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(-) Description

Title :  STRUCTURE OF DIPHTHERIA TOXIN REPRESSOR
 
Authors :  X. Qiu, E. Pohl, W. G. Hol
Date :  26 Jul 96  (Deposition) - 20 Aug 97  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transcription Regulation, Repressor, Dna-Binding, Iron (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Qiu, E. Pohl, R. K. Holmes, W. G. Hol
High-Resolution Structure Of The Diphtheria Toxin Repressor Complexed With Cobalt And Manganese Reveals An Sh3-Like Third Domain And Suggests A Possible Role Of Phosphate As Co-Corepressor.
Biochemistry V. 35 12292 1996
PubMed-ID: 8823163  |  Reference-DOI: 10.1021/BI960861D
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DIPHTHERIA TOXIN REPRESSOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: T
    Expression System Plasmid: PMS298
    Expression System Taxid: 562
    Gene: T
    Organism Scientific: CORYNEBACTERIUM DIPHTHERIAE
    Organism Taxid: 1717
    Strain: C7(-)
    Synonym: DTXR

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1CO1Ligand/IonCOBALT (II) ION
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION
2SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:79 , ARG A:80 , GLU A:83 , HIS A:98 , SER A:126 , PHE A:128 , ASN A:130 , CO A:291 , HOH A:303 , HOH A:419BINDING SITE FOR RESIDUE SO4 A 290
2AC2SOFTWAREHIS A:79 , GLU A:83 , HIS A:98 , SO4 A:290BINDING SITE FOR RESIDUE CO A 291

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (11, 11)

Asymmetric Unit (11, 11)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_DTXR_CORDI_001 *R47HDTXR_CORDI  ---  ---AR47H
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)
Biological Unit 1 (11, 22)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_DTXR_CORDI_001 *R47HDTXR_CORDI  ---  ---AR47H
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, 1)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2DTR)

(-) Sequences/Alignments

Asymmetric 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:214
 aligned with DTXR_CORDI | P0DJL7 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:223
                                    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 LVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEACRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELGVGNSDAAVPGTRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVDRDGHITLSHNGKDVELIDDLAHTIRIEEL 226
               SCOP domains d2dtra1 A:4-64 Diphtheria toxin repressor (DtxR)             d2dtra2 A:65-140 Diphtheria toxin repressor (DtxR)                                 d2dtra3 A:148-226 Diphtheria toxin repressor (DtxR)                             SCOP domains
               CATH domains 2dtrA01 A:4-74 'winged helix' repressor DNA binding domain             2dtrA02 A:75-140 Diphtheria Toxin Repressor, domain 2             -------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh......hhhhhhhh...hhhhhhhhhhhhh...eee.....eee.hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh...hhhhhhhhhh................hhh..-------....hhhh.....eeeeeee..hhh......hhhhhh.......eeeee..--..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
                 2dtr A   4 LVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEACRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELGV-------PGTRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVDR--HITLSHNGKDVELLDDLAHTIRIEEL 226
                                    13        23        33        43        53        63        73        83        93       103       113       123       133      |  -    |  153       163       173       183       193    |  203       213       223   
                                                                                                                                                                  140     148                                               198  |                         
                                                                                                                                                                                                                               201                         


Chain A from PDB  Type:PROTEIN  Length:214
 aligned with DTXR_CORDW | H2I233 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:223
                                    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 LVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEACRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELGVGNSDAAAPGTRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVDRDGHITLSHNGKDVELLDDLAHTIRIEEL 226
               SCOP domains d2dtra1 A:4-64 Diphtheria toxin repressor (DtxR)             d2dtra2 A:65-140 Diphtheria toxin repressor (DtxR)                                 d2dtra3 A:148-226 Diphtheria toxin repressor (DtxR)                             SCOP domains
               CATH domains 2dtrA01 A:4-74 'winged helix' repressor DNA binding domain             2dtrA02 A:75-140 Diphtheria Toxin Repressor, domain 2             -------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh......hhhhhhhh...hhhhhhhhhhhhh...eee.....eee.hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh...hhhhhhhhhh................hhh..-------....hhhh.....eeeeeee..hhh......hhhhhh.......eeeee..--..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
                 2dtr A   4 LVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEACRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELGV-------PGTRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVDR--HITLSHNGKDVELLDDLAHTIRIEEL 226
                                    13        23        33        43        53        63        73        83        93       103       113       123       133      |  -    |  153       163       173       183       193    |  203       213       223   
                                                                                                                                                                  140     148                                               198  |                         
                                                                                                                                                                                                                               201
   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  (3, 3)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DTR)

(-) Gene Ontology  (7, 14)

Asymmetric Unit(hide GO term definitions)
Chain A   (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.

Chain A   (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.

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  2dtr
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  DTXR_CORDW | H2I233
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 Related Entries

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

UniProtKB/Swiss-Prot
        DTXR_CORDI | P0DJL7: 1bi0 1bi1 1bi2 1bi3 1bym 1c0w 1ddn 1dpr 1f5t 1fwz 1g3s 1g3t 1g3w 1g3y 1p92 1qvp 1qw1 1xcv 2qq9 2qqa 2qqb 2tdx 3glx
        DTXR_CORDW | H2I233: 1bi0 1bi1 1bi2 1bi3 1bym 1c0w 1ddn 1dpr 1f5t 1fwz 1g3s 1g3t 1g3w 1g3y 1p92 1qvp 1qw1 1xcv 2qq9 2qqa 2qqb 2tdx 3glx

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2DTR)