP + 2 H(+) + kanamycin 3'-phosphate.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016773    phosphotransferase activity, alcohol group as acceptor    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.

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