1XCB

X-ray Structure of a Rex-Family Repressor/NADH Complex from Thermus Aquaticus

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
A	d1xcba1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Transcriptional repressor Rex, N-terminal domain	Transcriptional repressor Rex, N-terminal domain	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
A	d1xcba2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Transcriptional repressor Rex, C-terminal domain	Transcriptional repressor Rex, C-terminal domain	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
B	d1xcbb1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Transcriptional repressor Rex, N-terminal domain	Transcriptional repressor Rex, N-terminal domain	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
B	d1xcbb2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Transcriptional repressor Rex, C-terminal domain	Transcriptional repressor Rex, C-terminal domain	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
C	d1xcbc1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Transcriptional repressor Rex, N-terminal domain	Transcriptional repressor Rex, N-terminal domain	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
C	d1xcbc2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Transcriptional repressor Rex, C-terminal domain	Transcriptional repressor Rex, C-terminal domain	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
D	d1xcbd1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Transcriptional repressor Rex, N-terminal domain	Transcriptional repressor Rex, N-terminal domain	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
D	d1xcbd2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Transcriptional repressor Rex, C-terminal domain	Transcriptional repressor Rex, C-terminal domain	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
E	d1xcbe1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Transcriptional repressor Rex, N-terminal domain	Transcriptional repressor Rex, N-terminal domain	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
E	d1xcbe2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Transcriptional repressor Rex, C-terminal domain	Transcriptional repressor Rex, C-terminal domain	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
F	d1xcbf1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Transcriptional repressor Rex, N-terminal domain	Transcriptional repressor Rex, N-terminal domain	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
F	d1xcbf2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Transcriptional repressor Rex, C-terminal domain	Transcriptional repressor Rex, C-terminal domain	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
G	d1xcbg1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Transcriptional repressor Rex, N-terminal domain	Transcriptional repressor Rex, N-terminal domain	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
G	d1xcbg2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Transcriptional repressor Rex, C-terminal domain	Transcriptional repressor Rex, C-terminal domain	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Put_DNA-bind_N	e1xcbA1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Put_DNA-bind_N	ECOD (1.6)
A	CoA_binding_1	e1xcbA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: CoA_binding_1	ECOD (1.6)
B	Put_DNA-bind_N	e1xcbB1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Put_DNA-bind_N	ECOD (1.6)
B	CoA_binding_1	e1xcbB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: CoA_binding_1	ECOD (1.6)
C	Put_DNA-bind_N	e1xcbC1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Put_DNA-bind_N	ECOD (1.6)
C	CoA_binding_1	e1xcbC2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: CoA_binding_1	ECOD (1.6)
D	Put_DNA-bind_N	e1xcbD1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Put_DNA-bind_N	ECOD (1.6)
D	CoA_binding_1	e1xcbD2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: CoA_binding_1	ECOD (1.6)
E	Put_DNA-bind_N	e1xcbE1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Put_DNA-bind_N	ECOD (1.6)
E	CoA_binding_1	e1xcbE2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: CoA_binding_1	ECOD (1.6)
F	Put_DNA-bind_N	e1xcbF1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Put_DNA-bind_N	ECOD (1.6)
F	CoA_binding_1	e1xcbF2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: CoA_binding_1	ECOD (1.6)
G	Put_DNA-bind_N	e1xcbG1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Put_DNA-bind_N	ECOD (1.6)
G	CoA_binding_1	e1xcbG2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: CoA_binding_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
C	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
C	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
D	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
D	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
E	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
E	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
F	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
F	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
G	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
G	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like 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	PF06971	Putative DNA-binding protein N-terminus (Put_DNA-bind_N)	Putative DNA-binding protein N-terminus	-	Family
A, B, C, D, E A, B, C, D, E, F, G	PF02629	CoA binding domain (CoA_binding)	CoA binding domain	This domain has a Rossmann fold and is found in a number of proteins including succinyl CoA synthetases, malate and ATP-citrate ligases.	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	Redox-sensing transcriptional repressor rex	DNA binding binding organic cyclic compound binding nucleic acid binding transcription regulator activity DNA-binding transcription factor activity identical protein binding protein binding	regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process cellular process response to stimulus response to redox state	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G	IPR009718	Rex DNA-binding, C-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F, G	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G	IPR022876	Redox-sensing transcriptional repressor Rex	Family
A, B, C, D, E A, B, C, D, E, F, G	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G	IPR003781	CoA-binding	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.