1XCV - JenaLib

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Title :   CRYSTAL STRUCTURE OF (H79AC102D)DTXR COMPLEXED WITH NICKEL(II)

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

Date :   03 Sep 04 (Deposition) - 16 Aug 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Helix-Turn-Helix, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. A. D'Aquino, J. Tetenbaum-Novatt, A. White, F. Berkovitch, D. Ring
Mechanism Of Metal Ion Activation Of The Diphtheria Toxin Repressor Dtxr.
Proc. Natl. Acad. Sci. Usa V. 102 18408 2005
PubMed-ID: 16352732 | Reference-DOI: 10.1073/PNAS.0500908102

Molecule 1 - DIPHTHERIA TOXIN REPRESSOR MUTANT
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	DTXR
	Mutation	:	YES
	Organism Scientific	:	CORYNEBACTERIUM DIPHTHERIAE
	Organism Taxid	:	1717
	Synonym	:	(H79AC102D)DTXR, IRON-DEPENDENT DIPHTHERIA TOX REGULATORY ELEMENT, TOX REGULATORY FACTOR

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	NI	1	Ligand/Ion	NICKEL (II) ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	NI	-1	Ligand/Ion	NICKEL (II) ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	MET A:10 , ASP A:102 , GLU A:105 , HIS A:106	BINDING SITE FOR RESIDUE NI A 252

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

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

Asymmetric Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_DTXR_CORDI_001 *	R	47	H	DTXR_CORDI	---	---	A	R	47	H
	* ID not provided by source

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

Biological Unit 1 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_DTXR_CORDI_001 *	R	47	H	DTXR_CORDI	---	---	A	R	47	H
	* 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, 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 1XCV)

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: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 d1xcva1 A:1-64 Diphtheria toxin repressor (DtxR)                d1xcva2 A:65-139 Diphtheria toxin repressor (DtxR)                          SCOP domains
               CATH domains --1xcvA01 A:3-75 'winged helix' repressor DNA binding domain               1xcvA02 A:76-136 Diphtheria Toxin Repressor, domain 2        --- CATH domains
               Pfam domains --Fe_dep_repress-1xcvA02 A:3-62                               --Fe_dep_repr_C-1xcvA01 A:65-135                                         ---- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhhhhhhhh..eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhh................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------H-------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---HTH_DTXR  PDB: A:4-65 UniProt: 4-65                           -------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xcv A   1 MKDLVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKARLAERLLTDIIGLDINKVHDEADRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELG 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 d1xcva1 A:1-64 Diphtheria toxin repressor (DtxR)                d1xcva2 A:65-139 Diphtheria toxin repressor (DtxR)                          SCOP domains
               CATH domains --1xcvA01 A:3-75 'winged helix' repressor DNA binding domain               1xcvA02 A:76-136 Diphtheria Toxin Repressor, domain 2        --- CATH domains
               Pfam domains --Fe_dep_repress-1xcvA02 A:3-62                               --Fe_dep_repr_C-1xcvA01 A:65-135                                         ---- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhhhhhhhh..eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhh................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------H-------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---HTH_DTXR  PDB: A:4-65 UniProt: 4-65                           -------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xcv A   1 MKDLVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKARLAERLLTDIIGLDINKVHDEADRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELG 139
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

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 '\|'

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: Fe_dep_repr_C (11)

Corynebacterium diphtheriae (7)

Fe_dep_repr_C-1xcvA01

A:65-135

Family: Fe_dep_repress (10)

Corynebacterium diphtheriae (6)

Fe_dep_repress-1xcvA02

A:3-62

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.

Asymmetric Unit
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	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1xcv)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Jmol
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Access by PDB/NDB ID
	1xcv
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	DTXR_CORDW \| H2I233
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1p92	CRYSTAL STRUCTURE OF (H79A)DTXR
2tdx	DIPHTHERIA TOX REPRESSOR (C102D MUTANT) COMPLEXED WITH NICKEL

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

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

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SCOP Domains (2, 2)

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