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(-) Description

Title :  CRYSTAL STRUCTURE OF STREPTOGRAMIN GROUP A ANTIBIOTIC ACETYLTRANSFERASE VATA FROM STAPHYLOCOCCUS AUREUS IN COMPLEX WITH VIRGINIAMYCIN M1
 
Authors :  P. J. Stogios, G. Minasov, E. Evdokimova, Z. Wawrzak, V. Yim, M. Krishna R. Di Leo, P. Courvalin, A. Savchenko, W. F. Anderson, Center For St Genomics Of Infectious Diseases (Csgid)
Date :  03 Nov 12  (Deposition) - 21 Nov 12  (Release) - 24 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.36
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Structural Genomics, Antibiotic Resistance, Center For Structural Genomics Of Infectious Diseases (Csgid), Niaid, National Institute Of Allergy And Infectious Diseases, Xenobiotic Acyltransferase (Xat) Family, Hexapeptide Repeat Acyltransferase, Streptogramin Group A Antibiotic Acetyltransferase, Streptogramin Group A Antibiotics, Streptogramin A, Virginiamycin M1, Dalfopristin, Acetyl Coenzyme A, Coenzyme A, Intracellular, Transferase-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. J. Stogios, M. L. Kuhn, E. Evdokimova, P. Courvalin, W. F. Anderson, A. Savchenko
Potential For Reduction Of Streptogramin A Resistance Revealed By Structural Analysis Of Acetyltransferase Vata.
Antimicrob. Agents Chemother. V. 58 7083 2014
PubMed-ID: 25223995  |  Reference-DOI: 10.1128/AAC.03743-14

(-) Compounds

Molecule 1 - VIRGINIAMYCIN A ACETYLTRANSFERASE
    Chains: A, B, C
    EC Number: 2.3.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P15TV LIC
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: VAT
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Strain: BM3093

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 40)

Asymmetric/Biological Unit (7, 40)
No.NameCountTypeFull Name
1CL9Ligand/IonCHLORIDE ION
2EDO15Ligand/Ion1,2-ETHANEDIOL
3NA1Ligand/IonSODIUM ION
4PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
5PGE2Ligand/IonTRIETHYLENE GLYCOL
6SO48Ligand/IonSULFATE ION
7VIR1Ligand/IonVIRGINIAMYCIN M1

(-) Sites  (40, 40)

Asymmetric Unit (40, 40)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:70 , LEU A:189 , MET A:191 , HOH A:503BINDING SITE FOR RESIDUE SO4 A 301
02AC2SOFTWAREASN A:203 , ARG C:88 , ASP C:112 , EDO C:307BINDING SITE FOR RESIDUE SO4 A 302
03AC3SOFTWARELYS A:153 , LEU A:166 , LYS A:167 , PHE A:168 , HOH A:478BINDING SITE FOR RESIDUE SO4 A 303
04AC4SOFTWAREASN A:164 , HOH A:422 , ASN B:164 , HOH B:417 , ASN C:164 , HOH C:514BINDING SITE FOR RESIDUE NA A 304
05AC5SOFTWAREGLY A:117 , ASP A:118 , LYS A:138BINDING SITE FOR RESIDUE CL A 305
06AC6SOFTWAREARG A:100 , HOH A:518BINDING SITE FOR RESIDUE CL A 306
07AC7SOFTWARELYS A:171BINDING SITE FOR RESIDUE CL A 307
08AC8SOFTWAREGLU A:60BINDING SITE FOR RESIDUE CL A 308
09AC9SOFTWAREGLY A:84 , LEU A:216BINDING SITE FOR RESIDUE EDO A 309
10BC1SOFTWARELYS A:46 , ARG A:47BINDING SITE FOR RESIDUE EDO A 310
11BC2SOFTWAREASP A:53 , THR A:79 , HOH A:420 , HOH A:532 , CL B:306BINDING SITE FOR RESIDUE EDO A 311
12BC3SOFTWARELYS A:138 , GLY A:140 , VAL A:155 , HOH A:562BINDING SITE FOR RESIDUE EDO A 312
13BC4SOFTWAREGLU A:12 , LYS A:27 , PRO A:28 , HOH A:522 , ARG B:211BINDING SITE FOR RESIDUE PEG A 313
14BC5SOFTWAREPRO A:76 , GLY A:128 , ARG A:129 , ALA A:146 , ALA A:147 , HOH A:410 , TYR C:57 , HOH C:511BINDING SITE FOR RESIDUE PEG A 314
15BC6SOFTWAREALA A:146 , HOH A:454BINDING SITE FOR RESIDUE PEG A 315
16BC7SOFTWAREASN A:20 , LEU A:23 , TYR A:42 , ASP A:44 , HOH A:410 , HOH A:412 , HOH A:488 , HOH A:588 , TYR C:59 , GLY C:84 , ASN C:86 , HIS C:87 , HIS C:97 , LEU C:98 , PRO C:108 , LEU C:113 , HOH C:571BINDING SITE FOR RESIDUE VIR A 316
17BC8SOFTWARELYS B:153 , LEU B:166 , LYS B:167 , PHE B:168 , HOH B:553BINDING SITE FOR RESIDUE SO4 B 301
18BC9SOFTWARELYS B:27 , GLY B:38 , GLU B:39 , ARG B:70 , HOH B:449BINDING SITE FOR RESIDUE SO4 B 302
19CC1SOFTWAREARG B:88 , ASN C:203BINDING SITE FOR RESIDUE SO4 B 303
20CC2SOFTWAREILE B:139BINDING SITE FOR RESIDUE CL B 304
21CC3SOFTWARESER B:174 , GLY B:176BINDING SITE FOR RESIDUE CL B 305
22CC4SOFTWAREEDO A:311 , LYS B:46 , ARG B:47BINDING SITE FOR RESIDUE CL B 306
23CC5SOFTWARELYS B:214 , HOH B:527BINDING SITE FOR RESIDUE EDO B 307
24CC6SOFTWARETRP B:126 , GLY B:128 , ALA B:146 , ALA B:147 , PEG B:312 , PGE B:314 , HOH B:471BINDING SITE FOR RESIDUE EDO B 308
25CC7SOFTWAREASN B:154 , HOH B:531BINDING SITE FOR RESIDUE EDO B 309
26CC8SOFTWAREGLU B:39 , ARG B:70 , LEU B:189 , MET B:191BINDING SITE FOR RESIDUE EDO B 310
27CC9SOFTWARETYR B:57 , TYR B:59BINDING SITE FOR RESIDUE EDO B 311
28DC1SOFTWAREALA B:146 , EDO B:308 , HOH B:537BINDING SITE FOR RESIDUE PEG B 312
29DC2SOFTWAREHIS B:87 , LEU B:98 , TYR C:42 , ASP C:44 , HOH C:506 , HOH C:529 , HOH C:632BINDING SITE FOR RESIDUE PGE B 313
30DC3SOFTWARETYR A:57 , HIS A:87 , HOH A:476 , TYR B:42 , ASP B:44 , GLY B:75 , TRP B:126 , ILE B:127 , ARG B:129 , EDO B:308 , HOH B:471BINDING SITE FOR RESIDUE PGE B 314
31DC4SOFTWARELYS C:27 , GLU C:39 , ARG C:70 , HOH C:579BINDING SITE FOR RESIDUE SO4 C 301
32DC5SOFTWARELYS C:153 , LYS C:167 , PHE C:168 , HOH C:615BINDING SITE FOR RESIDUE SO4 C 302
33DC6SOFTWAREARG C:47BINDING SITE FOR RESIDUE CL C 303
34DC7SOFTWAREARG C:100BINDING SITE FOR RESIDUE CL C 304
35DC8SOFTWAREALA C:146 , ILE C:160BINDING SITE FOR RESIDUE EDO C 305
36DC9SOFTWAREASN C:13 , ILE C:14BINDING SITE FOR RESIDUE EDO C 306
37EC1SOFTWAREPRO A:199 , SO4 A:302 , MET C:107BINDING SITE FOR RESIDUE EDO C 307
38EC2SOFTWARELYS C:111 , GLN C:185 , ASN C:188 , HOH C:604BINDING SITE FOR RESIDUE EDO C 308
39EC3SOFTWAREASP C:10 , PRO C:11 , GLU C:39 , HOH C:611BINDING SITE FOR RESIDUE EDO C 309
40EC4SOFTWAREGLU C:33 , ASN C:34 , GLU C:60BINDING SITE FOR RESIDUE EDO C 310

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HUS)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Asn A:164 -Pro A:165
2Asn B:164 -Pro B:165
3Asn C:164 -Pro C:165

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HUS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HUS)

(-) Exons   (0, 0)

(no "Exon" information available for 4HUS)

(-) 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:212
                                                                                                                                                                                                                                                    
               SCOP domains d4husa_ A: automated matches                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eee.hhhh....eee....eee......hhh.ee..hhhhh..eee....ee....eee.hhhh........hhhhhh.hhhhhh.hhhhh.....eee....ee....ee....ee....ee....ee.......eeee....eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hus A   7 HGPDPENILPIKGNRNLQFIKPTITNENILVGEYSYYDSKRGESFEDQVLYHYEVIGDKLIIGRFCSIGPGTTFIMNGANHRMDGSTYPFHLFRMGWEKYMPSLKDLPLKGDIEIGNDVWIGRDVTIMPGVKIGDGAIIAAEAVVTKNVAPYSIVGGNPLKFIRKRFSDGVIEEWLALQWWNLDMKIINENLPFIINGDIEMLKRKRKLLDD 218
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216  


Chain B from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains d4husb_ B: automated matches                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eee.hhhh....eee....eee......hhh.ee.........eee....ee....eee.hhhh........hhhhhh.hhhhhh.hhhhh.....eee....ee....ee....ee....ee....ee.......eeee....eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hus B   6 DHGPDPENILPIKGNRNLQFIKPTITNENILVGEYSYYDSKRGESFEDQVLYHYEVIGDKLIIGRFCSIGPGTTFIMNGANHRMDGSTYPFHLFRMGWEKYMPSLKDLPLKGDIEIGNDVWIGRDVTIMPGVKIGDGAIIAAEAVVTKNVAPYSIVGGNPLKFIRKRFSDGVIEEWLALQWWNLDMKIINENLPFIINGDIEMLKRKRKLLDDT 219
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215    


Chain C from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                 
               SCOP domains d4husc_ C: automated matches                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eee.hhhh....eee....eee.....hhhh.ee.........eee....ee....eee.hhhh........hhhhhh.hhhhhh.hhhhh.....eee....ee....ee....ee....ee....ee.......eeee....eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hus C   7 HGPDPENILPIKGNRNLQFIKPTITNENILVGEYSYYDSKRGESFEDQVLYHYEVIGDKLIIGRFCSIGPGTTFIMNGANHRMDGSTYPFHLFRMGWEKYMPSLKDLPLKGDIEIGNDVWIGRDVTIMPGVKIGDGAIIAAEAVVTKNVAPYSIVGGNPLKFIRKRFSDGVIEEWLALQWWNLDMKIINENLPFIINGDIEMLKRKRKL 215
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206
   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, 3)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HUS)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HUS)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

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  4hus
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 Related Entries

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

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        VATA_STAAU | P26839: 4hur 4myo

(-) Related Entries Specified in the PDB File

4e8l CRYSTAL STRUCTURE OF STREPTOGRAMIN GROUP A ANTIBIOTIC ACETYLTRANSFERASE VATA FROM STAPHYLOCOCCUS AUREUS
4hur CRYSTAL STRUCTURE OF STREPTOGRAMIN GROUP A ANTIBIOTIC ACETYLTRANSFERASE VATA FROM STAPHYLOCOCCUS AUREUS IN COMPLEX WITH ACETYL COENZYME A RELATED ID: CSGID-IDP91546 RELATED DB: TARGETTRACK