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(-) Description

Title :  CRYSTAL STRUCTURE OF AMINOGLYCOSIDE 6'-ACETYLTRANSFERASE TYPE II IN COMPLEX WITH COENZYME A
 
Authors :  D. L. Burk, N. Ghuman, L. E. Wybenga-Groot, A. M. Berghuis
Date :  12 Nov 02  (Deposition) - 18 Mar 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A (1x),B (1x),C (1x),D (1x)
Keywords :  Aminoglycoside 6'-N-Acetyltransferase, Antibiotic Resistance, Coenzyme A (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. L. Burk, N. Ghuman, L. E. Wybenga-Groot, A. M. Berghuis
X-Ray Structure Of The Aac(6')-Ii Antibiotic Resistance Enzyme At 1. 8 A Resolution; Examination Of Oligomeric Arrangements In Gnat Superfamily Members
Protein Sci. V. 12 426 2003
PubMed-ID: 12592013  |  Reference-DOI: 10.1110/PS.0233503
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AAC(6')-II
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPLAAC-1
    Expression System Taxid: 562
    Organism Scientific: ENTEROCOCCUS FAECIUM
    Organism Taxid: 1352

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD
Biological Unit 3 (1x): A (1x)B (1x)C (1x)D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
1COA4Ligand/IonCOENZYME A
2SO45Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1COA2Ligand/IonCOENZYME A
2SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (2, 7)
No.NameCountTypeFull Name
1COA2Ligand/IonCOENZYME A
2SO45Ligand/IonSULFATE ION
Biological Unit 3 (2, 7)
No.NameCountTypeFull Name
1COA2Ligand/IonCOENZYME A
2SO45Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS C:153 , HOH C:909 , HIS D:128 , THR D:129 , HOH D:924 , HOH D:934 , HOH D:999BINDING SITE FOR RESIDUE SO4 C 900
2AC2SOFTWARETHR A:123 , LYS A:132 , PRO A:177 , HOH A:635 , HOH A:665 , HIS C:116 , GLN C:122 , HOH C:1027 , HOH C:1031 , HOH C:1041BINDING SITE FOR RESIDUE SO4 C 901
3AC3SOFTWARETYR C:126 , GLU C:127 , HIS C:128 , THR C:129 , HOH C:919 , HOH C:1023 , LYS D:153BINDING SITE FOR RESIDUE SO4 C 902
4AC4SOFTWAREHIS B:116 , GLN B:122 , THR D:123 , LYS D:132 , HOH D:942 , HOH D:951 , HOH D:991 , HOH D:1001BINDING SITE FOR RESIDUE SO4 D 903
5AC5SOFTWAREARG C:90 , HOH C:942 , HOH C:995 , HOH C:1019BINDING SITE FOR RESIDUE SO4 C 904
6AC6SOFTWARETRP A:25 , LEU A:76 , VAL A:78 , ARG A:83 , LYS A:84 , ASN A:85 , GLN A:86 , ILE A:87 , GLY A:88 , THR A:89 , GLY A:110 , THR A:111 , ASN A:138 , GLU A:141 , HIS A:142 , PRO A:143 , GLU A:145 , PHE A:146 , TYR A:147 , LYS A:149 , HOH A:607 , HOH A:649 , HOH A:661 , HOH A:663 , HOH A:677 , HOH A:684BINDING SITE FOR RESIDUE COA A 601
7AC7SOFTWARETHR B:24 , TRP B:25 , LEU B:76 , VAL B:77 , VAL B:78 , ARG B:83 , LYS B:84 , ASN B:85 , GLN B:86 , ILE B:87 , GLY B:88 , THR B:89 , THR B:111 , GLU B:141 , HIS B:142 , PHE B:146 , TYR B:147 , LYS B:149 , HOH B:640 , HOH B:674 , HOH B:678BINDING SITE FOR RESIDUE COA B 602
8AC8SOFTWAREHOH B:675 , THR C:24 , TRP C:25 , LEU C:76 , VAL C:77 , VAL C:78 , ARG C:83 , LYS C:84 , ASN C:85 , GLN C:86 , ILE C:87 , GLY C:88 , THR C:89 , THR C:111 , GLU C:141 , HIS C:142 , PHE C:146 , TYR C:147 , LYS C:149 , HOH C:921 , HOH C:986 , HOH C:1015 , HOH C:1016 , HOH C:1032BINDING SITE FOR RESIDUE COA C 603
9AC9SOFTWARETRP D:25 , LEU D:76 , VAL D:78 , ARG D:83 , LYS D:84 , ASN D:85 , GLN D:86 , ILE D:87 , GLY D:88 , THR D:89 , GLY D:110 , GLU D:141 , HIS D:142 , PRO D:143 , GLU D:145 , PHE D:146 , TYR D:147 , LYS D:149 , HOH D:907 , HOH D:970 , HOH D:973 , HOH D:990BINDING SITE FOR RESIDUE COA D 604

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1N71)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1His A:74 -Pro A:75
2His B:74 -Pro B:75
3His C:74 -Pro C:75
4His D:74 -Pro D:75

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1N71)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1N71)

(-) Exons   (0, 0)

(no "Exon" information available for 1N71)

(-) Sequences/Alignments

Asymmetric 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:180
 aligned with Q47764_ENTFC | Q47764 from UniProtKB/TrEMBL  Length:182

    Alignment length:180
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
         Q47764_ENTFC     1 MIISEFDRNNPVLKDQLSDLLRLTWPEEYGDSSAEEVEEMMNPERIAVAAVDQDELVGFIGAIPQYGITGWELHPLVVESSRRKNQIGTRLVNYLEKEVASRGGITIYLGTDDLDHGTTLSQTDLYVHTFDKVASIQNLREHPYEFYEKLGYKIVGVLPNANGWDKPDIWMAKTIIPRPD 180
               SCOP domains d1n71a_ A: Aminoglycoside 6'-N-acetyltransferase                                                                                                                                     SCOP domains
               CATH domains 1n71A00 A:1-180  [code=3.40.630.30, no name defined]                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee....hhhhhhhhhhhhhhhh......hhhhhhhhhh....eeeeeee..eeeeeeeeeeee...eeeeeeeee.......hhhhhhhhhhhhhhhhh...eeeeeee...............hhhhhhhh.......hhhhhhhh..eeeeee.........eeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1n71 A   1 MIISEFDRNNPVLKDQLSDLLRLTWPEEYGDSSAEEVEEMMNPERIAVAAVDQDELVGFIGAIPQYGITGWELHPLVVESSRRKNQIGTRLVNYLEKEVASRGGITIYLGTDDLDHGTTLSQTDLYEHTFDKVASIQNLREHPYEFYEKLGYKIVGVLPNANGWDKPDIWMAKTIIPRPD 180
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180


Chain B from PDB  Type:PROTEIN  Length:179
 aligned with Q47764_ENTFC | Q47764 from UniProtKB/TrEMBL  Length:182

    Alignment length:179
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170         
         Q47764_ENTFC     1 MIISEFDRNNPVLKDQLSDLLRLTWPEEYGDSSAEEVEEMMNPERIAVAAVDQDELVGFIGAIPQYGITGWELHPLVVESSRRKNQIGTRLVNYLEKEVASRGGITIYLGTDDLDHGTTLSQTDLYVHTFDKVASIQNLREHPYEFYEKLGYKIVGVLPNANGWDKPDIWMAKTIIPRP 179
               SCOP domains d1n71b_ B: Aminoglycoside 6'-N-acetyltransferase                                                                                                                                    SCOP domains
               CATH domains 1n71B00 B:1-179  [code=3.40.630.30, no name defined]                                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....hhhhhhhhhhhhhhhh......hhhhhhhhh.....eeeeeee..eeeeeeeeeeee...eeeeeeeee.hhhh..hhhhhhhhhhhhhhhhh...eeeeeee...............hhhhhhhh.......hhhhhhh...eeeeee.........eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n71 B   1 MIISEFDRNNPVLKDQLSDLLRLTWPEEYGDSSAEEVEEMMNPERIAVAAVDQDELVGFIGAIPQYGITGWELHPLVVESSRRKNQIGTRLVNYLEKEVASRGGITIYLGTDDLDHGTTLSQTDLYEHTFDKVASIQNLREHPYEFYEKLGYKIVGVLPNANGWDKPDIWMAKTIIPRP 179
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170         


Chain C from PDB  Type:PROTEIN  Length:179
 aligned with Q47764_ENTFC | Q47764 from UniProtKB/TrEMBL  Length:182

    Alignment length:179
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170         
         Q47764_ENTFC     1 MIISEFDRNNPVLKDQLSDLLRLTWPEEYGDSSAEEVEEMMNPERIAVAAVDQDELVGFIGAIPQYGITGWELHPLVVESSRRKNQIGTRLVNYLEKEVASRGGITIYLGTDDLDHGTTLSQTDLYVHTFDKVASIQNLREHPYEFYEKLGYKIVGVLPNANGWDKPDIWMAKTIIPRP 179
               SCOP domains d1n71c_ C: Aminoglycoside 6'-N-acetyltransferase                                                                                                                                    SCOP domains
               CATH domains 1n71C00 C:1-179  [code=3.40.630.30, no name defined]                                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....hhhhhhhhhhhhhhhh......hhhhhhhhhh....eeeeeee..eeeeeeeeeeee...eeeeeeeee.hhhh..hhhhhhhhhhhhhhhhh...eeeeeee...............hhhhhhhh.......hhhhhhhh..eeeeee.........eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n71 C   1 MIISEFDRNNPVLKDQLSDLLRLTWPEEYGDSSAEEVEEMMNPERIAVAAVDQDELVGFIGAIPQYGITGWELHPLVVESSRRKNQIGTRLVNYLEKEVASRGGITIYLGTDDLDHGTTLSQTDLYEHTFDKVASIQNLREHPYEFYEKLGYKIVGVLPNANGWDKPDIWMAKTIIPRP 179
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170         


Chain D from PDB  Type:PROTEIN  Length:180
 aligned with Q47764_ENTFC | Q47764 from UniProtKB/TrEMBL  Length:182

    Alignment length:180
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
         Q47764_ENTFC     1 MIISEFDRNNPVLKDQLSDLLRLTWPEEYGDSSAEEVEEMMNPERIAVAAVDQDELVGFIGAIPQYGITGWELHPLVVESSRRKNQIGTRLVNYLEKEVASRGGITIYLGTDDLDHGTTLSQTDLYVHTFDKVASIQNLREHPYEFYEKLGYKIVGVLPNANGWDKPDIWMAKTIIPRPD 180
               SCOP domains d1n71d_ D: Aminoglycoside 6'-N-acetyltransferase                                                                                                                                     SCOP domains
               CATH domains 1n71D00 D:1-180  [code=3.40.630.30, no name defined]                                                                                                                                 CATH domains
           Pfam domains (1) -------------------------------------------------Acetyltransf_1-1n71D01 D:50-119                                       ------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------Acetyltransf_1-1n71D02 D:50-119                                       ------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -------------------------------------------------Acetyltransf_1-1n71D03 D:50-119                                       ------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -------------------------------------------------Acetyltransf_1-1n71D04 D:50-119                                       ------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author .eeee....hhhhhhhhhhhhhhhh......hhhhhhhhhh....eeeeeee..eeeeeeeeeeee...eeeeeeeee.hhhh..hhhhhhhhhhhhhhhhh...eeeeeee...............hhhhhhhh.......hhhhhhhh..eeeeee.........eeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1n71 D   1 MIISEFDRNNPVLKDQLSDLLRLTWPEEYGDSSAEEVEEMMNPERIAVAAVDQDELVGFIGAIPQYGITGWELHPLVVESSRRKNQIGTRLVNYLEKEVASRGGITIYLGTDDLDHGTTLSQTDLYEHTFDKVASIQNLREHPYEFYEKLGYKIVGVLPNANGWDKPDIWMAKTIIPRPD 180
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
   Legend:   → Mismatch (orange background)
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  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, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Acetyltrans (109)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q47764_ENTFC | Q47764)
molecular function
    GO:0008080    N-acetyltransferase activity    Catalysis of the transfer of an acetyl group to a nitrogen atom on the acceptor molecule.

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  1n71
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  Q47764_ENTFC | Q47764
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 Related Entries

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

UniProtKB/TrEMBL
        Q47764_ENTFC | Q47764: 1b87 2a4n 5e96

(-) Related Entries Specified in the PDB File

1b87 AMINOGLYCOSIDE 6'-ACETYLTRANSFERASE TYPE II IN COMPLEX WITH ACETYL COENZYME A