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(-) Description

Title :  AMINOGLYCOSIDE PHOSPHOTRANSFERASE (2'')-IA (CTD OF AAC(6')-IE/APH(2'')-IA) S214A MUTANT IN COMPLEX WITH GMPPNP AND MAGNESIUM
 
Authors :  S. J. Caldwell, A. M. Berghuis
Date :  10 Mar 16  (Deposition) - 25 May 16  (Release) - 15 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Kinase, Antibiotic, Aminoglycoside, Resistance, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. J. Caldwell, Y. Huang, A. M. Berghuis
Antibiotic Binding Drives Catalytic Activation Of Aminoglycoside Kinase Aph(2)-Ia.
Structure V. 24 935 2016
PubMed-ID: 27161980  |  Reference-DOI: 10.1016/J.STR.2016.04.002

(-) Compounds

Molecule 1 - BIFUNCTIONAL AAC/APH
    ChainsA, B, C, D
    EC Number2.3.1.-, 2.7.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET-22B-APH(2'')-IA
    Expression System StrainBL21(LDE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL DOMAIN (UNP RESIDUES 175-479)
    GeneAACA-APHD, R015, VRA0030
    MutationYES
    Organism ScientificSTAPHYLOCOCCUS AUREUS
    Organism Taxid1280
    Other DetailsC-TERMINAL DOMAIN OF AAC(6')-IE/APH(2'')-IA BIFUNCTIONAL ENZYME, RESIDUES 175-479. S214A MUTANT

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 19)

Asymmetric Unit (4, 19)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2GNP4Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
3GOL3Ligand/IonGLYCEROL
4MG9Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
3GOL1Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
3GOL1Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
3GOL-1Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
3GOL1Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:208 , ILE A:224 , LYS A:226 , TYR A:274 , GLU A:276 , ILE A:277 , PHE A:281 , HIS A:379 , ILE A:392 , ASP A:393 , MG A:700 , MG A:702 , HOH A:900 , HOH A:902 , HOH A:906 , HOH A:909 , HOH A:923 , HOH A:1093 , HOH A:1154 , HOH A:1286binding site for residue GNP A 500
02AC2SOFTWAREHIS A:379 , ASP A:393 , GNP A:500 , HOH A:900binding site for residue MG A 700
03AC3SOFTWAREASP A:393 , GNP A:500 , HOH A:902 , HOH A:903binding site for residue MG A 702
04AC4SOFTWAREGLN A:462 , ARG A:469binding site for residue CL A 802
05AC5SOFTWARELYS A:201 , ASN A:220binding site for residue GOL A 804
06AC6SOFTWAREILE B:208 , ILE B:224 , LYS B:226 , TYR B:274 , GLU B:276 , ILE B:277 , PHE B:281 , HIS B:379 , ILE B:392 , ASP B:393 , MG B:700 , MG B:702 , HOH B:900 , HOH B:902 , HOH B:903 , HOH B:906 , HOH B:909 , HOH B:911 , HOH B:923 , HOH B:1023 , HOH B:1057 , HOH B:1093 , HOH B:1260 , HOH B:1287binding site for residue GNP B 500
07AC7SOFTWAREHIS B:379 , ASP B:393 , GNP B:500 , HOH B:900binding site for residue MG B 700
08AC8SOFTWAREASP B:393 , GNP B:500 , HOH B:902 , HOH B:903binding site for residue MG B 702
09AC9SOFTWAREGLN B:462 , ILE B:465 , GLU B:466 , ARG B:469 , HOH B:1107binding site for residue CL B 802
10AD1SOFTWAREASN B:199 , LYS B:201 , ASN B:220 , GLU B:222 , HOH B:1183binding site for residue GOL B 804
11AD2SOFTWAREILE C:208 , SER C:210 , ILE C:224 , LYS C:226 , TYR C:274 , GLU C:276 , ILE C:277 , PHE C:281 , HIS C:379 , ILE C:392 , ASP C:393 , MG C:700 , MG C:702 , HOH C:900 , HOH C:902 , HOH C:906 , HOH C:909 , HOH C:923 , HOH C:1083 , HOH C:1093 , HOH C:1154 , HOH C:1260 , HOH C:1571binding site for residue GNP C 500
12AD3SOFTWAREHIS C:379 , ASP C:393 , GNP C:500 , HOH C:900binding site for residue MG C 700
13AD4SOFTWAREASP C:393 , GNP C:500 , HOH C:902 , HOH C:903binding site for residue MG C 702
14AD5SOFTWAREASN C:385 , HOH C:1636 , HOH C:1637 , HOH C:1638binding site for residue MG C 800
15AD6SOFTWAREGLN C:462 , ARG C:469binding site for residue CL C 802
16AD7SOFTWARESER D:210 , GLY D:211 , ILE D:224 , LYS D:226 , TYR D:274 , GLU D:276 , ILE D:277 , PHE D:281 , HIS D:379 , ILE D:392 , ASP D:393 , MG D:700 , MG D:702 , HOH D:900 , HOH D:902 , HOH D:903 , HOH D:906 , HOH D:909 , HOH D:1023 , HOH D:1057 , HOH D:1299 , HOH D:1501binding site for residue GNP D 500
17AD8SOFTWAREHIS D:379 , ASP D:393 , GNP D:500 , HOH D:900binding site for residue MG D 700
18AD9SOFTWAREASP D:393 , GNP D:500 , HOH D:902 , HOH D:903binding site for residue MG D 702
19AE1SOFTWAREPHE D:200 , LYS D:201 , ASN D:220 , GLU D:222 , TYR D:223binding site for residue GOL D 804

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5IQH)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5IQH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5IQH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5IQH)

(-) Exons   (0, 0)

(no "Exon" information available for 5IQH)

(-) 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:294
                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh.......eeeeee...eeeeee...eeeeee.....hhhhhhhhhhhhhhh........eeeeee....eeeeee....ee.hhhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee....hhh.eee.....eeee......eeee.hhhhh..........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5iqh A 182 NATNVKAMKYLIEHYFDNFKVDSIEIIGSGYDAVAYLVNNEYIFKTKFSKKGYAKEKAIYNFLNTNLETNVKIPNIEYSYISDELSILGYKEIKGTFLTPEIYSTMSEEEQNLLKRDIASFLRQMHGLDYTDISECTIDNKQNVLEEYILLRETIYNDLTDIEKDYIESFMERLNATTVFEGKKCLCHNDFSCNHLLLDGNNRLTGIIDFGDSGIIDEYCDFIYLLEDSEEEIGTNFGEDILRMYGNIDIEKAKEYQDIVEEYYPIETIVYGIKNIKQEFIENGRKEIYKRTYK 478
                                   191       201       211       221       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474    
                                                                          230|                                                                                                                                                                                                                                                    
                                                                           234                                                                                                                                                                                                                                                    

Chain B from PDB  Type:PROTEIN  Length:293
                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.......eeeeee...eeeeee...eeeeee....hhhhhhhhhhhhhhh........eeeeee....eeeeee....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee....hhh.eee.....eeee......eeee.hhhhh..........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iqh B 183 ATNVKAMKYLIEHYFDNFKVDSIEIIGSGYDAVAYLVNNEYIFKTKFSKGYAKEKAIYNFLNTNLETNVKIPNIEYSYISDELSILGYKEIKGTFLTPEIYSTMSEEEQNLLKRDIASFLRQMHGLDYTDISECTIDNKQNVLEEYILLRETIYNDLTDIEKDYIESFMERLNATTVFEGKKCLCHNDFSCNHLLLDGNNRLTGIIDFGDSGIIDEYCDFIYLLEDSEEEIGTNFGEDILRMYGNIDIEKAKEYQDIVEEYYPIETIVYGIKNIKQEFIENGRKEIYKRTYKD 479
                                   192       202       212       222       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476   
                                                                         230|                                                                                                                                                                                                                                                    
                                                                          235                                                                                                                                                                                                                                                    

Chain C from PDB  Type:PROTEIN  Length:288
                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.......eeeee..eeeeee...eeeeeee..hhhhhhhhhhhhhh........eeeeee...eeeeeee....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee....hhh.eee.....eeee......eeee.hhhhh..........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5iqh C 183 ATNVKAMKYLIEHYFDNFKVDSIEIIGSDAVAYLVNNEYIFKTKFSYAKEKAIYNFLNTNLETNVKIPNIEYSYISDELSILGYKEIKGTFLTPEIYSTMSEEEQNLLKRDIASFLRQMHGLDYTDISECTIDNKQNVLEEYILLRETIYNDLTDIEKDYIESFMERLNATTVFEGKKCLCHNDFSCNHLLLDGNNRLTGIIDFGDSGIIDEYCDFIYLLEDSEEEIGTNFGEDILRMYGNIDIEKAKEYQDIVEEYYPIETIVYGIKNIKQEFIENGRKEIYKRTYK 478
                                   192       202       214       224     ||240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470        
                                                     210|              230|                                                                                                                                                                                                                                                 
                                                      213               237                                                                                                                                                                                                                                                 

Chain D from PDB  Type:PROTEIN  Length:291
                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.......eeeeeee..eeeeee...eeeeee....hhhhhhhhhhhhhhh........eeeeee....eeeeee....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee....hhh.eee.....eeee......eeee.hhhhh..........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iqh D 183 ATNVKAMKYLIEHYFDNFKVDSIEIIGSGYDAVAYLVNNEYIFKTKFSKGYAKEKAIYNFLNTNLETNVKIPNIEYSYISDELSILGYKEIKGTFLTPEIYSTMSEEEQNLLKRDIASFLRQMHGLDYTDISECTIDNKQNVLEEYILLRETIYNDLTDIEKDYIESFMERLNATTVFEGKKCLCHNDFSCNHLLLDGNNRLTGIIDFGDSGIIDEYCDFIYLLEDSEEEIGTNFGEDILRMYGNIDIEKAKEYQDIVEEYYPIETIVYGIKNIKQEFIENGRKEIYKRTY 477
                                   192       202       212       222       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476 
                                                                         230|                                                                                                                                                                                                                                                  
                                                                          235                                                                                                                                                                                                                                                  

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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  (0, 0)

(no "SCOP Domain" information available for 5IQH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5IQH)

(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (11, 11)

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 Related Entries

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        AACA_STAAU | P0A0C14ork 5byl 5iqa 5iqb 5iqc 5iqd 5iqe 5iqf 5iqg 5iqi

(-) Related Entries Specified in the PDB File

5byl 5iqa 5iqb 5iqc 5iqd 5iqe 5iqf 5iqg 5iqi