2P5T | pdb_00002p5t

Molecular and structural characterization of the PezAT chromosomal toxin-antitoxin system of the human pathogen Streptococcus pneumoniae

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)
I [auth H]	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8056333	3002021	SCOP2B (2022-06-29)
G [auth F]	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8056333	3002021	SCOP2B (2022-06-29)
E [auth D]	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8056333	3002021	SCOP2B (2022-06-29)
C [auth B]	SCOP2 Family	Zeta toxin-like	8056332	4003002	SCOP2 (2022-06-29)
C [auth B]	SCOP2 Superfamily	P-loop nucleotide/nucleoside kinase-like	8056333	3002021	SCOP2 (2022-06-29)
H [auth G]	SCOP2B Superfamily	epsilon antitoxin-like	8056334	3001049	SCOP2B (2022-06-29)
F [auth E]	SCOP2B Superfamily	epsilon antitoxin-like	8056334	3001049	SCOP2B (2022-06-29)
D [auth C]	SCOP2B Superfamily	epsilon antitoxin-like	8056334	3001049	SCOP2B (2022-06-29)
B [auth A]	SCOP2 Family	epsilon antitoxin-like	8019195	4002284	SCOP2 (2022-06-29)
B [auth A]	SCOP2 Superfamily	epsilon antitoxin-like	8056334	3001049	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)
I [auth H]	Biopterin_H	e2p5tH1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Biopterin_H	ECOD (v294.1)
G [auth F]	Biopterin_H	e2p5tF1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Biopterin_H	ECOD (v294.1)
E [auth D]	Biopterin_H	e2p5tD1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Biopterin_H	ECOD (v294.1)
C [auth B]	SoxZ	e2p5tB1	A: a/b three-layered sandwiches	X: Profilin-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: SoxZ	ECOD (v294.1)
H [auth G]	Biopterin_H	e2p5tG1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Biopterin_H	ECOD (v294.1)
F [auth E]	Biopterin_H	e2p5tE1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Biopterin_H	ECOD (v294.1)
D [auth C]	Biopterin_H	e2p5tC1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Biopterin_H	ECOD (v294.1)
B [auth A]	TetR_C_21	e2p5tA1	A: a/b three-layered sandwiches	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases	T: Metallo-dependent phosphatases	F: TetR_C_21	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
I [auth H]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
G [auth F]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
E [auth D]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C [auth B]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
H [auth G]	1.10.8.130	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
F [auth E]	1.10.8.130	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
D [auth C]	1.10.8.130	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
B [auth A]	1.10.8.130	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth B], E [auth D], G [auth F], I [auth H]	PF06414	Zeta toxin (Zeta_toxin)	Zeta toxin	This family consists of several bacterial zeta toxin proteins. Zeta toxin is thought to be part of a postregulational killing system in bacteria. It relies on antitoxin/toxin systems that secure stable inheritance of low and medium copy number plasmi ...	This family consists of several bacterial zeta toxin proteins. Zeta toxin is thought to be part of a postregulational killing system in bacteria. It relies on antitoxin/toxin systems that secure stable inheritance of low and medium copy number plasmids during cell division and kill cells that have lost the plasmid [1].	Domain
B [auth A], D [auth C], F [auth E], H [auth G]	PF08998	Bacterial epsilon antitoxin (Epsilon_antitox)	Bacterial epsilon antitoxin	The epsilon antitoxin, produced by various prokaryotes, forms part of a postsegregational killing system which is involved in the initiation of programmed cell death of plasmid-free cells. The protein is folded into a three-helix bundle that directly ...	The epsilon antitoxin, produced by various prokaryotes, forms part of a postsegregational killing system which is involved in the initiation of programmed cell death of plasmid-free cells. The protein is folded into a three-helix bundle that directly interacts with the zeta toxin, inactivating it [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth B], E [auth D], G [auth F], I [auth H]	PezT	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 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 kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	-	-
B [auth A], D [auth C], F [auth E], H [auth G]	Putative transcriptional regulator PezA	DNA binding binding nucleic acid binding toxic substance binding	response to stimulus response to chemical response to toxic substance regulation of biological process regulation of cellular process biological regulation negative regulation of cellular process negative regulation of biological process regulation of cell killing cellular process negative regulation of cell killing cell killing	-
A [auth X]	fragment of PezA helix-turn-helix motif	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth B], E [auth D], G [auth F], I [auth H]	IPR048180	Toxin PezT	Family
C [auth B], E [auth D], G [auth F], I [auth H]	IPR010488	Zeta toxin domain	Domain
C [auth B], E [auth D], G [auth F], I [auth H]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B [auth A], D [auth C], F [auth E], H [auth G]	IPR035569	Antitoxin epsilon/PezA domain superfamily	Homologous Superfamily
B [auth A], D [auth C], F [auth E], H [auth G]	IPR001387	Cro/C1-type, helix-turn-helix domain	Domain
B [auth A], D [auth C], F [auth E], H [auth G]	IPR048181	Antitoxin PezA	Family
B [auth A], D [auth C], F [auth E], H [auth G]	IPR015090	Antitoxin epsilon/PezA domain	Domain
B [auth A], D [auth C], F [auth E], H [auth G]	IPR010982	Lambda repressor-like, DNA-binding domain superfamily	Homologous Superfamily

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.