2HS5

Structural Genomics, the crystal structure of a putative transcriptional regulator GntR from Rhodococcus sp. RHA1

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)
A	d2hs5a1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	GntR-like transcriptional regulators	Putative transcriptional regulator RHA1_ro03477	(Rhodococcus jostii RHA1 ) [TaxId: 101510 ],	SCOPe (2.08)
A	d2hs5a2	All alpha proteins	GntR ligand-binding domain-like	GntR ligand-binding domain-like	GntR ligand-binding domain-like	Putative transcriptional regulator RHA1_ro03477	(Rhodococcus jostii RHA1 ) [TaxId: 101510 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	GntR-like transcriptional regulators	8002696	4000155	SCOP2 (2022-06-29)
A	SCOP2 Family	FadR effector domain-like	8002697	4000215	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Winged helix DNA-binding domain	8017669	3000034	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	FadR effector domain-like	8017667	3000064	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)
A	GntR	e2hs5A1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: GntR	ECOD (1.6)
A	FCD	e2hs5A2	A: alpha bundles	X: Fatty acid responsive transcription factor FadR, C-terminal domain (From Topology)	H: Fatty acid responsive transcription factor FadR, C-terminal domain (From Topology)	T: Fatty acid responsive transcription factor FadR, C-terminal domain	F: FCD	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	1.20.120.530	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	GntR ligand-binding domain-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF07729	FCD domain (FCD)	FCD domain	This domain is the C-terminal ligand binding domain of many members of the GntR family. This domain binds to a range of effector molecules, including Lactate, Zn(II), Ni(II), Ca(II), Mg(II), citrate, sugar acids, sialic acid and N-acetylglucosamine-6 ...	This domain is the C-terminal ligand binding domain of many members of the GntR family. This domain binds to a range of effector molecules, including Lactate, Zn(II), Ni(II), Ca(II), Mg(II), citrate, sugar acids, sialic acid and N-acetylglucosamine-6-P, that regulate the transcription of genes through the action of the N-terminal DNA-binding domain Pfam:PF00392 (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). This domain is found in Swiss:P45427 and Swiss:P31460 that are regulators of sugar biosynthesis operons. It is also in the known structure of FadR where it binds to acyl-coA, the domain is alpha helical [1]. This family has been named as FCD for (FadR C-terminal Domain).	Domain
A	PF00392	Bacterial regulatory proteins, gntR family (GntR)	Bacterial regulatory proteins, gntR family	This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector-binding/oligomerisation domain. The GntR-like proteins include the following sub-fam ...	This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector-binding/oligomerisation domain. The GntR-like proteins include the following sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA, DevA, DasR [1-2][4][5]. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships [3]. The DasR regulator has been shown to be a global regulator of primary metabolism and development in Streptomyces coelicolor [5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	putative transcriptional regulator GntR	DNA binding binding nucleic acid binding transcription regulator activity DNA-binding transcription factor activity	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A	IPR008920	Transcription regulator FadR/GntR, C-terminal	Homologous Superfamily
A	IPR000524	Transcription regulator HTH, GntR	Domain
A	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
A	IPR011711	GntR, C-terminal	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.