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(-) Description

Title :  STRUCTURE OF APO-AND HOLO-DIPHTHERIA TOXIN REPRESSOR
 
Authors :  E. Pohl, W. G. J. Hol
Date :  21 Jun 98  (Deposition) - 22 Jun 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Repressor, Transcription Regulation, Dna-Binding, Iron (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Pohl, R. K. Holmes, W. G. Hol
Motion Of The Dna-Binding Domain With Respect To The Core Of The Diphtheria Toxin Repressor (Dtxr) Revealed In The Crystal Structures Of Apo- And Holo-Dtxr.
J. Biol. Chem. V. 273 22420 1998
PubMed-ID: 9712865  |  Reference-DOI: 10.1074/JBC.273.35.22420
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DIPHTHERIA TOXIN REPRESSOR
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System GeneT
    Expression System PlasmidPMS298
    Expression System StrainDH5-ALPHA
    Expression System Taxid562
    GeneDTXR
    Organism ScientificCORYNEBACTERIUM DIPHTHERIAE
    Organism Taxid1717
    StrainC7(-)
    SynonymDTXR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1CSS2Mod. Amino AcidS-MERCAPTOCYSTEINE
2SO42Ligand/IonSULFATE ION
3ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:79 , GLU A:83 , HIS A:98 , SO4 A:292BINDING SITE FOR RESIDUE ZN A 291
2AC2SOFTWAREHIS B:79 , GLU B:83 , HIS B:98 , SO4 B:1292BINDING SITE FOR RESIDUE ZN B 1291
3AC3SOFTWAREMET A:76 , HIS A:79 , ARG A:80 , GLU A:83 , HIS A:98 , SER A:126 , PHE A:128 , ASN A:130 , ZN A:291 , HOH A:318BINDING SITE FOR RESIDUE SO4 A 292
4AC4SOFTWAREHIS B:79 , ARG B:80 , GLU B:83 , HIS B:98 , SER B:126 , PHE B:128 , ASN B:130 , HOH B:335 , ZN B:1291BINDING SITE FOR RESIDUE SO4 B 1292

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1BI3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1BI3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (11, 12)

Asymmetric/Biological Unit (11, 12)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_DTXR_CORDI_001 *R47HDTXR_CORDI  ---  ---A/BR47H
02UniProtVAR_DTXR_CORDI_004 *I165VDTXR_CORDI  ---  ---AI165V
03UniProtVAR_DTXR_CORDI_005 *V174ADTXR_CORDI  ---  ---AV174A
04UniProtVAR_DTXR_CORDI_006 *S191TDTXR_CORDI  ---  ---AS191T
05UniProtVAR_DTXR_CORDI_008 *H201RDTXR_CORDI  ---  ---AH201R
06UniProtVAR_DTXR_CORDI_009 *S205RDTXR_CORDI  ---  ---AS205R
07UniProtVAR_DTXR_CORDI_010 *I214LDTXR_CORDI  ---  ---AL214L
08UniProtVAR_DTXR_CORDI_011 *I214YDTXR_CORDI  ---  ---AL214Y
09UniProtVAR_DTXR_CORDI_012 *A218TDTXR_CORDI  ---  ---AA218T
10UniProtVAR_DTXR_CORDI_013 *I221MDTXR_CORDI  ---  ---AI221M
11UniProtVAR_DTXR_CORDI_014 *I221TDTXR_CORDI  ---  ---AI221T
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_DTXRPS50944 DtxR-type HTH domain profile.DTXR_CORDI4-65
 
  2A:4-65
B:4-65
DTXR_CORDW4-65
 
  2A:4-65
B:4-65

(-) Exons   (0, 0)

(no "Exon" information available for 1BI3)

(-) 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
 aligned with DTXR_CORDI | P0DJL7 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:222
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223  
           DTXR_CORDI     4 LVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEACRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELGVGNSDAAVPGTRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVDRDGHITLSHNGKDVELIDDLAHTIRIEE 225
               SCOP domains d1bi3a1 A:4-64 Diphtheria toxin repressor (DtxR)             d1bi3a2 A:65-140 Diphtheria toxin repressor (DtxR)                                 d1bi3a3 A:148-225 Diphtheria toxin repressor (DtxR   )                         SCOP domains
               CATH domains 1bi3A01 A:4-74 'winged helix' repressor DNA binding domain             1bi3A02 A:75-140 Diphtheria Toxin Repressor, domain 2                    1bi3A03 A:148-223  [code=2.30.30.90, no name defin   ed]                    -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh.....hhhhhhhh...hhhhhhhhhhhhh...eee.....eee.hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh...hhhhhhhhhh...............hhhh..-------....hhhh.....eeeeeee..hhh.....hhhhhhh.......eeee..---..eeee..eeee..hhhhhh.eee. Sec.struct. author
             SAPs(SNPs) (1) -------------------------------------------H---------------------------------------------------------------------------------------------------------------------V--------A----------------T---------R---R--------L---T--M---- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Y------T---- SAPs(SNPs) (2)
                PROSITE (2) HTH_DTXR  PDB: A:4-65 UniProt: 4-65                           ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1bi3 A   4 LVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEAcRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELGV-------PGTRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVD---HITLSHNGKDVELLDDLAHTIRIEE 225
                                    13        23        33        43        53        63        73        83        93       103       113       123       133      |  -    |  153       163       173       183       193   |   203       213       223  
                                                                                                                            102-CSS                               140     148                                              197 201                        

Chain A from PDB  Type:PROTEIN  Length:212
 aligned with DTXR_CORDW | H2I233 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:222
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223  
           DTXR_CORDW     4 LVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEACRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELGVGNSDAAAPGTRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVDRDGHITLSHNGKDVELLDDLAHTIRIEE 225
               SCOP domains d1bi3a1 A:4-64 Diphtheria toxin repressor (DtxR)             d1bi3a2 A:65-140 Diphtheria toxin repressor (DtxR)                                 d1bi3a3 A:148-225 Diphtheria toxin repressor (DtxR   )                         SCOP domains
               CATH domains 1bi3A01 A:4-74 'winged helix' repressor DNA binding domain             1bi3A02 A:75-140 Diphtheria Toxin Repressor, domain 2                    1bi3A03 A:148-223  [code=2.30.30.90, no name defin   ed]                    -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh.....hhhhhhhh...hhhhhhhhhhhhh...eee.....eee.hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh...hhhhhhhhhh...............hhhh..-------....hhhh.....eeeeeee..hhh.....hhhhhhh.......eeee..---..eeee..eeee..hhhhhh.eee. Sec.struct. author
             SAPs(SNPs) (1) -------------------------------------------H---------------------------------------------------------------------------------------------------------------------V--------A----------------T---------R---R--------L---T--M---- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Y------T---- SAPs(SNPs) (2)
                    PROSITE HTH_DTXR  PDB: A:4-65 UniProt: 4-65                           ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1bi3 A   4 LVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEAcRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELGV-------PGTRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVD---HITLSHNGKDVELLDDLAHTIRIEE 225
                                    13        23        33        43        53        63        73        83        93       103       113       123       133      |  -    |  153       163       173       183       193   |   203       213       223  
                                                                                                                            102-CSS                               140     148                                              197 201                        

Chain B from PDB  Type:PROTEIN  Length:137
 aligned with DTXR_CORDI | P0DJL7 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:137
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       
           DTXR_CORDI     4 LVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEACRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELGV 140
               SCOP domains d1bi3b1 B:4-64 Diphtheria toxin repressor (DtxR)             d1bi3b2 B:65-140 Diphtheria toxin repressor (DtxR)                           SCOP domains
               CATH domains 1bi3B01 B:4-75 'winged helix' repressor DNA binding domain              1bi3B02 B:76-136 Diphtheria Toxin Repressor, domain 2        ---- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh.....hhhhhhhh...hhhhhhhhhhhhh...eee.....eee.hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh...hhhhhhhhhh...............hhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------H--------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) HTH_DTXR  PDB: B:4-65 UniProt: 4-65                           --------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bi3 B   4 LVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEAcRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELGV 140
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       
                                                                                                                            102-CSS                                  

Chain B from PDB  Type:PROTEIN  Length:137
 aligned with DTXR_CORDW | H2I233 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:137
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       
           DTXR_CORDW     4 LVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEACRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELGV 140
               SCOP domains d1bi3b1 B:4-64 Diphtheria toxin repressor (DtxR)             d1bi3b2 B:65-140 Diphtheria toxin repressor (DtxR)                           SCOP domains
               CATH domains 1bi3B01 B:4-75 'winged helix' repressor DNA binding domain              1bi3B02 B:76-136 Diphtheria Toxin Repressor, domain 2        ---- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh.....hhhhhhhh...hhhhhhhhhhhhh...eee.....eee.hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh...hhhhhhhhhh...............hhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------H--------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE HTH_DTXR  PDB: B:4-65 UniProt: 4-65                           --------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bi3 B   4 LVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEAcRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELGV 140
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       
                                                                                                                            102-CSS                                  

   Legend:   → Mismatch (orange background)
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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  (3, 5)

Asymmetric/Biological Unit

(-) CATH Domains  (3, 5)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BI3)

(-) Gene Ontology  (7, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DTXR_CORDW | H2I233)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0046914    transition metal ion binding    Interacting selectively and non-covalently with a transition metal ions; a transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver.
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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain A,B   (DTXR_CORDI | P0DJL7)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0046914    transition metal ion binding    Interacting selectively and non-covalently with a transition metal ions; a transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver.
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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DTXR_CORDI | P0DJL71bi0 1bi1 1bi2 1bym 1c0w 1ddn 1dpr 1f5t 1fwz 1g3s 1g3t 1g3w 1g3y 1p92 1qvp 1qw1 1xcv 2dtr 2qq9 2qqa 2qqb 2tdx 3glx
        DTXR_CORDW | H2I2331bi0 1bi1 1bi2 1bym 1c0w 1ddn 1dpr 1f5t 1fwz 1g3s 1g3t 1g3w 1g3y 1p92 1qvp 1qw1 1xcv 2dtr 2qq9 2qqa 2qqb 2tdx 3glx

(-) Related Entries Specified in the PDB File

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