2TDX - JenaLib

Title :   DIPHTHERIA TOX REPRESSOR (C102D MUTANT) COMPLEXED WITH NICKEL

Authors :   A. White, X. Ding, H. Zheng, N. Schiering, D. Ringe, J. R. Murphy

Date :   22 Jun 98 (Deposition) - 14 Oct 98 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Dna-Binding Regulatory Protein, Diphtheria Tox Repressor, Transcription Regulation, Dna-Binding Protein, Iron-Regulated Repressor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. White, X. Ding, J. C. Vanderspek, J. R. Murphy, D. Ringe
Structure Of The Metal-Ion-Activated Diphtheria Toxin Repressor/Tox Operator Complex.
Nature V. 394 502 1998
PubMed-ID: 9697776 | Reference-DOI: 10.1038/28893
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (1, 1)

Exons (0, 0)

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
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Chain A from PDB  Type:PROTEIN  Length:139
 aligned with DTXR_CORDI | P0DJL7 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:139
                                    10        20        30        40        50        60        70        80        90       100       110       120       130         
           DTXR_CORDI     1 MKDLVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEACRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELG 139
               SCOP domains d2tdxa1 A:1-64 Diphtheria toxin repressor (DtxR)                d2tdxa2 A:65-139 Diphtheria toxin repressor (DtxR)                          SCOP domains
               CATH domains --2tdxA01 A:3-75 'winged helix' repressor DNA binding domain               2tdxA02 A:76-136 Diphtheria Toxin Repressor, domain 2        --- CATH domains
               Pfam domains --Fe_dep_repress-2tdxA02 A:3-62                               --Fe_dep_repr_C-2tdxA01 A:65-135                                         ---- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhh.....hhhhhhh....hhhhhhhhhhh.....eee.....eee.hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.....hhhhhhhhhh.................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------H-------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---HTH_DTXR  PDB: A:4-65 UniProt: 4-65                           -------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2tdx A   1 MKDLVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEADRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELG 139
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain A from PDB  Type:PROTEIN  Length:139
 aligned with DTXR_CORDW | H2I233 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:139
                                    10        20        30        40        50        60        70        80        90       100       110       120       130         
           DTXR_CORDW     1 MKDLVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEACRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELG 139
               SCOP domains d2tdxa1 A:1-64 Diphtheria toxin repressor (DtxR)                d2tdxa2 A:65-139 Diphtheria toxin repressor (DtxR)                          SCOP domains
               CATH domains --2tdxA01 A:3-75 'winged helix' repressor DNA binding domain               2tdxA02 A:76-136 Diphtheria Toxin Repressor, domain 2        --- CATH domains
               Pfam domains --Fe_dep_repress-2tdxA02 A:3-62                               --Fe_dep_repr_C-2tdxA01 A:65-135                                         ---- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhh.....hhhhhhh....hhhhhhhhhhh.....eee.....eee.hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.....hhhhhhhhhh.................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------H-------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---HTH_DTXR  PDB: A:4-65 UniProt: 4-65                           -------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2tdx A   1 MKDLVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEADRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELG 139
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

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 (2, 2)

CATH Domains (2, 2)

Pfam Domains (2, 2)

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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