3C1Y | pdb_00003c1y

Structure of bacterial DNA damage sensor protein with co-purified and co-crystallized ligand

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	DisA linker domain-like	8045280	4004389	SCOP2 (2022-06-29)
B	SCOP2 Family	DacA-like	8089950	4003884	SCOP2 (2022-06-29)
B	SCOP2 Family	Hef domain-like	8089952	4001374	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	DisA linker domain-like	8089949	3002406	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	DacA-like	8089951	3001724	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Helix-hairpin-helix tandem	8089953	3000163	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	Helix-hairpin-helix tandem	8089953	3000163	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DisA linker domain-like	8089949	3002406	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DacA-like	8089951	3001724	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B		e3c1yB4	A: HTH	X: SH3	H: SH3	T: HHH	F:	ECOD (20:10:01)
B		e3c1yB1	A: Nat/Ivy	X: Acyl-CoA N-acyltransferases (Nat)	H: Acyl-CoA N-acyltransferases (Nat)	T: Glyco_hydro_32C	F:	ECOD (20:10:01)
A		e3c1yA1	A: DisA nucleotide-binding domain	X: DisA nucleotide-binding domain	H: DisA nucleotide-binding domain	T: DAC	F:	ECOD (20:10:01)
A		e3c1yA2	A: HUP domain-like	X: Duffy-binding-like domain, C-terminal subdomain	H: Duffy-binding-like domain, C-terminal subdomain	T: PFEMP	F:	ECOD (20:10:01)
A		e3c1yA3	A: Anticodon-binding domain of Class II aaRS	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T:	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.1700.10	Alpha Beta	3-Layer(aba) Sandwich	YojJ-like (1	DNA integrity scanning protein, DisA, N-terminal domain	CATH (4.3.0)
B	1.20.1260.110	Mainly Alpha	Up-down Bundle	Ferritin	DNA integrity scanning linker region	CATH (4.3.0)
B	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
A	3.40.1700.10	Alpha Beta	3-Layer(aba) Sandwich	YojJ-like (1	DNA integrity scanning protein, DisA, N-terminal domain	CATH (4.3.0)
A	1.20.1260.110	Mainly Alpha	Up-down Bundle	Ferritin	DNA integrity scanning linker region	CATH (4.3.0)
A	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00633	Helix-hairpin-helix motif (HHH)	Helix-hairpin-helix motif	-	Motif
A, B	PF10635	DisA bacterial checkpoint controller linker region (DisA-linker)	DisA bacterial checkpoint controller linker region	The DisA protein is a bacterial checkpoint protein that dimerises into an octameric complex. The protein consists of three distinct domains. the first, N-terminal region, from 1-145 is globular and is represented by family DisA_N, Pfam:PF02457; the n ...	The DisA protein is a bacterial checkpoint protein that dimerises into an octameric complex. The protein consists of three distinct domains. the first, N-terminal region, from 1-145 is globular and is represented by family DisA_N, Pfam:PF02457; the next 146-289 residues is this domain that consists of an elongated bundle of three alpha helices (alpha-6, alpha-10, and alpha-11), one side of which carries an additional three helices (alpha7-9), thus forming a spine like-linker between domains 1 and 3. The C-terminal residues of domain 3 are family HHH, Pfam:PF00633, the specific DNA-binding domain. The octameric complex thus has structurally linked nucleotide-binding and DNA-binding HhH domains and the nucleotide-binding domains are bound to a cyclic di-adenosine phosphate such that DisA is a specific di-adenylate cyclase. The di-adenylate cyclase activity is strongly suppressed by binding to branched DNA, but not to duplex or single-stranded DNA, suggesting a role for DisA as a monitor of the presence of stalled replication forks or recombination intermediates via DNA structure-modulated c-di-AMP synthesis [1].	Domain
A, B	PF02457	DisA bacterial checkpoint controller nucleotide-binding (DAC)	DisA bacterial checkpoint controller nucleotide-binding	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	DNA integrity scanning protein disA	catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid catalytic activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid catalytic activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding phosphorus-oxygen lyase activity cyclase activity lyase activity adenylate cyclase activity hydrolase activity diadenylate cyclase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups	cellular response to stimulus 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	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR023763	DNA integrity scanning protein, DisA	Family
A, B	IPR000445	Helix-hairpin-helix motif	Conserved Site
A, B	IPR018906	DNA integrity scanning, DisA, linker region	Domain
A, B	IPR038331	DisA, linker domain superfamily	Homologous Superfamily
A, B	IPR010994	RuvA domain 2-like	Homologous Superfamily
A, B	IPR050338	DNA integrity scanning protein DisA	Family
A, B	IPR036888	DNA integrity scanning protein, DisA, N-terminal domain superfamily	Homologous Superfamily
A, B	IPR003390	DNA integrity scanning protein, DisA, N-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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.