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Description

Title :   CRYSTAL STRUCTURE OF SOXR IN COMPLEX WITH DNA

Authors :   S. Watanabe, A. Kita, K. Kobayashi, K. Miki

Date :   05 Feb 08 (Deposition) - 25 Mar 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Oxidative Stress, Merr Family, Activator, Dna-Binding, Iron, Iron- Sulfur, Metal-Binding, Transcription, Transcription Regulation, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Watanabe, A. Kita, K. Kobayashi, K. Miki
Crystal Structure Of The [2Fe-2S] Oxidative-Stress Sensor Soxr Bound To Dna
Proc. Natl. Acad. Sci. Usa V. 105 4121 2008
PubMed-ID: 18334645 | Reference-DOI: 10.1073/PNAS.0709188105

Compounds

Molecule 1 - REDOX-SENSITIVE TRANSCRIPTIONAL ACTIVATOR SOXR
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-3XA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	SOXR
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12

*Molecule 2 - DNA (5'- D(DGPDCPDCPDTPDCPDAPDAPDGPDTPDTPDAPDAPDCPDTPDTPDGPDA PDGPDGPDC)-3')*
	Chains	:	B
	Engineered	:	YES
	Synthetic	:	YES

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 3)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	DTT	1	Ligand/Ion	2,3-DIHYDROXY-1,4-DITHIOBUTANE
2	FES	1	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER
3	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	DTT	2	Ligand/Ion	2,3-DIHYDROXY-1,4-DITHIOBUTANE
2	FES	2	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER
3	GOL	2	Ligand/Ion	GLYCEROL

Sites (3, 3)

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:119 , CYS A:122 , GLY A:123 , CYS A:124 , LEU A:125 , CYS A:130	BINDING SITE FOR RESIDUE FES A 501
2	AC2	SOFTWARE	HIS A:107	BINDING SITE FOR RESIDUE DTT A 901
3	AC3	SOFTWARE	ARG A:20 , LEU A:54 , ARG A:127 , ARG A:133	BINDING SITE FOR RESIDUE GOL A 801

SS Bonds (0, 0)

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

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 2ZHG)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

Asymmetric Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_SOXR_ECOLI_001 *	R	20	C	SOXR_ECOLI	---	---	A	R	20	C
	* 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_SOXR_ECOLI_001 *	R	20	C	SOXR_ECOLI	---	---	A	R	20	C
	* ID not provided by source

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

PROSITE Motifs (2, 2)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_MERR_2	PS50937	MerR-type HTH domain profile.	SOXR_ECOLI	11-79	1	A:11-79
2	HTH_MERR_1	PS00552	MerR-type HTH domain signature.	SOXR_ECOLI	15-37	1	A:15-37

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_MERR_2	PS50937	MerR-type HTH domain profile.	SOXR_ECOLI	11-79	2	A:11-79
2	HTH_MERR_1	PS00552	MerR-type HTH domain signature.	SOXR_ECOLI	15-37	2	A:15-37

Exons (0, 0)

(no "Exon" information available for 2ZHG)

Sequences/Alignments

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:121
 aligned with SOXR_ECOLI | P0ACS2 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:126
                                    19        29        39        49        59        69        79        89        99       109       119       129      
           SOXR_ECOLI    10 ALLTPGEVAKRSGVAVSALHFYESKGLITSIRNSGNQRRYKRDVLRYVAIIKIAQRIGIPLATIGEAFGVLPEGHTLSAKEWKQLSSQWREELDRRIHTLVALRDELDGCIGCGCLSRSDCPLRNP 135
               SCOP domains d2zhga_ A: automated matches                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ---MerR-2zhgA01 A:13-49                 ----MerR-DNA-bind-2zhgA02 A:54     -119                               ---------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh.hhhhhhhhhhh.....ee.....ee...hhhhhhhhhhhhhhhh.hhhhhhhhhh.-----..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------C------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -HTH_MERR_2  PDB: A:11-79 UniProt: 11-79                              -------------------------------------------------------- PROSITE (1)
                PROSITE (2) -----HTH_MERR_1  PDB: A:15-3-------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2zhg A  10 ALLTPGEVAKRSGVAVSALHFYESKGLITSIRNSGNQRRYKRDVLRYVAIIKIAQRIGIPLATIGEAFGV-----TLSAKEWKQLSSQWREELDRRIHTLVALRDELDGCIGCGCLSRSDCPLRNP 135
                                    19        29        39        49        59        69        79     |  89        99       109       119       129      
                                                                                                79    85

Chain B from PDB  Type:DNA  Length:20
                                                    
                 2zhg B   1 GCCTCAAGTTAACTTGAGGC  20
                                    10        20

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Putative DNA-binding domain (45)

Superfamily: Putative DNA-binding domain (45)

Family: automated matches (2)

Protein domain: automated matches (2)

Escherichia coli K-12 [TaxId: 83333] (1)

d2zhga_

CATH Domains (0, 0)

(no "CATH Domain" information available for 2ZHG)

Pfam Domains (2, 2)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: MerR (15)

Escherichia coli (strain K12) (5)

MerR-2zhgA01

A:13-49

Family: MerR-DNA-bind (12)

Escherichia coli (strain K12) (8)

MerR-DNA-bind-2zhgA02

A:54-119

Gene Ontology (8, 8)

Asymmetric Unit(hide GO term definitions)

Chain A (SOXR_ECOLI | P0ACS2)

molecular function
	GO:0051537	2 iron, 2 sulfur cluster binding	Interacting selectively and non-covalently with a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0051536	iron-sulfur cluster binding	Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006979	response to oxidative stress	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
	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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	Cis Peptide Bonds
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Databases and Analysis Tools

Databases

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	2zhg
		Family and Domain Information	:	ProDom \| SYSTERS
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	SOXR_ECOLI \| P0ACS2
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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	SOXR_ECOLI \| P0ACS2	:	2zhh

Related Entries Specified in the PDB File

2zhh	THE SAME PROTEIN WITHOUT DNA