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(-) Description

Title :  CRYSTAL STRUCTURE OF 3',5"-AMINOGLYCOSIDE PHOSPHOTRANSFERASE TYPE IIIA AMPPNP COMPLEX
 
Authors :  D. L. Burk, W. C. Hon, A. K. -W. Leung, A. M. Berghuis
Date :  18 May 01  (Deposition) - 08 Aug 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Antibiotic Resistance, Kinase, Atp-Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. L. Burk, W. C. Hon, A. K. Leung, A. M. Berghuis
Structural Analyses Of Nucleotide Binding To An Aminoglycoside Phosphotransferase.
Biochemistry V. 40 8756 2001
PubMed-ID: 11467935  |  Reference-DOI: 10.1021/BI010504P
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AMINOGLYCOSIDE 3'-PHOSPHOTRANSFERASE
    Chains: A, B
    EC Number: 2.7.1.95
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PPCRG6
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: ENTEROCOCCUS FAECALIS
    Organism Taxid: 1351
    Synonym: APH(3')III

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MG4Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:195 , ASP A:208 , ANP A:303 , HOH A:349 , HOH A:390BINDING SITE FOR RESIDUE MG A 301
2AC2SOFTWAREASP A:208 , ANP A:303 , HOH A:347 , HOH A:348BINDING SITE FOR RESIDUE MG A 302
3AC3SOFTWAREASN B:195 , ASP B:208 , ANP B:304 , HOH B:390 , HOH B:391BINDING SITE FOR RESIDUE MG B 301
4AC4SOFTWAREASP B:208 , ANP B:304 , HOH B:353 , HOH B:354BINDING SITE FOR RESIDUE MG B 302
5AC5SOFTWAREASP A:22 , SER A:27 , VAL A:31 , TYR A:42 , LYS A:44 , MET A:90 , SER A:91 , GLU A:92 , ALA A:93 , SER A:194 , ASN A:195 , PHE A:197 , ILE A:207 , ASP A:208 , MG A:301 , MG A:302 , HOH A:342 , HOH A:347 , HOH A:348 , HOH A:349 , HOH A:354 , HOH A:390 , HOH A:394 , HOH A:395BINDING SITE FOR RESIDUE ANP A 303
6AC6SOFTWAREASP B:22 , MET B:26 , SER B:27 , VAL B:31 , TYR B:42 , LYS B:44 , MET B:90 , SER B:91 , GLU B:92 , ALA B:93 , LEU B:97 , ASP B:190 , SER B:194 , ASN B:195 , PHE B:197 , ILE B:207 , ASP B:208 , MG B:301 , MG B:302 , HOH B:313 , HOH B:341 , HOH B:348 , HOH B:353 , HOH B:354 , HOH B:390 , HOH B:391 , HOH B:394 , HOH B:399BINDING SITE FOR RESIDUE ANP B 304

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:19 -B:156
2A:156 -B:19

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1J7U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J7U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1J7U)

(-) Exons   (0, 0)

(no "Exon" information available for 1J7U)

(-) 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:263
 aligned with KKA3_ENTFL | P0A3Y5 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:263
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261   
           KKA3_ENTFL     2 AKMRISPELKKLIEKYRCVKDTEGMSPAKVYKLVGENENLYLKMTDSRYKGTTYDVEREKDMMLWLEGKLPVPKVLHFERHDGWSNLLMSEADGVLCSEEYEDEQSPEKIIELYAECIRLFHSIDISDCPYTNSLDSRLAELDYLLNNDLADVDCENWEEDTPFKDPRELYDFLKTEKPEEELVFSHGDLGDSNIFVKDGKVSGFIDLGRSGRADKWYDIAFCVRSIREDIGEEQYVELFFDLLGIKPDWEKIKYYILLDELF 264
               SCOP domains d1j7ua_ A: Type IIIa 3',5-aminoglycoside phosphotransferase                                                                                                                                                                                                             SCOP domains
               CATH domains 1j7uA01 A:2-91 Phosphorylase Kinase; domain 1                                             1j7uA02 A:92-264  [code=3.90.1200.10, no name defined]                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhh...eeee........eeeeee....eeeeeeehhhhh....hhhhhhhhhhhh........eeeeeee..eeeeeee....eehhhhh....hhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhh.....hhhhhh......hhhhhhhhhhhh.....eeee........eee....eeee......eeeehhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j7u A   2 AKMRISPELKKLIEKYRCVKDTEGMSPAKVYKLVGENENLYLKMTDSRYKGTTYDVEREKDMMLWLEGKLPVPKVLHFERHDGWSNLLMSEADGVLCSEEYEDEQSPEKIIELYAECIRLFHSIDISDCPYTNSLDSRLAELDYLLNNDLADVDCENWEEDTPFKDPRELYDFLKTEKPEEELVFSHGDLGDSNIFVKDGKVSGFIDLGRSGRADKWYDIAFCVRSIREDIGEEQYVELFFDLLGIKPDWEKIKYYILLDELF 264
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261   


Chain B from PDB  Type:PROTEIN  Length:263
 aligned with KKA3_ENTFL | P0A3Y5 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:263
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261   
           KKA3_ENTFL     2 AKMRISPELKKLIEKYRCVKDTEGMSPAKVYKLVGENENLYLKMTDSRYKGTTYDVEREKDMMLWLEGKLPVPKVLHFERHDGWSNLLMSEADGVLCSEEYEDEQSPEKIIELYAECIRLFHSIDISDCPYTNSLDSRLAELDYLLNNDLADVDCENWEEDTPFKDPRELYDFLKTEKPEEELVFSHGDLGDSNIFVKDGKVSGFIDLGRSGRADKWYDIAFCVRSIREDIGEEQYVELFFDLLGIKPDWEKIKYYILLDELF 264
               SCOP domains d1j7ub_ B: Type IIIa 3',5-aminoglycoside phosphotransferase                                                                                                                                                                                                             SCOP domains
               CATH domains 1j7uB01 B:2-91 Phosphorylase Kinase; domain 1                                             1j7uB02 B:92-264  [code=3.90.1200.10, no name defined]                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhh..eeee........eeeeee....eeeeeeehhhhh....hhhhhhhhhhhh........eeeeeee..eeeeeee....eehhhhhh...hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh.................hhhhhhhhhhhh.....eeee........eeee..eeeee......eeeehhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j7u B   2 AKMRISPELKKLIEKYRCVKDTEGMSPAKVYKLVGENENLYLKMTDSRYKGTTYDVEREKDMMLWLEGKLPVPKVLHFERHDGWSNLLMSEADGVLCSEEYEDEQSPEKIIELYAECIRLFHSIDISDCPYTNSLDSRLAELDYLLNNDLADVDCENWEEDTPFKDPRELYDFLKTEKPEEELVFSHGDLGDSNIFVKDGKVSGFIDLGRSGRADKWYDIAFCVRSIREDIGEEQYVELFFDLLGIKPDWEKIKYYILLDELF 264
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261
   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
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J7U)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (KKA3_ENTFL | P0A3Y5)
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: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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        KKA3_ENTFL | P0A3Y5: 1j7i 1j7l 1l8t 2b0q 2bkk 3q2j 3tm0

(-) Related Entries Specified in the PDB File

1j7i 1J7I CONTAINS THE APOENZYME FORM OF THIS ENZYME
1j7l 1J7L CONTAINS THE SAME ENZYME COMPLEXED WITH ADP