1BI3 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (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 :   2.40

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)

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)

Asymmetric/Biological Unit (3, 6)

No.	Name	Count	Type	Full Name
1	CSS	2	Mod. Amino Acid	S-MERCAPTOCYSTEINE
2	SO4	2	Ligand/Ion	SULFATE ION
3	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:79 , GLU A:83 , HIS A:98 , SO4 A:292	BINDING SITE FOR RESIDUE ZN A 291
2	AC2	SOFTWARE	HIS B:79 , GLU B:83 , HIS B:98 , SO4 B:1292	BINDING SITE FOR RESIDUE ZN B 1291
3	AC3	SOFTWARE	MET 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:318	BINDING SITE FOR RESIDUE SO4 A 292
4	AC4	SOFTWARE	HIS 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:1291	BINDING SITE FOR RESIDUE SO4 B 1292

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

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

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 1BI3)

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)
	-	→ 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 1BI3)

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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Description

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Ligands, Modified Residues, Ions (3, 6)

Sites (4, 4)

SS Bonds (0, 0)

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