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(-) Description

Title :  SIMOCYCLINONE D8 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  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1CL6Ligand/IonCHLORIDE ION
2SM82Ligand/IonSIMOCYCLINONE D8

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:189 , GLY A:193 , GLN A:197 , LEU A:212 , THR A:215 , PRO A:218 , HIS A:219 , ILE B:83 , THR B:86 , ALA B:103 , LYS B:107 , PRO B:126 , GLN B:136 , VAL B:139 , LEU B:154 , TYR B:160 , ASN B:161 , HOH B:2037BINDING SITE FOR RESIDUE SM8 A 501
2AC2SOFTWAREVAL A:45 , TRP A:116BINDING SITE FOR RESIDUE CL A1247
3AC3SOFTWAREMET A:50 , LYS A:71BINDING SITE FOR RESIDUE CL A1248
4AC4SOFTWAREASP A:184 , MET A:185BINDING SITE FOR RESIDUE CL A1249
5AC5SOFTWAREGLU A:43 , ALA A:47 , ILE A:83 , THR A:86 , ALA A:103 , LYS A:107 , GLN A:135 , GLN A:136 , VAL A:139 , LEU A:154 , ILE A:157 , TYR A:160 , ASN A:161 , MET B:189 , SER B:192 , GLY B:193 , GLN B:197 , VAL B:200 , LEU B:212 , HIS B:219BINDING SITE FOR RESIDUE SM8 B 501
6AC6SOFTWAREGLY B:44 , VAL B:45 , TRP B:116BINDING SITE FOR RESIDUE CL B1248
7AC7SOFTWARELYS B:71BINDING SITE FOR RESIDUE CL B1249
8AC8SOFTWARETRP B:174 , MET B:185BINDING SITE FOR RESIDUE CL B1250

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y30)

(-) Cis Peptide Bonds  (1, 1)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y30)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y30)

(-) Exons   (0, 0)

(no "Exon" information available for 2Y30)

(-) 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:227
 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 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......---------------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh.hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh.hhhhhh.......hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y30 A   5 EPVSIWM---------------LSRDQIVRAAVKVADTEGVEAASMRRVAAELGAGTMSLYYYVPTKEDLVELMVDEVIGETRLPDRPGPDWRAALTLAANEKRALWLRHPWLATAWRNGHPVWGPNSLRQQEFVLGTLGVFDLQVDELLSLIGLYNGYVESFVRNEVGWLEEARRTKVDMREWMRRSGPYAQQLVDSGEYPMFARVLAETVAPHMGPDQRFRSGLERLLDSIGASLDRLSP 246
                                  |  -         -  |     34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244  
                                 11              27                                                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:223
 aligned with Q9AMH9_STRAT | Q9AMH9 from UniProtKB/TrEMBL  Length:261

    Alignment length:240
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249
         Q9AMH9_STRAT    10 SIWMHPEPAGRRSARSHRTLSRDQIVRAAVKVADTEGVEAASMRRVAAELGAGTMSLYYYVPTKEDLVELMVDEVIGETRLPDRPGPDWRAALTLAANEKRALWLRHPWLATAWRNGHPVWGPNSLRQQEFVLGTLGVFDLQVDELLSLIGLYNGYVESFVRNEVGWLEEARRTKVDMREWMRRSGPYAQQLVDSGEYPMFARVLAETVAPHMGPDQRFRSGLERLLDSIGASLDRLSPP 249
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ------------------------TetR_N-2y30B01 B:32-78                         ---------TetR_C-2y30B03 B:88-241                                                                                                                                   ------ Pfam domains (1)
           Pfam domains (2) ------------------------TetR_N-2y30B02 B:32-78                         ---------TetR_C-2y30B04 B:88-241                                                                                                                                   ------ Pfam domains (2)
         Sec.struct. author ...-----------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2y30 B   8 SIW-----------------SRDQIVRAAVKVADTEGVEAASMRRVAAELGAGTMSLYYYVPTKEDLVELMVDEVIGETRLPDRPGPDWRAALTLAANEKRALWLRHPWLATAWRNGHPVWGPNSLRQQEFVLGTLGVFDLQVDELLSLIGLYNGYVESFVRNEVGWLEEARRTKVDMREWMRRSGPYAQQLVDSGEYPMFARVLAETVAPHMGPDQRFRSGLERLLDSIGASLDRLSPP 247
                              |      -         -|       37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247
                             10                28
   Legend:   → Mismatch (orange background)
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  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 2Y30)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y30)

(-) 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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  2y30
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 Related Entries

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

UniProtKB/TrEMBL
        Q9AMH9_STRAT | Q9AMH9: 2y2z 2y31 3zql

(-) Related Entries Specified in the PDB File

2y2z LIGAND-FREE FORM OF TETR-LIKE REPRESSOR SIMR
2y31 SIMOCYCLINONE C4 BOUND FORM OF TETR-LIKE REPRESSOR SIMR