1P92 - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF (H79A)DTXR

Authors :   J. A. D'Aquino, D. Ringe

Date :   08 May 03 (Deposition) - 25 May 04 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Diphtheria Toxin Repressor, Dtxr, Dna-Binding Protein, Helix-Turn- Helix, Sh3-Like, Metal Ion Binding Site, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. A. D'Aquino, D. Ringe
Determinants Of The Src Homology Domain 3-Like Fold.
J. Bacteriol. V. 185 4081 2003
PubMed-ID: 12837782 | Reference-DOI: 10.1128/JB.185.14.4081-4086.2003

Molecule 1 - DIPHTHERIA TOXIN REPRESSOR
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	DTXR
	Mutation	:	YES
	Organism Scientific	:	CORYNEBACTERIUM DIPHTHERIAE
	Organism Taxid	:	1717
	Synonym	:	IRON-DEPENDENT DIPHTHERIA TOX REGULATORY ELEMENT, TOX REGULATORY FACTOR

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	BME	2	Ligand/Ion	BETA-MERCAPTOETHANOL

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:102	BINDING SITE FOR RESIDUE BME A 550

(no "SS Bond" information available for 1P92)

(no "Cis Peptide Bond" information available for 1P92)

Asymmetric Unit (12, 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	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_007 *	D	199	V	DTXR_CORDI	---	---	A	D	199	V
06	UniProt	VAR_DTXR_CORDI_008 *	H	201	R	DTXR_CORDI	---	---	A	H	201	R
07	UniProt	VAR_DTXR_CORDI_009 *	S	205	R	DTXR_CORDI	---	---	A	S	205	R
08	UniProt	VAR_DTXR_CORDI_010 *	I	214	L	DTXR_CORDI	---	---	A	L	214	L
09	UniProt	VAR_DTXR_CORDI_011 *	I	214	Y	DTXR_CORDI	---	---	A	L	214	Y
10	UniProt	VAR_DTXR_CORDI_012 *	A	218	T	DTXR_CORDI	---	---	A	A	218	T
11	UniProt	VAR_DTXR_CORDI_013 *	I	221	M	DTXR_CORDI	---	---	A	I	221	M
12	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)

Biological Unit 1 (12, 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	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_007 *	D	199	V	DTXR_CORDI	---	---	A	D	199	V
06	UniProt	VAR_DTXR_CORDI_008 *	H	201	R	DTXR_CORDI	---	---	A	H	201	R
07	UniProt	VAR_DTXR_CORDI_009 *	S	205	R	DTXR_CORDI	---	---	A	S	205	R
08	UniProt	VAR_DTXR_CORDI_010 *	I	214	L	DTXR_CORDI	---	---	A	L	214	L
09	UniProt	VAR_DTXR_CORDI_011 *	I	214	Y	DTXR_CORDI	---	---	A	L	214	Y
10	UniProt	VAR_DTXR_CORDI_012 *	A	218	T	DTXR_CORDI	---	---	A	A	218	T
11	UniProt	VAR_DTXR_CORDI_013 *	I	221	M	DTXR_CORDI	---	---	A	I	221	M
12	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)

Biological Unit 2 (12, 24)

								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	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_007 *	D	199	V	DTXR_CORDI	---	---	A	D	199	V
06	UniProt	VAR_DTXR_CORDI_008 *	H	201	R	DTXR_CORDI	---	---	A	H	201	R
07	UniProt	VAR_DTXR_CORDI_009 *	S	205	R	DTXR_CORDI	---	---	A	S	205	R
08	UniProt	VAR_DTXR_CORDI_010 *	I	214	L	DTXR_CORDI	---	---	A	L	214	L
09	UniProt	VAR_DTXR_CORDI_011 *	I	214	Y	DTXR_CORDI	---	---	A	L	214	Y
10	UniProt	VAR_DTXR_CORDI_012 *	A	218	T	DTXR_CORDI	---	---	A	A	218	T
11	UniProt	VAR_DTXR_CORDI_013 *	I	221	M	DTXR_CORDI	---	---	A	I	221	M
12	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 Unit (1, 1)

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

Biological Unit 1 (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	1	A:4-65
1	HTH_DTXR	PS50944	DtxR-type HTH domain profile.	DTXR_CORDW	4-65	1	A:4-65

Biological Unit 2 (1, 4)

	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
1	HTH_DTXR	PS50944	DtxR-type HTH domain profile.	DTXR_CORDW	4-65	2	A:4-65

(no "Exon" information available for 1P92)

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:218
 aligned with DTXR_CORDI | P0DJL7 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:226
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      
           DTXR_CORDI     1 MKDLVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEACRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELGVGNSDAAVPGTRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVDRDGHITLSHNGKDVELIDDLAHTIRIEEL 226
               SCOP domains d1p92a1 A:1-64 Diphtheria toxin repressor (DtxR)                d1p92a2 A:65-139 Diphtheria toxin repressor (DtxR)                         --------d1p92a3 A:148-226 Diphtheria toxin repressor (DtxR)                             SCOP domains
               CATH domains 1p92A01 A:1-74 'winged helix' repressor DNA binding domain                1p92A02 A:75-139 Diphtheria Toxin Repressor, domain 2            --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --Fe_dep_repress-1p92A02 A:3-62                               --Fe_dep_repr_C-1p92A01 A:65-135                                         -------------------FeoA-1p92A03 A:155-225                                                 - Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhh....hhhhhhhhhhhh..eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhh.............hhhhhh--------..eehhhhh............hhhhh...hhhhhhhhh............................hhhhhhhhee... Sec.struct. author
             SAPs(SNPs) (1) ----------------------------------------------H---------------------------------------------------------------------------------------------------------------------V--------A----------------T-------V-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
                 1p92 A   1 MKDLVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKARLAERLLTDIIGLDINKVHDEACRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELG--------PGTRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVDRDGHITLSHNGKDVELLDDLAHTIRIEEL 226
                                    10        20        30        40        50        60        70        80        90       100       110       120       130        |-       150       160       170       180       190       200       210       220      
                                                                                                                                                                    139      148

Chain A from PDB  Type:PROTEIN  Length:218
 aligned with DTXR_CORDW | H2I233 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:226
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      
           DTXR_CORDW     1 MKDLVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEACRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELGVGNSDAAAPGTRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVDRDGHITLSHNGKDVELLDDLAHTIRIEEL 226
               SCOP domains d1p92a1 A:1-64 Diphtheria toxin repressor (DtxR)                d1p92a2 A:65-139 Diphtheria toxin repressor (DtxR)                         --------d1p92a3 A:148-226 Diphtheria toxin repressor (DtxR)                             SCOP domains
               CATH domains 1p92A01 A:1-74 'winged helix' repressor DNA binding domain                1p92A02 A:75-139 Diphtheria Toxin Repressor, domain 2            --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --Fe_dep_repress-1p92A02 A:3-62                               --Fe_dep_repr_C-1p92A01 A:65-135                                         -------------------FeoA-1p92A03 A:155-225                                                 - Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhh....hhhhhhhhhhhh..eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhh.............hhhhhh--------..eehhhhh............hhhhh...hhhhhhhhh............................hhhhhhhhee... Sec.struct. author
             SAPs(SNPs) (1) ----------------------------------------------H---------------------------------------------------------------------------------------------------------------------V--------A----------------T-------V-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
                 1p92 A   1 MKDLVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKARLAERLLTDIIGLDINKVHDEACRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELG--------PGTRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVDRDGHITLSHNGKDVELLDDLAHTIRIEEL 226
                                    10        20        30        40        50        60        70        80        90       100       110       120       130        |-       150       160       170       180       190       200       210       220      
                                                                                                                                                                    139      148

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	-	→ Gap	(green background, '-', border residues have a numbering label)
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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 '\|'

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: Fe_dep_repr_C (11)

Corynebacterium diphtheriae (7)

Fe_dep_repr_C-1p92A01

A:65-135

Family: Fe_dep_repress (10)

Corynebacterium diphtheriae (6)

Fe_dep_repress-1p92A02

A:3-62

Clan: TRB (15)

Family: FeoA (11)

Corynebacterium diphtheriae (6)

FeoA-1p92A03

A:155-225

Asymmetric Unit(hide GO term definitions)

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.

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.

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	1p92
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	DTXR_CORDW \| H2I233
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1ddn	DIPHTHERIA TOX REPRESSOR (C102D MUTANT) COMPLEXED WITH NICKEL AND WITH TOX DNA OPERATOR
1dpr	STRUCTURES OF THE APO- AND THE METAL ION-ACTIVATED FORMS OF THE DIPHTHERIA TOX REPRESSOR FROM CORYNEBACTERIUM DIPHTHERIAE
2tdx	DIPHTHERIA TOX REPRESSOR (C102D MUTANT) COMPLEXED WITH NICKEL

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

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SS Bonds (0, 0)

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SAPs(SNPs)/Variants (12, 12)

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Exons (0, 0)

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SCOP Domains (3, 3)

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Related Entries

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Related Entries Specified in the PDB File