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(-) Description

Title :  CRYSTAL STRUCTURE OF THE OPERATOR-BINDING FORM OF THE MULTI-DRUG BINDING TRANSCRIPTIONAL REPRESSOR CGMR
 
Authors :  H. Itou, Y. Shirakihara, I. Tanaka
Date :  12 Apr 07  (Deposition) - 15 Apr 08  (Release) - 13 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H
Keywords :  Protein-Dna Complex, Helix-Turn-Helix, Tetr-Family, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Itou, N. Watanabe, M. Yao, Y. Shirakihara, I. Tanaka
Crystal Structures Of The Multidrug Binding Repressor Corynebacteriumglutamicum Cgmr In Complex With Inducers And With An Operator
J. Mol. Biol. V. 403 174 2010
PubMed-ID: 20691702  |  Reference-DOI: 10.1016/J.JMB.2010.07.042

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET26B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CGL2612
    Organism Scientific: CORYNEBACTERIUM GLUTAMICUM
    Organism Taxid: 196627
    Strain: ATCC13032
    Synonym: BACTERIAL REGULATORY PROTEIN, TETR FAMILY
 
Molecule 2 - 5'-D(*DTP*DAP*DAP*DCP*DTP*DGP*DTP*DAP*DCP*DCP*DGP*DAP*DCP*D C)-3'
    Chains: E, G
    Engineered: YES
    Other Details: CGL2612 OPERATOR DNA UPPER STRAND
    Other Details - Source: SEQUENCE FOUND IN THE C.GLUTAMICUM GENOME.
    Synthetic: YES
 
Molecule 3 - 5'-D(*DGP*DGP*DTP*DCP*DGP*DGP*DTP*DAP*DCP*DAP*DGP*DTP*DTP*D A)-3'
    Chains: F, H
    Engineered: YES
    Other Details: CGL2612 OPERATOR DNA LOWER STRAND
    Other Details - Source: SEQUENCE FOUND IN THE C.GLUTAMICUM GENOME.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit : ABCDEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric/Biological Unit (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2YVH)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2YVH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2YVH)

(-) 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:171
 aligned with Q8NMG3_CORGL | Q8NMG3 from UniProtKB/TrEMBL  Length:177

    Alignment length:171
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173 
         Q8NMG3_CORGL     4 SKKEMILRTAIDYIGEYSLETLSYDSLAEATGLSKSGLIYHFPSRHALLLGMHELLADDWDKELRDITRDPEDPLERLRAVVVTLAENVSRPELLLLIDAPSHPDFLNAWRTVNHQWIPDTDDLENDAHKRAVYLVQLAADGLFVHDYIHDDVLSKSKRQAMLETILELIP 174
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2yvhA00 A:4-174 Tetracycline Repressor, domain 2                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhh.hhhhhhhhhhh..hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yvh A   4 SKKEmILRTAIDYIGEYSLETLSYDSLAEATGLSKSGLIYHFPSRHALLLGmHELLADDWDKELRDITRDPEDPLERLRAVVVTLAENVSRPELLLLIDAPSHPDFLNAWRTVNHQWIPDTDDLENDAHKRAVYLVQLAADGLFVHDYIHDDVLSKSKRQAmLETILELIP 174
                                |   13        23        33        43        53 |      63        73        83        93       103       113       123       133       143       153       163 |     173 
                                |                                             55-MSE                                                                                                       165-MSE     
                                8-MSE                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:172
 aligned with Q8NMG3_CORGL | Q8NMG3 from UniProtKB/TrEMBL  Length:177

    Alignment length:172
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172  
         Q8NMG3_CORGL     3 TSKKEMILRTAIDYIGEYSLETLSYDSLAEATGLSKSGLIYHFPSRHALLLGMHELLADDWDKELRDITRDPEDPLERLRAVVVTLAENVSRPELLLLIDAPSHPDFLNAWRTVNHQWIPDTDDLENDAHKRAVYLVQLAADGLFVHDYIHDDVLSKSKRQAMLETILELIP 174
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2yvhB00 B:3-174 Tetracycline Repressor, domain 2                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh.hhhhhhhhhhh..hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yvh B   3 TSKKEmILRTAIDYIGEYSLETLSYDSLAEATGLSKSGLIYHFPSRHALLLGmHELLADDWDKELRDITRDPEDPLERLRAVVVTLAENVSRPELLLLIDAPSHPDFLNAWRTVNHQWIPDTDDLENDAHKRAVYLVQLAADGLFVHDYIHDDVLSKSKRQAmLETILELIP 174
                                 |  12        22        32        42        52  |     62        72        82        92       102       112       122       132       142       152       162  |    172  
                                 8-MSE                                         55-MSE                                                                                                       165-MSE     


Chain C from PDB  Type:PROTEIN  Length:171
 aligned with Q8NMG3_CORGL | Q8NMG3 from UniProtKB/TrEMBL  Length:177

    Alignment length:171
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173 
         Q8NMG3_CORGL     4 SKKEMILRTAIDYIGEYSLETLSYDSLAEATGLSKSGLIYHFPSRHALLLGMHELLADDWDKELRDITRDPEDPLERLRAVVVTLAENVSRPELLLLIDAPSHPDFLNAWRTVNHQWIPDTDDLENDAHKRAVYLVQLAADGLFVHDYIHDDVLSKSKRQAMLETILELIP 174
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2yvhC00 C:4-174 Tetracycline Repressor, domain 2                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh.hhhhhhhhhhh..hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yvh C   4 SKKEmILRTAIDYIGEYSLETLSYDSLAEATGLSKSGLIYHFPSRHALLLGmHELLADDWDKELRDITRDPEDPLERLRAVVVTLAENVSRPELLLLIDAPSHPDFLNAWRTVNHQWIPDTDDLENDAHKRAVYLVQLAADGLFVHDYIHDDVLSKSKRQAmLETILELIP 174
                                |   13        23        33        43        53 |      63        73        83        93       103       113       123       133       143       153       163 |     173 
                                8-MSE                                         55-MSE                                                                                                       165-MSE     


Chain D from PDB  Type:PROTEIN  Length:172
 aligned with Q8NMG3_CORGL | Q8NMG3 from UniProtKB/TrEMBL  Length:177

    Alignment length:172
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172  
         Q8NMG3_CORGL     3 TSKKEMILRTAIDYIGEYSLETLSYDSLAEATGLSKSGLIYHFPSRHALLLGMHELLADDWDKELRDITRDPEDPLERLRAVVVTLAENVSRPELLLLIDAPSHPDFLNAWRTVNHQWIPDTDDLENDAHKRAVYLVQLAADGLFVHDYIHDDVLSKSKRQAMLETILELIP 174
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2yvhD00 D:3-174 Tetracycline Repressor, domain 2                                                                                                                             CATH domains
           Pfam domains (1) ------TetR_N-2yvhD01 D:9-55                          ----------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------TetR_N-2yvhD02 D:9-55                          ----------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ------TetR_N-2yvhD03 D:9-55                          ----------------------------------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) ------TetR_N-2yvhD04 D:9-55                          ----------------------------------------------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhhhhhhhhh..hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yvh D   3 TSKKEmILRTAIDYIGEYSLETLSYDSLAEATGLSKSGLIYHFPSRHALLLGmHELLADDWDKELRDITRDPEDPLERLRAVVVTLAENVSRPELLLLIDAPSHPDFLNAWRTVNHQWIPDTDDLENDAHKRAVYLVQLAADGLFVHDYIHDDVLSKSKRQAmLETILELIP 174
                                 |  12        22        32        42        52  |     62        72        82        92       102       112       122       132       142       152       162  |    172  
                                 8-MSE                                         55-MSE                                                                                                       165-MSE     


Chain E from PDB  Type:DNA  Length:14
                                              
                 2yvh E   3 TAACTGTACCGACC  16
                                    12    


Chain F from PDB  Type:DNA  Length:14
                                              
                 2yvh F  17 GGTCGGTACAGTTA  30
                                    26    


Chain G from PDB  Type:DNA  Length:14
                                              
                 2yvh G   3 TAACTGTACCGACC  16
                                    12    


Chain H from PDB  Type:DNA  Length:14
                                              
                 2yvh H  17 GGTCGGTACAGTTA  30
                                    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 2YVH)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 4)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q8NMG3_CORGL | Q8NMG3)
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: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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 Related Entries

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

UniProtKB/TrEMBL
        Q8NMG3_CORGL | Q8NMG3: 2yve 2zoy 2zoz

(-) Related Entries Specified in the PDB File

2yve THE SAME PROTEIN COMPLEXED WITH METHYLENE BLUE
2zoy THE SAME PROTEIN IN LIGAND-FREE STATE
2zoz THE SAME PROTEIN COMPLEXED WITH ETHIDIUM