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(-) Description

Title :  SIMOCYCLINONE C4 BOUND FORM OF TETR-LIKE REPRESSOR SIMR
 
Authors :  T. B. K. Le, C. E. M. Stevenson, H. -P. Fiedler, A. Maxwell, D. M. Lawson, M. J. Buttner
Date :  17 Dec 10  (Deposition) - 09 Mar 11  (Release) - 25 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transcription, Tetr-Family (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. B. K. Le, C. E. M. Stevenson, H. -P. Fiedler, A. Maxwell, D. M. Lawson, M. J. Buttner
Structures Of The Tetr-Like Simocyclinone Efflux Pump Repressor, Simr, And The Mechanism Of Ligand- Mediated Derepression.
J. Mol. Biol. V. 408 40 2011
PubMed-ID: 21354180  |  Reference-DOI: 10.1016/J.JMB.2011.02.035

(-) Compounds

Molecule 1 - PUTATIVE REPRESSOR SIMREG2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PIJ10499
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: PLYSS
    Expression System Vector: PET20B
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 3-261
    Organism Scientific: STREPTOMYCES ANTIBIOTICUS
    Organism Taxid: 1890
    Strain: TU 6040
    Synonym: SIMR, SIM16

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 13)

Asymmetric/Biological Unit (5, 13)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2CA1Ligand/IonCALCIUM ION
3CL8Ligand/IonCHLORIDE ION
4PG41Ligand/IonTETRAETHYLENE GLYCOL
5SMQ2Ligand/IonSIMOCYCLINONE C4

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREMET A:185 , MET A:189 , GLY A:193 , GLN A:197 , LEU A:212 , HIS A:219 , HOH A:2140 , HOH A:2166 , HOH A:2168 , PRO B:126 , GLN B:135 , GLN B:136 , LEU B:154 , ASN B:161 , HOH B:2057BINDING SITE FOR RESIDUE SMQ A 501
02AC2SOFTWARELYS A:107 , PRO A:126 , GLN A:135 , GLN A:136 , LEU A:154 , ASN A:161 , HOH A:2097 , MET B:189 , GLY B:193 , GLN B:197 , LEU B:212 , PRO B:218 , HIS B:219 , HOH B:2099BINDING SITE FOR RESIDUE SMQ B 501
03AC3SOFTWAREARG A:232 , ASP A:235 , SER A:236 , HOH A:2159 , HOH A:2169 , SER B:240 , ARG B:243 , LEU B:244BINDING SITE FOR RESIDUE 1PE A1248
04AC4SOFTWARELEU A:88 , PRO A:89 , ASP A:90 , ARG A:134 , GLU A:137 , PHE A:138 , HOH A:2045BINDING SITE FOR RESIDUE PG4 A1249
05AC5SOFTWARELEU A:244 , HOH A:2088 , HOH A:2090 , ASP B:235 , HOH B:2040 , HOH B:2041BINDING SITE FOR RESIDUE CA B1247
06AC6SOFTWAREHOH A:2073 , GLY B:44 , VAL B:45 , TRP B:116 , HOH B:2018 , HOH B:2053BINDING SITE FOR RESIDUE CL B1248
07AC7SOFTWARELYS B:71 , HOH B:2024BINDING SITE FOR RESIDUE CL B1249
08AC8SOFTWAREMET B:185 , HOH B:2092BINDING SITE FOR RESIDUE CL B1250
09AC9SOFTWARETRP A:174 , ASP A:184 , MET A:185 , HOH A:2106 , HOH A:2120BINDING SITE FOR RESIDUE CL A1250
10BC1SOFTWAREMET B:50 , HOH B:2020 , HOH B:2024BINDING SITE FOR RESIDUE CL B1251
11BC2SOFTWAREGLY A:44 , VAL A:45 , HOH A:2018 , HOH B:2056BINDING SITE FOR RESIDUE CL A1251
12BC3SOFTWAREGLY B:221 , ASP B:223 , GLN B:224BINDING SITE FOR RESIDUE CL B1252
13BC4SOFTWAREGLY A:221 , ASP A:223 , GLN A:224 , HOH A:2145BINDING SITE FOR RESIDUE CL A1252

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y31)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:246 -Pro A:247

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y31)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y31)

(-) Exons   (0, 0)

(no "Exon" information available for 2Y31)

(-) 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:242
 aligned with Q9AMH9_STRAT | Q9AMH9 from UniProtKB/TrEMBL  Length:261

    Alignment length:242
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247  
         Q9AMH9_STRAT     8 PVSIWMHPEPAGRRSARSHRTLSRDQIVRAAVKVADTEGVEAASMRRVAAELGAGTMSLYYYVPTKEDLVELMVDEVIGETRLPDRPGPDWRAALTLAANEKRALWLRHPWLATAWRNGHPVWGPNSLRQQEFVLGTLGVFDLQVDELLSLIGLYNGYVESFVRNEVGWLEEARRTKVDMREWMRRSGPYAQQLVDSGEYPMFARVLAETVAPHMGPDQRFRSGLERLLDSIGASLDRLSPP 249
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................hhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhh....hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y31 A   6 PVSIWMHPEPAGRRSARSHRTLSRDQIVRAAVKVADTEGVEAASMRRVAAELGAGTMSLYYYVPTKEDLVELMVDEVIGETRLPDRPGPDWRAALTLAANEKRALWLRHPWLATAWRNGHPVWGPNSLRQQEFVLGTLGVFDLQVDELLSLIGLYNGYVESFVRNEVGWLEEARRTKVDMREWMRRSGPYAQQLVDSGEYPMFARVLAETVAPHMGPDQRFRSGLERLLDSIGASLDRLSPP 247
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245  


Chain B from PDB  Type:PROTEIN  Length:232
 aligned with Q9AMH9_STRAT | Q9AMH9 from UniProtKB/TrEMBL  Length:261

    Alignment length:242
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246  
         Q9AMH9_STRAT     7 EPVSIWMHPEPAGRRSARSHRTLSRDQIVRAAVKVADTEGVEAASMRRVAAELGAGTMSLYYYVPTKEDLVELMVDEVIGETRLPDRPGPDWRAALTLAANEKRALWLRHPWLATAWRNGHPVWGPNSLRQQEFVLGTLGVFDLQVDELLSLIGLYNGYVESFVRNEVGWLEEARRTKVDMREWMRRSGPYAQQLVDSGEYPMFARVLAETVAPHMGPDQRFRSGLERLLDSIGASLDRLSP 248
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------TetR_N-2y31B01 B:32-78                         ---------TetR_C-2y31B03 B:88-241                                                                                                                                   ----- Pfam domains (1)
           Pfam domains (2) ---------------------------TetR_N-2y31B02 B:32-78                         ---------TetR_C-2y31B04 B:88-241                                                                                                                                   ----- Pfam domains (2)
         Sec.struct. author ...hhhhh...----------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh....hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y31 B   5 EPVSIWMHPEP----------TLSRDQIVRAAVKVADTEGVEAASMRRVAAELGAGTMSLYYYVPTKEDLVELMVDEVIGETRLPDRPGPDWRAALTLAANEKRALWLRHPWLATAWRNGHPVWGPNSLRQQEFVLGTLGVFDLQVDELLSLIGLYNGYVESFVRNEVGWLEEARRTKVDMREWMRRSGPYAQQLVDSGEYPMFARVLAETVAPHMGPDQRFRSGLERLLDSIGASLDRLSP 246
                                    14|        - |      34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244  
                                     15         26
   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  (0, 0)

(no "SCOP Domain" information available for 2Y31)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y31)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)
(-)
Clan: TetR_C (33)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9AMH9_STRAT | Q9AMH9)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

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  2y31
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 Related Entries

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

UniProtKB/TrEMBL
        Q9AMH9_STRAT | Q9AMH9: 2y2z 2y30 3zql

(-) Related Entries Specified in the PDB File

2y2z LIGAND-FREE FORM OF TETR-LIKE REPRESSOR SIMR
2y30 SIMOCYCLINONE D8 BOUND FORM OF TETR-LIKE REPRESSOR SIMR