1BI2 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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 :   2.30

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)

Molecule 1 - DIPHTHERIA TOXIN REPRESSOR
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Gene	:	T
	Expression System Plasmid	:	PMS298
	Expression System Strain	:	DH5-ALPHA
	Expression System Taxid	:	562
	Gene	:	DTXR
	Organism Scientific	:	CORYNEBACTERIUM DIPHTHERIAE
	Organism Taxid	:	1717
	Strain	:	C7(-)
	Synonym	:	DTXR

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1BI2)

(no "Site" information available for 1BI2)

(no "SS Bond" information available for 1BI2)

(no "Cis Peptide Bond" information available for 1BI2)

Asymmetric/Biological Unit (11, 12)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_DTXR_CORDI_001 *	R	47	H	DTXR_CORDI	---	---	A/B	R	47	H
02	UniProt	VAR_DTXR_CORDI_004 *	I	165	V	DTXR_CORDI	---	---	A	I	165	V
03	UniProt	VAR_DTXR_CORDI_005 *	V	174	A	DTXR_CORDI	---	---	A	V	174	A
04	UniProt	VAR_DTXR_CORDI_006 *	S	191	T	DTXR_CORDI	---	---	A	S	191	T
05	UniProt	VAR_DTXR_CORDI_008 *	H	201	R	DTXR_CORDI	---	---	A	H	201	R
06	UniProt	VAR_DTXR_CORDI_009 *	S	205	R	DTXR_CORDI	---	---	A	S	205	R
07	UniProt	VAR_DTXR_CORDI_010 *	I	214	L	DTXR_CORDI	---	---	A	L	214	L
08	UniProt	VAR_DTXR_CORDI_011 *	I	214	Y	DTXR_CORDI	---	---	A	L	214	Y
09	UniProt	VAR_DTXR_CORDI_012 *	A	218	T	DTXR_CORDI	---	---	A	A	218	T
10	UniProt	VAR_DTXR_CORDI_013 *	I	221	M	DTXR_CORDI	---	---	A	I	221	M
11	UniProt	VAR_DTXR_CORDI_014 *	I	221	T	DTXR_CORDI	---	---	A	I	221	T
	* ID not provided by source

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_DTXR	PS50944	DtxR-type HTH domain profile.	DTXR_CORDI	4-65	2	A:4-65 B:4-65
1	HTH_DTXR	PS50944	DtxR-type HTH domain profile.	DTXR_CORDW	4-65	2	A:4-65 B:4-65

(no "Exon" information available for 1BI2)

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

    Alignment length:223
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222   
           DTXR_CORDI     3 DLVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEACRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELGVGNSDAAVPGTRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVDRDGHITLSHNGKDVELIDDLAHTIRIEE 225
               SCOP domains d1bi2a1 A:3-64 Diphtheria toxin repressor (DtxR)              d1bi2a2 A:65-140 Diphtheria toxin repressor (DtxR)                                 d1bi2a3 A:148-225 Diphtheria toxin repressor (DtxR)                            SCOP domains
               CATH domains 1bi2A01 A:3-74 'winged helix' repressor DNA binding domain              1bi2A02 A:75-140 Diphtheria Toxin Repressor, domain 2                    1bi2A03 A:148-223  [code=2.30.30.90, no name define  d]                     -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh.....hhhhhhhh...hhhhhhhhhhhhh...eee.....eee.hhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhh...hhhhhhhhhh...............hhhh..-------....hhhh.....eeeeeee..hhh......hhhhhh.......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
                 1bi2 A   3 DLVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEACRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELGV-------PGTRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVDR--HITLSHNGKDVELLDDLAHTIRIEE 225
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       | -     | 152       162       172       182       192     | 202       212       222   
                                                                                                                                                                   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
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222   
           DTXR_CORDW     3 DLVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEACRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELGVGNSDAAAPGTRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVDRDGHITLSHNGKDVELLDDLAHTIRIEE 225
               SCOP domains d1bi2a1 A:3-64 Diphtheria toxin repressor (DtxR)              d1bi2a2 A:65-140 Diphtheria toxin repressor (DtxR)                                 d1bi2a3 A:148-225 Diphtheria toxin repressor (DtxR)                            SCOP domains
               CATH domains 1bi2A01 A:3-74 'winged helix' repressor DNA binding domain              1bi2A02 A:75-140 Diphtheria Toxin Repressor, domain 2                    1bi2A03 A:148-223  [code=2.30.30.90, no name define  d]                     -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh.....hhhhhhhh...hhhhhhhhhhhhh...eee.....eee.hhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhh...hhhhhhhhhh...............hhhh..-------....hhhh.....eeeeeee..hhh......hhhhhh.......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
                 1bi2 A   3 DLVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEACRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELGV-------PGTRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVDR--HITLSHNGKDVELLDDLAHTIRIEE 225
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       | -     | 152       162       172       182       192     | 202       212       222   
                                                                                                                                                                   140     148                                               198  |                        
                                                                                                                                                                                                                                201

Chain B from PDB  Type:PROTEIN  Length:138
 aligned with DTXR_CORDI | P0DJL7 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:138
                                    12        22        32        42        52        62        72        82        92       102       112       122       132        
           DTXR_CORDI     3 DLVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEACRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELGV 140
               SCOP domains d1bi2b1 B:3-64 Diphtheria toxin repressor (DtxR)              d1bi2b2 B:65-140 Diphtheria toxin repressor (DtxR)                           SCOP domains
               CATH domains 1bi2B01 B:3-75 'winged helix' repressor DNA binding domain               1bi2B02 B:76-136 Diphtheria Toxin Repressor, domain 2        ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh.....hhhhhhhh...hhhhhhhhhhhhh...eee.....eee.hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh..hhhhhhhhhh...............hhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------H--------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -HTH_DTXR  PDB: B:4-65 UniProt: 4-65                           --------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1bi2 B   3 DLVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEACRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELGV 140
                                    12        22        32        42        52        62        72        82        92       102       112       122       132

Chain B from PDB  Type:PROTEIN  Length:138
 aligned with DTXR_CORDW | H2I233 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:138
                                    12        22        32        42        52        62        72        82        92       102       112       122       132        
           DTXR_CORDW     3 DLVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEACRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELGV 140
               SCOP domains d1bi2b1 B:3-64 Diphtheria toxin repressor (DtxR)              d1bi2b2 B:65-140 Diphtheria toxin repressor (DtxR)                           SCOP domains
               CATH domains 1bi2B01 B:3-75 'winged helix' repressor DNA binding domain               1bi2B02 B:76-136 Diphtheria Toxin Repressor, domain 2        ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh.....hhhhhhhh...hhhhhhhhhhhhh...eee.....eee.hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh..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
                 1bi2 B   3 DLVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEACRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELGV 140
                                    12        22        32        42        52        62        72        82        92       102       112       122       132

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 '\|'

(no "Pfam Domain" information available for 1BI2)

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.

Asymmetric/Biological Unit
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