1TJL | pdb_00001tjl

Crystal structure of transcription factor DksA from E. coli

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
J	d1tjlj1	All alpha proteins	Long alpha-hairpin	DnaK suppressor protein DksA, alpha-hairpin domain	DnaK suppressor protein DksA, alpha-hairpin domain	DnaK suppressor protein DksA, alpha-hairpin domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
J	d1tjlj2	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	Prokaryotic DksA/TraR C4-type zinc finger	DnaK suppressor protein DksA, zinc finger domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
I	d1tjli1	All alpha proteins	Long alpha-hairpin	DnaK suppressor protein DksA, alpha-hairpin domain	DnaK suppressor protein DksA, alpha-hairpin domain	DnaK suppressor protein DksA, alpha-hairpin domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
I	d1tjli2	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	Prokaryotic DksA/TraR C4-type zinc finger	DnaK suppressor protein DksA, zinc finger domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
H	d1tjlh1	All alpha proteins	Long alpha-hairpin	DnaK suppressor protein DksA, alpha-hairpin domain	DnaK suppressor protein DksA, alpha-hairpin domain	DnaK suppressor protein DksA, alpha-hairpin domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
H	d1tjlh2	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	Prokaryotic DksA/TraR C4-type zinc finger	DnaK suppressor protein DksA, zinc finger domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
G	d1tjlg1	All alpha proteins	Long alpha-hairpin	DnaK suppressor protein DksA, alpha-hairpin domain	DnaK suppressor protein DksA, alpha-hairpin domain	DnaK suppressor protein DksA, alpha-hairpin domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
G	d1tjlg2	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	Prokaryotic DksA/TraR C4-type zinc finger	DnaK suppressor protein DksA, zinc finger domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d1tjlf1	All alpha proteins	Long alpha-hairpin	DnaK suppressor protein DksA, alpha-hairpin domain	DnaK suppressor protein DksA, alpha-hairpin domain	DnaK suppressor protein DksA, alpha-hairpin domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d1tjlf2	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	Prokaryotic DksA/TraR C4-type zinc finger	DnaK suppressor protein DksA, zinc finger domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d1tjle1	All alpha proteins	Long alpha-hairpin	DnaK suppressor protein DksA, alpha-hairpin domain	DnaK suppressor protein DksA, alpha-hairpin domain	DnaK suppressor protein DksA, alpha-hairpin domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d1tjle2	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	Prokaryotic DksA/TraR C4-type zinc finger	DnaK suppressor protein DksA, zinc finger domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d1tjld1	All alpha proteins	Long alpha-hairpin	DnaK suppressor protein DksA, alpha-hairpin domain	DnaK suppressor protein DksA, alpha-hairpin domain	DnaK suppressor protein DksA, alpha-hairpin domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d1tjld2	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	Prokaryotic DksA/TraR C4-type zinc finger	DnaK suppressor protein DksA, zinc finger domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1tjlc1	All alpha proteins	Long alpha-hairpin	DnaK suppressor protein DksA, alpha-hairpin domain	DnaK suppressor protein DksA, alpha-hairpin domain	DnaK suppressor protein DksA, alpha-hairpin domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1tjlc2	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	Prokaryotic DksA/TraR C4-type zinc finger	DnaK suppressor protein DksA, zinc finger domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1tjlb1	All alpha proteins	Long alpha-hairpin	DnaK suppressor protein DksA, alpha-hairpin domain	DnaK suppressor protein DksA, alpha-hairpin domain	DnaK suppressor protein DksA, alpha-hairpin domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1tjlb2	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	Prokaryotic DksA/TraR C4-type zinc finger	DnaK suppressor protein DksA, zinc finger domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1tjla1	All alpha proteins	Long alpha-hairpin	DnaK suppressor protein DksA, alpha-hairpin domain	DnaK suppressor protein DksA, alpha-hairpin domain	DnaK suppressor protein DksA, alpha-hairpin domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1tjla2	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	Prokaryotic DksA/TraR C4-type zinc finger	DnaK suppressor protein DksA, zinc finger domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
J	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8040230	3000068	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	DnaK suppressor protein DksA, alpha-hairpin domain	8040228	3000986	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8040230	3000068	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	DnaK suppressor protein DksA, alpha-hairpin domain	8040228	3000986	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	DnaK suppressor protein DksA, alpha-hairpin domain	8040228	3000986	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8040230	3000068	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8040230	3000068	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	DnaK suppressor protein DksA, alpha-hairpin domain	8040228	3000986	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8040230	3000068	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	DnaK suppressor protein DksA, alpha-hairpin domain	8040228	3000986	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	DnaK suppressor protein DksA, alpha-hairpin domain	8040228	3000986	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8040230	3000068	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	DnaK suppressor protein DksA, alpha-hairpin domain	8040228	3000986	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8040230	3000068	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DnaK suppressor protein DksA, alpha-hairpin domain	8040228	3000986	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8040230	3000068	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DnaK suppressor protein DksA, alpha-hairpin domain	8040228	3000986	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8040230	3000068	SCOP2B (2022-06-29)
A	SCOP2 Family	DnaK suppressor protein DksA, alpha-hairpin domain	8027849	4002240	SCOP2 (2022-06-29)
A	SCOP2 Family	Prokaryotic DksA/TraR C4-type zinc finger	8027851	4003090	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	DnaK suppressor protein DksA, alpha-hairpin domain	8040228	3000986	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8040230	3000068	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
J	dksA	e1tjlJ1	A: alpha bundles	X: Long alpha-hairpin	H: DnaK suppressor protein DksA, alpha-hairpin domain (From Topology)	T: DnaK suppressor protein DksA, alpha-hairpin domain	F: dksA	ECOD (1.6)
J	zf-dskA_traR	e1tjlJ2	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: zf-dskA_traR	ECOD (1.6)
I	dksA	e1tjlI1	A: alpha bundles	X: Long alpha-hairpin	H: DnaK suppressor protein DksA, alpha-hairpin domain (From Topology)	T: DnaK suppressor protein DksA, alpha-hairpin domain	F: dksA	ECOD (1.6)
I	zf-dskA_traR	e1tjlI2	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: zf-dskA_traR	ECOD (1.6)
H	dksA	e1tjlH1	A: alpha bundles	X: Long alpha-hairpin	H: DnaK suppressor protein DksA, alpha-hairpin domain (From Topology)	T: DnaK suppressor protein DksA, alpha-hairpin domain	F: dksA	ECOD (1.6)
H	zf-dskA_traR	e1tjlH2	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: zf-dskA_traR	ECOD (1.6)
G	dksA	e1tjlG1	A: alpha bundles	X: Long alpha-hairpin	H: DnaK suppressor protein DksA, alpha-hairpin domain (From Topology)	T: DnaK suppressor protein DksA, alpha-hairpin domain	F: dksA	ECOD (1.6)
G	zf-dskA_traR	e1tjlG2	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: zf-dskA_traR	ECOD (1.6)
F	dksA	e1tjlF1	A: alpha bundles	X: Long alpha-hairpin	H: DnaK suppressor protein DksA, alpha-hairpin domain (From Topology)	T: DnaK suppressor protein DksA, alpha-hairpin domain	F: dksA	ECOD (1.6)
F	zf-dskA_traR	e1tjlF2	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: zf-dskA_traR	ECOD (1.6)
E	dksA	e1tjlE1	A: alpha bundles	X: Long alpha-hairpin	H: DnaK suppressor protein DksA, alpha-hairpin domain (From Topology)	T: DnaK suppressor protein DksA, alpha-hairpin domain	F: dksA	ECOD (1.6)
E	zf-dskA_traR	e1tjlE2	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: zf-dskA_traR	ECOD (1.6)
D	dksA	e1tjlD1	A: alpha bundles	X: Long alpha-hairpin	H: DnaK suppressor protein DksA, alpha-hairpin domain (From Topology)	T: DnaK suppressor protein DksA, alpha-hairpin domain	F: dksA	ECOD (1.6)
D	zf-dskA_traR	e1tjlD2	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: zf-dskA_traR	ECOD (1.6)
C	dksA	e1tjlC1	A: alpha bundles	X: Long alpha-hairpin	H: DnaK suppressor protein DksA, alpha-hairpin domain (From Topology)	T: DnaK suppressor protein DksA, alpha-hairpin domain	F: dksA	ECOD (1.6)
C	zf-dskA_traR	e1tjlC2	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: zf-dskA_traR	ECOD (1.6)
B	dksA	e1tjlB1	A: alpha bundles	X: Long alpha-hairpin	H: DnaK suppressor protein DksA, alpha-hairpin domain (From Topology)	T: DnaK suppressor protein DksA, alpha-hairpin domain	F: dksA	ECOD (1.6)
B	zf-dskA_traR	e1tjlB2	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: zf-dskA_traR	ECOD (1.6)
A	dksA	e1tjlA1	A: alpha bundles	X: Long alpha-hairpin	H: DnaK suppressor protein DksA, alpha-hairpin domain (From Topology)	T: DnaK suppressor protein DksA, alpha-hairpin domain	F: dksA	ECOD (1.6)
A	zf-dskA_traR	e1tjlA2	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: zf-dskA_traR	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
J	1.20.120.910	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	DksA, coiled-coil domain	CATH (4.3.0)
I	1.20.120.910	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	DksA, coiled-coil domain	CATH (4.3.0)
H	1.20.120.910	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	DksA, coiled-coil domain	CATH (4.3.0)
G	1.20.120.910	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	DksA, coiled-coil domain	CATH (4.3.0)
F	1.20.120.910	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	DksA, coiled-coil domain	CATH (4.3.0)
E	1.20.120.910	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	DksA, coiled-coil domain	CATH (4.3.0)
D	1.20.120.910	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	DksA, coiled-coil domain	CATH (4.3.0)
C	1.20.120.910	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	DksA, coiled-coil domain	CATH (4.3.0)
B	1.20.120.910	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	DksA, coiled-coil domain	CATH (4.3.0)
A	1.20.120.910	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	DksA, coiled-coil domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	PF21157	DnaK suppressor protein DksA, N-terminal domain (DksA_N)	DnaK suppressor protein DksA, N-terminal domain	DksA is a transcription factor that directly binds RNA polymerase and controls the bacteria response to stress and starvation. DksA is all helical and comprises a coiled-coil (CC) and globular domains [1-4]. This is the N-terminal domain which extend ...	DksA is a transcription factor that directly binds RNA polymerase and controls the bacteria response to stress and starvation. DksA is all helical and comprises a coiled-coil (CC) and globular domains [1-4]. This is the N-terminal domain which extends through the secondary channel toward the RNAP active site and serves as a conduit for the substrate NTPs. This domain consists of two helices arranged in an antiparallel alpha-hairpin with left-handed twist.	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	PF01258	Prokaryotic dksA/traR C4-type zinc finger (zf-dskA_traR)	Prokaryotic dksA/traR C4-type zinc finger	This domain is found in the members of the DksA/TraR family. It adopts a treble clef fold [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	DnaK suppressor protein	guanosine tetraphosphate binding guanyl nucleotide binding binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding guanosine tetraphosphate binding guanyl nucleotide binding binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cation binding transition metal ion binding zinc ion binding metal ion binding	cellular response to stimulus double-strand break repair response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair cellular response to stimulus double-strand break repair response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair regulation of cellular process RNA metabolic process regulation of primary metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR020458	Zinc finger, DksA/TraR C4-type conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR037187	DksA, N-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR000962	Zinc finger, DksA/TraR C4-type	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR020460	Zinc finger, DksA/TraR C4-type, bacteria	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR048489	DnaK suppressor protein DksA, N-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR012784	RNA polymerase-binding transcription factor DksA	Family