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(-) Description

Title :  KANAMYCIN NUCLEOTIDYLTRANSFERASE
 
Authors :  L. C. Pedersen, M. M. Benning, H. M. Holden
Date :  07 Jul 95  (Deposition) - 17 Aug 96  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Antibiotic Resistance, Transferase, Plasmid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. C. Pedersen, M. M. Benning, H. M. Holden
Structural Investigation Of The Antibiotic And Atp-Binding Sites In Kanamycin Nucleotidyltransferase.
Biochemistry V. 34 13305 1995
PubMed-ID: 7577914  |  Reference-DOI: 10.1021/BI00041A005
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - KANAMYCIN NUCLEOTIDYLTRANSFERASE
    Chains: A, B
    EC Number: 2.7.7.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PX(T7)TK101
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Synonym: KNTASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1APC2Ligand/IonDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2KAN2Ligand/IonKANAMYCIN A
3MG2Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:39 , ASP A:50 , GLU A:52 , APC A:556BINDING SITE FOR RESIDUE MG A 603
2AC2SOFTWARESER B:39 , ASP B:50 , GLU B:52 , APC B:557BINDING SITE FOR RESIDUE MG B 604
3AC3SOFTWAREGLY A:38 , SER A:39 , ARG A:42 , SER A:49 , ASP A:50 , GLU A:52 , LEU A:98 , THR A:99 , GLN A:102 , THR A:186 , THR A:187 , SER A:188 , MG A:603 , HOH A:608 , HOH A:611 , HOH A:631 , GLU B:145 , LYS B:149 , KAN B:559BINDING SITE FOR RESIDUE APC A 556
4AC4SOFTWAREGLU A:145 , LYS A:149 , KAN A:558 , TYR B:37 , GLY B:38 , SER B:39 , ARG B:42 , SER B:49 , ASP B:50 , GLU B:52 , LEU B:98 , THR B:99 , THR B:186 , THR B:187 , SER B:188 , MG B:604 , HOH B:619BINDING SITE FOR RESIDUE APC B 557
5AC5SOFTWARESER A:94 , ASP A:95 , GLU A:141 , GLU A:142 , GLU A:145 , GLU B:67 , GLU B:76 , APC B:557 , KAN B:559BINDING SITE FOR RESIDUE KAN A 558
6AC6SOFTWAREGLU A:67 , LYS A:74 , GLU A:76 , APC A:556 , KAN A:558 , SER B:94 , ASP B:95 , GLU B:141 , GLU B:145BINDING SITE FOR RESIDUE KAN B 559

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:157 -Pro A:158
2Gly B:157 -Pro B:158

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1KNY)

(-) 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:253
 aligned with KANU_STAAU | P05057 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:253
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   
           KANU_STAAU     1 MNGPIIMTREERMKIVHEIKERILDKYGDDVKAIGVYGSLGRQTDGPYSDIEMMCVMSTEEAEFSHEWTTGEWKVEVNFDSEEILLDYASQVESDWPLTHGQFFSILPIYDSGGYLEKVYQTAKSVEAQTFHDAICALIVEELFEYAGKWRNIRVQGPTTFLPSLTVQVAMAGAMLIGLHHRICYTTSASVLTEAVKQSDLPSGYDHLCQFVMSGQLSDSEKLLESLENFWNGIQEWTERHGYIVDVSKRIPF 253
               SCOP domains d1knya2 A:1-125 Kanamycin nucleotidyltransferase (KNTase), N-terminal domain                                                 d1knya1 A:126-253 Kanamycin nucleotidyltransferase (KNTase), C-terminal domain                                                   SCOP domains
               CATH domains 1knyA01 A:1-125 Beta Polymerase, domain 2                                                                                    1knyA02 A:126-253 Nucleotidyltransferases  domain 2                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhheeeeeeehhhhh........eeeeeee.....eeeeeee....eeeeeeeehhhhhhhhh.....hhhhhhhh...eeeee...hhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.........hhhhhhh.......hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kny A   1 MNGPIIMTREERMKIVHEIKERILDKYGDDVKAIGVYGSLGRQTDGPYSDIEMMCVMSTEEAEFSHEWTTGEWKVEVNFYSEEILLDYASQVESDWPLTHGQFFSILPIYDSGGYLEKVYQTAKSVEAQTFHDAICALIVEELFEYAGKWRNIRVQGPTTFLPSLTVQVAMAGAMLIGLHHRICYTTSASVLTEAVKQSDLPSGYDHLCQFVMSGQLSDSEKLLESLENFWNGIQEWTERHGYIVDVSKRIPF 253
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   


Chain B from PDB  Type:PROTEIN  Length:253
 aligned with KANU_STAAU | P05057 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:253
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   
           KANU_STAAU     1 MNGPIIMTREERMKIVHEIKERILDKYGDDVKAIGVYGSLGRQTDGPYSDIEMMCVMSTEEAEFSHEWTTGEWKVEVNFDSEEILLDYASQVESDWPLTHGQFFSILPIYDSGGYLEKVYQTAKSVEAQTFHDAICALIVEELFEYAGKWRNIRVQGPTTFLPSLTVQVAMAGAMLIGLHHRICYTTSASVLTEAVKQSDLPSGYDHLCQFVMSGQLSDSEKLLESLENFWNGIQEWTERHGYIVDVSKRIPF 253
               SCOP domains d1knyb2 B:1-125 Kanamycin nucleotidyltransferase (KNTase), N-terminal domain                                                 d1knyb1 B:126-253 Kanamycin nucleotidyltransferase (KNTase), C-terminal domain                                                   SCOP domains
               CATH domains 1knyB01 B:1-125 Beta Polymerase, domain 2                                                                                    1knyB02 B:126-253 Nucleotidyltransferases  domain 2                                                                              CATH domains
           Pfam domains (1) ---------------NTP_transf_2-1knyB03 B:16-110                                                                  KNTase_C-1knyB01 B:111-253                                                                                                                      Pfam domains (1)
           Pfam domains (2) ---------------NTP_transf_2-1knyB04 B:16-110                                                                  KNTase_C-1knyB02 B:111-253                                                                                                                      Pfam domains (2)
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhheeeeeeehhhhh........eeeeeee.....eeeeeee....eeeeeeeehhhhhhhh......hhhhhhhh...eeeee...hhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh.......hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kny B   1 MNGPIIMTREERMKIVHEIKERILDKYGDDVKAIGVYGSLGRQTDGPYSDIEMMCVMSTEEAEFSHEWTTGEWKVEVNFYSEEILLDYASQVESDWPLTHGQFFSILPIYDSGGYLEKVYQTAKSVEAQTFHDAICALIVEELFEYAGKWRNIRVQGPTTFLPSLTVQVAMAGAMLIGLHHRICYTTSASVLTEAVKQSDLPSGYDHLCQFVMSGQLSDSEKLLESLENFWNGIQEWTERHGYIVDVSKRIPF 253
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: KNTase_C (11)
(-)
Clan: NTP_transf (45)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (KANU_STAAU | P05057)
molecular function
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    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: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

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UniProtKB/Swiss-Prot
        KANU_STAAU | P05057: 1kan

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