2QQ9 - JenaLib

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Asymmetric Unit (Jmol Viewer)

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF DTXR(D6A C102D) COMPLEXED WITH NICKEL(II)

Authors :   J. A. D'Aquino, J. R. Lattimer, A. Denninger, K. E. D'Aquino, D. Ringe

Date :   26 Jul 07 (Deposition) - 30 Oct 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.71

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

Keywords :   Repressor, Regulator, Dtxr, Helix-Turn-Helix, Metal Ion, Activation, Dna-Binding, Ferrous Iron, Transcription, Transcription Regulation, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. A. D'Aquino, J. R. Lattimer, A. Denninger, K. E. D'Aquino, D. Ringe
Role Of The N-Terminal Helix In The Metal Ion-Induced Activation Of The Diphtheria Toxin Repressor Dtxr.
Biochemistry V. 46 11761 2007
PubMed-ID: 17902703 | Reference-DOI: 10.1021/BI7007883

Molecule 1 - DIPHTHERIA TOXIN REPRESSOR
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Strain	:	BL-21(DE3)
	Expression System Taxid	:	469008
	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 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	NI	2	Ligand/Ion	NICKEL (II) ION
2	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	NI	-1	Ligand/Ion	NICKEL (II) ION
2	PO4	2	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:79 , GLU A:83 , HIS A:98 , PO4 A:600 , HOH A:629 , HOH A:642	BINDING SITE FOR RESIDUE NI A 551
2	AC2	SOFTWARE	MET A:10 , ASP A:102 , GLU A:105 , HIS A:106 , HOH A:616	BINDING SITE FOR RESIDUE NI A 552
3	AC3	SOFTWARE	HIS A:79 , ARG A:80 , GLU A:83 , SER A:126 , PHE A:128 , ASN A:130 , NI A:551 , HOH A:629 , HOH A:642	BINDING SITE FOR RESIDUE PO4 A 600

(no "SS Bond" information available for 2QQ9)

Asymmetric Unit

No.	Residues
1	His A:201	-	Ile A:202
2	Glu A:225	-	Leu A:226

Asymmetric Unit (11, 11)

								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_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)

Biological Unit 1 (11, 22)

								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_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 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 2QQ9)

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:212
 aligned with DTXR_CORDI | P0DJL7 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:224
                                    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 DLVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEACRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELGVGNSDAAVPGTRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVDRDGHITLSHNGKDVELIDDLAHTIRIEEL 226
               SCOP domains d2qq9a1 A:3-64 Diphtheria toxin repressor (DtxR)              d2qq9a2 A:65-139 Diphtheria toxin repressor (DtxR)                                   d2qq9a3 A:150-226 Diphtheria toxin repressor (Dtx  R)                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Fe_dep_repress-2qq9A02 A:3-62                               --Fe_dep_repr_C-2qq9A01 A:65-135                                         ----          -----FeoA-2qq9A03 A:155-225                                                 - Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh..eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhh.............hhhhhh----------.hhhhhh....eeeeeee.hhhhh..hhhhhhhhhh.....eeeee...--..eee....eee.hhhhhhhheee.. 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
                 2qq9 A   3 DLVATTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEADRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELG----------TRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVDR--HITLSHNGKDVELLDDLAHTIRIEEL 226
                                    12        22        32        42        52        62        72        82        92       102       112       122       132      |  -       152       162       172       182       192     | 202       212       222    
                                                                                                                                                                  139        150                                             198  |                         
                                                                                                                                                                                                                                201

Chain A from PDB  Type:PROTEIN  Length:212
 aligned with DTXR_CORDW | H2I233 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:224
                                    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 DLVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEACRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELGVGNSDAAAPGTRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVDRDGHITLSHNGKDVELLDDLAHTIRIEEL 226
               SCOP domains d2qq9a1 A:3-64 Diphtheria toxin repressor (DtxR)              d2qq9a2 A:65-139 Diphtheria toxin repressor (DtxR)                                   d2qq9a3 A:150-226 Diphtheria toxin repressor (Dtx  R)                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Fe_dep_repress-2qq9A02 A:3-62                               --Fe_dep_repr_C-2qq9A01 A:65-135                                         ----          -----FeoA-2qq9A03 A:155-225                                                 - Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh..eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhh.............hhhhhh----------.hhhhhh....eeeeeee.hhhhh..hhhhhhhhhh.....eeeee...--..eee....eee.hhhhhhhheee.. 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
                 2qq9 A   3 DLVATTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEADRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELG----------TRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVDR--HITLSHNGKDVELLDDLAHTIRIEEL 226
                                    12        22        32        42        52        62        72        82        92       102       112       122       132      |  -       152       162       172       182       192     | 202       212       222    
                                                                                                                                                                  139        150                                             198  |                         
                                                                                                                                                                                                                                201

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 "CATH Domain" information available for 2QQ9)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: Fe_dep_repr_C (11)

Corynebacterium diphtheriae (7)

Fe_dep_repr_C-2qq9A01

A:65-135

Family: Fe_dep_repress (10)

Corynebacterium diphtheriae (6)

Fe_dep_repress-2qq9A02

A:3-62

Clan: TRB (15)

Family: FeoA (11)

Corynebacterium diphtheriae (6)

FeoA-2qq9A03

A:155-225

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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	Cis Peptide Bonds
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		His A:201 - Ile A:202	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	2qq9
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	DTXR_CORDW \| H2I233
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Description

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Ligands, Modified Residues, Ions (2, 3)

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