2Y7W - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   DNTR INDUCER BINDING DOMAIN

Authors :   L. Devesse, I. Smirnova, R. Lonneborg, U. Kapp, P. Brzezinski, G. A. Leo C. Dian

Date :   02 Feb 11 (Deposition) - 20 Jul 11 (Release) - 20 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.89

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

Keywords :   Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Devesse, I. Smirnova, R. Lonneborg, U. Kapp, P. Brzezinski, G. A. Leonard, C. Dian
Crystal Structures Of Dntr Inducer Binding Domains In Complex With Salicylate Offer Insights Into The Activation Of Lysr-Type Transcriptional Regulators.
Mol. Microbiol. V. 81 354 2011
PubMed-ID: 21692874 | Reference-DOI: 10.1111/J.1365-2958.2011.07673.X

Molecule 1 - LYSR-TYPE REGULATORY PROTEIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	INDUCER BINDING DOMAIN, RESIDUES 80-301
	Mutation	:	YES
	Organism Scientific	:	BURKHOLDERIA SP.
	Organism Taxid	:	233098
	Strain	:	DNT

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	PG4	3	Ligand/Ion	TETRAETHYLENE GLYCOL
2	SAL	3	Ligand/Ion	2-HYDROXYBENZOIC ACID

Biological Unit 1 (2, 5)

No.	Name	Count	Type	Full Name
1	PG4	3	Ligand/Ion	TETRAETHYLENE GLYCOL
2	SAL	2	Ligand/Ion	2-HYDROXYBENZOIC ACID

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	PG4	-1	Ligand/Ion	TETRAETHYLENE GLYCOL
2	SAL	1	Ligand/Ion	2-HYDROXYBENZOIC ACID

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:104 , ILE A:106 , GLY A:107 , PHE A:111 , HIS A:169 , ILE A:273	BINDING SITE FOR RESIDUE SAL A1300
2	AC2	SOFTWARE	VAL A:199 , VAL A:200 , ALA A:201 , GLY A:207 , GLU A:208 , VAL A:209 , ASP A:210 , ARG A:220 , THR A:244	BINDING SITE FOR RESIDUE PG4 A1301
3	AC3	SOFTWARE	ARG A:97 , THR A:98 , ASN A:100 , GLY A:145 , ASP A:148 , TYR A:281	BINDING SITE FOR RESIDUE PG4 A1302
4	AC4	SOFTWARE	THR B:104 , ILE B:106 , GLY B:107 , PHE B:111 , HIS B:169 , THR B:204 , HIS B:206 , ILE B:273	BINDING SITE FOR RESIDUE SAL B1300
5	AC5	SOFTWARE	ARG A:220 , PRO B:124 , HIS B:125 , ILE B:126	BINDING SITE FOR RESIDUE PG4 B1301
6	AC6	SOFTWARE	THR C:104 , ILE C:106 , GLY C:107 , PHE C:111 , PHE C:167 , HIS C:169 , ILE C:273	BINDING SITE FOR RESIDUE SAL C1300

(no "SS Bond" information available for 2Y7W)

Asymmetric Unit

No.	Residues
1	Ser A:184	-	Pro A:185
2	Ser B:184	-	Pro B:185
3	Gly B:205	-	His B:206
4	His B:206	-	Gly B:207
5	Lys C:177	-	Asp C:178
6	Ser C:184	-	Pro C:185
7	His C:206	-	Gly C:207
8	Ser D:184	-	Pro D:185
9	Ala D:201	-	Leu D:202
10	Leu D:202	-	Asn D:203
11	Gly D:205	-	His D:206
12	His D:206	-	Gly D:207

(no "SAP(SNP)/Variant" information available for 2Y7W)

(no "PROSITE Motif" information available for 2Y7W)

(no "Exon" information available for 2Y7W)

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:207
 aligned with Q7WT50_9BURK | Q7WT50 from UniProtKB/TrEMBL  Length:301

    Alignment length:212
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298  
         Q7WT50_9BURK    89 SFDPFASTRTFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLPELQTGFFQRRLFRHRYVCMFRKDHPSAKSPMSLKQFTELEHVGVVALNTGHGEVDGLLERAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFSE 300
               SCOP domains d2y7wa_ A: automated matches                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeehhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhh...eeee........eeeeeeeee.eeeeee..........hhhhhhhheeeee..-----.hhhhhhhhh....eeeeee....hhhhhhhh...eeeeehhhhhhhhhhhheeeee.......eeeeeeee.hhh.hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y7w A  89 SFDPFASTRTFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLPELQTGFFQRRLFRHRYVCMFRKDHPSAKSPMSLKQFTELEHVGVVA-----GEVDGLLERAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFSE 300
                                    98       108       118       128       138       148       158       168       178       188       198  |    208       218       228       238       248       258       268       278       288       298  
                                                                                                                                          201   207

Chain B from PDB  Type:PROTEIN  Length:207
 aligned with Q7WT50_9BURK | Q7WT50 from UniProtKB/TrEMBL  Length:301

    Alignment length:210
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299
         Q7WT50_9BURK    90 FDPFASTRTFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLPELQTGFFQRRLFRHRYVCMFRKDHPSAKSPMSLKQFTELEHVGVVALNTGHGEVDGLLERAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFS 299
               SCOP domains d2y7wb_ B: automated matches                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeeehhhhhhhhhhhhhhhhhhhh...eeeee....-..hhhhhh....eeee........eeeeeeeee.eeeeee..........hhhhhhhheeeee..--....hhhhhhhhh....eeeeee....hhhhhhhh....eeeehhhhhhhhhhhheeeee.......eeeeeeee.hhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2y7w B  90 FDPFASTRTFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNA-NLKEDMESGAVDLALGLLPELQTGFFQRRLFRHRYVCMFRKDHPSAKSPMSLKQFTELEHVGVVA--TGHGEVDGLLERAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFS 299
                                    99       109       119       129     | 139       149       159       169       179       189       199 |  |  209       219       229       239       249       259       269       279       289       299
                                                                       135 |                                                             201  |                                                                                               
                                                                         137                                                                204

Chain C from PDB  Type:PROTEIN  Length:207
 aligned with Q7WT50_9BURK | Q7WT50 from UniProtKB/TrEMBL  Length:301

    Alignment length:211
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298 
         Q7WT50_9BURK    89 SFDPFASTRTFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLPELQTGFFQRRLFRHRYVCMFRKDHPSAKSPMSLKQFTELEHVGVVALNTGHGEVDGLLERAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFS 299
               SCOP domains d2y7wc_ C: automated matches                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeehhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhh...eeee........eeeeeeeee.eeeeee..........hhhhhhhheeeee..----..hhhhhhhhh....eeeeee....hhhhhhhh...eeeeehhhhhhhhhhhheeeee.......eeeeeeee.hhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y7w C  89 SFDPFASTRTFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLPELQTGFFQRRLFRHRYVCMFRKDHPSAKSPMSLKQFTELEHVGVVA----HGEVDGLLERAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFS 299
                                    98       108       118       128       138       148       158       168       178       188       198  |    208       218       228       238       248       258       268       278       288       298 
                                                                                                                                          201  206

Chain D from PDB  Type:PROTEIN  Length:210
 aligned with Q7WT50_9BURK | Q7WT50 from UniProtKB/TrEMBL  Length:301

    Alignment length:211
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299 
         Q7WT50_9BURK    90 FDPFASTRTFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLPELQTGFFQRRLFRHRYVCMFRKDHPSAKSPMSLKQFTELEHVGVVALNTGHGEVDGLLERAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFSE 300
               SCOP domains d2y7wd_ D: automated matches                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeehhhhhhhhhhhhhhhhhhhh...eeeee.................eeee......-.eeeeeeeee.eeeeee..........hhhhhhhheeeee........hhhhhhhhh....eeeeee....hhhhhhhh....eeeehhhhhhhhhhhheeeee.......eeeeeeee.hhh.hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y7w D  90 FDPFASTRTFNLAMTDIGEMYFMPPLMEALAQRAPHIQISTLRPNAGNLKEDMESGAVDLALGLLPELQ-GFFQRRLFRHRYVCMFRKDHPSAKSPMSLKQFTELEHVGVVALNTGHGEVDGLLERAGIKRRMRLVVPHFIAIGPILHSTDLIATVPQRFAVRCEVPFGLTTSPHPAKLPDIAINLFWHAKYNRDPGNMWLRQLFVELFSE 300
                                    99       109       119       129       139       149        |-|      169       179       189       199       209       219       229       239       249       259       269       279       289       299 
                                                                                              158 |                                                                                                                                            
                                                                                                160

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

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Periplasmic binding protein-like II (813)

Superfamily: Periplasmic binding protein-like II (813)

Family: Phosphate binding protein-like (463)

Protein domain: automated matches (76)

Burkholderia sp. [TaxId: 233098] (5)

1a	d2y7wa_	A:
1b	d2y7wb_	B:
1c	d2y7wc_	C:
1d	d2y7wd_	D:

(no "CATH Domain" information available for 2Y7W)

(no "Pfam Domain" information available for 2Y7W)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Q7WT50_9BURK | Q7WT50)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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.
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.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		PG4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SAL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ala D:201 - Leu D:202	[ RasMol ]
		Gly B:205 - His B:206	[ RasMol ]
		Gly D:205 - His D:206	[ RasMol ]
		His B:206 - Gly B:207	[ RasMol ]
		His C:206 - Gly C:207	[ RasMol ]
		His D:206 - Gly D:207	[ RasMol ]
		Leu D:202 - Asn D:203	[ RasMol ]
		Lys C:177 - Asp C:178	[ RasMol ]
		Ser A:184 - Pro A:185	[ RasMol ]
		Ser B:184 - Pro B:185	[ RasMol ]
		Ser C:184 - Pro C:185	[ RasMol ]
		Ser D:184 - Pro D:185	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2y7w
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	Q7WT50_9BURK \| Q7WT50
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	Q7WT50_9BURK \| Q7WT50
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	Q7WT50_9BURK \| Q7WT50	:	1utb 1uth 2y7k 2y7p 2y7r 2y84 5ae4 5ae5

1utb	DNTR FROM BURKHOLDERIA SP. STRAIN DNT
1uth	DNTR FROM BURKHOLDERIA SP. STRAIN DNT IN COMPLEX WITH THIOCYANATE
2y7k	DNTR INDUCER BINDING DOMAIN IN COMPLEX WITH SALICYLATE. MONOCLINIC CRYSTAL FORM
2y7p	DNTR INDUCER BINDING DOMAIN IN COMPLEX WITH SALICYLATE. TRIGONAL CRYSTAL FORM
2y7r	DNTR INDUCER BINDING DOMAIN
2y84	DNTR INDUCER BINDING DOMAIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (12, 12)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (4, 4)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File