3OEI | pdb_00003oei

Crystal structure of Mycobacterium tuberculosis RelJK (Rv3357-Rv3358-RelBE3)

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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3oeia_	Alpha and beta proteins (a+b)	YefM-like	YefM-like	automated matches	automated matches	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
B	d3oeib_	Alpha and beta proteins (a+b)	YefM-like	YefM-like	automated matches	automated matches	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
I	d3oeii_	Alpha and beta proteins (a+b)	YefM-like	YefM-like	automated matches	automated matches	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
J	d3oeij_	Alpha and beta proteins (a+b)	YefM-like	YefM-like	automated matches	automated matches	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
M	d3oeim_	Alpha and beta proteins (a+b)	YefM-like	YefM-like	automated matches	automated matches	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
N	d3oein_	Alpha and beta proteins (a+b)	YefM-like	YefM-like	automated matches	automated matches	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
C	d3oeic1	Alpha and beta proteins (a+b)	RelE-like	RelE-like	automated matches	automated matches	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
C	d3oeic2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
D	d3oeid1	Alpha and beta proteins (a+b)	RelE-like	RelE-like	automated matches	automated matches	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
D	d3oeid2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
G	d3oeig_	Alpha and beta proteins (a+b)	RelE-like	RelE-like	automated matches	automated matches	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
H	d3oeih1	Alpha and beta proteins (a+b)	RelE-like	RelE-like	automated matches	automated matches	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
H	d3oeih2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
K	d3oeik_	Alpha and beta proteins (a+b)	RelE-like	RelE-like	automated matches	automated matches	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
L	d3oeil_	Alpha and beta proteins (a+b)	RelE-like	RelE-like	automated matches	automated matches	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
O	d3oeio_	Alpha and beta proteins (a+b)	RelE-like	RelE-like	automated matches	automated matches	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
P	d3oeip_	Alpha and beta proteins (a+b)	RelE-like	RelE-like	automated matches	automated matches	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
E	d3oeie_	Alpha and beta proteins (a+b)	YefM-like	YefM-like	automated matches	automated matches	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
F	d3oeif_	Alpha and beta proteins (a+b)	YefM-like	YefM-like	automated matches	automated matches	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	YefM-like	8082985	3000907	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	YefM-like	8082985	3000907	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	YefM-like	8082985	3000907	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	YefM-like	8082985	3000907	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	YefM-like	8082985	3000907	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	YefM-like	8082985	3000907	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RelE-like	8082989	3000741	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RelE-like	8082989	3000741	SCOP2B (2022-06-29)
G	SCOP2 Family	YoeB/Txe-like	8082988	4003384	SCOP2 (2022-06-29)
G	SCOP2 Superfamily	RelE-like	8082989	3000741	SCOP2 (2022-06-29)
H	SCOP2B Superfamily	RelE-like	8082989	3000741	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	RelE-like	8082989	3000741	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	RelE-like	8082989	3000741	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	RelE-like	8082989	3000741	SCOP2B (2022-06-29)
P	SCOP2B Superfamily	RelE-like	8082989	3000741	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	YefM-like	8082985	3000907	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	YefM-like	8082985	3000907	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)
A	PhdYeFM_antitox	e3oeiA1	A: a+b duplicates or obligate multimers	X: YefM-like (From Topology)	H: YefM-like (From Topology)	T: YefM-like	F: PhdYeFM_antitox	ECOD (1.6)
B	PhdYeFM_antitox	e3oeiB1	A: a+b duplicates or obligate multimers	X: YefM-like (From Topology)	H: YefM-like (From Topology)	T: YefM-like	F: PhdYeFM_antitox	ECOD (1.6)
I	PhdYeFM_antitox	e3oeiI1	A: a+b duplicates or obligate multimers	X: YefM-like (From Topology)	H: YefM-like (From Topology)	T: YefM-like	F: PhdYeFM_antitox	ECOD (1.6)
J	PhdYeFM_antitox	e3oeiJ1	A: a+b duplicates or obligate multimers	X: YefM-like (From Topology)	H: YefM-like (From Topology)	T: YefM-like	F: PhdYeFM_antitox	ECOD (1.6)
M	PhdYeFM_antitox	e3oeiM1	A: a+b duplicates or obligate multimers	X: YefM-like (From Topology)	H: YefM-like (From Topology)	T: YefM-like	F: PhdYeFM_antitox	ECOD (1.6)
N	PhdYeFM_antitox	e3oeiN1	A: a+b duplicates or obligate multimers	X: YefM-like (From Topology)	H: YefM-like (From Topology)	T: YefM-like	F: PhdYeFM_antitox	ECOD (1.6)
C	YoeB_toxin	e3oeiC1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: YoeB_toxin	ECOD (1.6)
D	YoeB_toxin	e3oeiD1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: YoeB_toxin	ECOD (1.6)
G	YoeB_toxin	e3oeiG1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: YoeB_toxin	ECOD (1.6)
H	YoeB_toxin	e3oeiH1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: YoeB_toxin	ECOD (1.6)
K	YoeB_toxin	e3oeiK1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: YoeB_toxin	ECOD (1.6)
L	YoeB_toxin	e3oeiL1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: YoeB_toxin	ECOD (1.6)
O	YoeB_toxin	e3oeiO1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: YoeB_toxin	ECOD (1.6)
P	YoeB_toxin	e3oeiP1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: YoeB_toxin	ECOD (1.6)
E	PhdYeFM_antitox	e3oeiE1	A: a+b duplicates or obligate multimers	X: YefM-like (From Topology)	H: YefM-like (From Topology)	T: YefM-like	F: PhdYeFM_antitox	ECOD (1.6)
F	PhdYeFM_antitox	e3oeiF1	A: a+b duplicates or obligate multimers	X: YefM-like (From Topology)	H: YefM-like (From Topology)	T: YefM-like	F: PhdYeFM_antitox	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.1620.10	Alpha Beta	3-Layer(aba) Sandwich	YefM-like fold	YefM-like domain	CATH (4.3.0)
A	6.10.250.330	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
B	3.40.1620.10	Alpha Beta	3-Layer(aba) Sandwich	YefM-like fold	YefM-like domain	CATH (4.3.0)
B	6.10.250.330	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
I	3.40.1620.10	Alpha Beta	3-Layer(aba) Sandwich	YefM-like fold	YefM-like domain	CATH (4.3.0)
I	6.10.250.330	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
J	3.40.1620.10	Alpha Beta	3-Layer(aba) Sandwich	YefM-like fold	YefM-like domain	CATH (4.3.0)
J	6.10.250.330	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
M	3.40.1620.10	Alpha Beta	3-Layer(aba) Sandwich	YefM-like fold	YefM-like domain	CATH (4.3.0)
M	6.10.250.330	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
N	3.40.1620.10	Alpha Beta	3-Layer(aba) Sandwich	YefM-like fold	YefM-like domain	CATH (4.3.0)
N	6.10.250.330	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
C	3.30.2310.20	Alpha Beta	2-Layer Sandwich	YaeB-like fold	RelE-like	CATH (4.3.0)
D	3.30.2310.20	Alpha Beta	2-Layer Sandwich	YaeB-like fold	RelE-like	CATH (4.3.0)
G	3.30.2310.20	Alpha Beta	2-Layer Sandwich	YaeB-like fold	RelE-like	CATH (4.3.0)
H	3.30.2310.20	Alpha Beta	2-Layer Sandwich	YaeB-like fold	RelE-like	CATH (4.3.0)
K	3.30.2310.20	Alpha Beta	2-Layer Sandwich	YaeB-like fold	RelE-like	CATH (4.3.0)
L	3.30.2310.20	Alpha Beta	2-Layer Sandwich	YaeB-like fold	RelE-like	CATH (4.3.0)
O	3.30.2310.20	Alpha Beta	2-Layer Sandwich	YaeB-like fold	RelE-like	CATH (4.3.0)
P	3.30.2310.20	Alpha Beta	2-Layer Sandwich	YaeB-like fold	RelE-like	CATH (4.3.0)
E	3.40.1620.10	Alpha Beta	3-Layer(aba) Sandwich	YefM-like fold	YefM-like domain	CATH (4.3.0)
E	6.10.250.330	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
F	3.40.1620.10	Alpha Beta	3-Layer(aba) Sandwich	YefM-like fold	YefM-like domain	CATH (4.3.0)
F	6.10.250.330	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, I, J, M A, B, I, J, M, N	PF02604	Antitoxin Phd_YefM, type II toxin-antitoxin system (PhdYeFM_antitox)	Antitoxin Phd_YefM, type II toxin-antitoxin system	Members of this family act as antitoxins in type II toxin-antitoxin systems [1]. When bound to their toxin partners, they can bind DNA via the N-terminus and repress the expression of operons containing genes encoding the toxin and the antitoxin [2] ...	Members of this family act as antitoxins in type II toxin-antitoxin systems [1]. When bound to their toxin partners, they can bind DNA via the N-terminus and repress the expression of operons containing genes encoding the toxin and the antitoxin [2]. This domain complexes with Txe toxins containing Pfam:PF06769, Fic/DOC toxins containing Pfam:PF02661 and YafO toxins containing Pfam:PF13957.	Domain
C, D, G, H, K C, D, G, H, K, L, O, P	PF06769	YoeB-like toxin of bacterial type II toxin-antitoxin system (YoeB_toxin)	YoeB-like toxin of bacterial type II toxin-antitoxin system	YoeB_toxin is a family of bacterial toxins that forms one component of the type II toxin-antitoxin system in E. coli whose antitoxin is represented by YefM, found in Pfam:PF02604. The plasmid encoded Axe-Txe proteins in Enterococcus faecium act as a ...	YoeB_toxin is a family of bacterial toxins that forms one component of the type II toxin-antitoxin system in E. coli whose antitoxin is represented by YefM, found in Pfam:PF02604. The plasmid encoded Axe-Txe proteins in Enterococcus faecium act as an antitoxin-toxin pair. When the plasmid is lost, the antitoxin is degraded relatively quickly by host enzymes. This allows the toxin to interact with its intracellular target, thus killing the cell or impeding cell growth [1]. These toxins are highly potent protein synthesis inhibitors, specifically blocking the initiation of translation. In the case of YoeB, it binds to the 50 S ribosomal subunit in 70 S ribosomes and interacts with the A site leading to mRNA cleavage at this site. As a result, the 3'-end portion of the mRNA is released from ribosomes, and translation initiation is effectively inhibited [2,3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, I, J, M A, B, I, J, M, N	RelJ (Antitoxin Rv3357)	DNA binding binding nucleic acid binding	regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound 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 primary metabolic process regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound 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 primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process	-
C, D, G, H, K C, D, G, H, K, L, O, P	RelK (Toxin Rv3358)	DNA binding binding nucleic acid binding endonuclease activity nuclease activity hydrolase activity, acting on ester bonds hydrolase activity catalytic activity	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process catabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleic acid catabolic process RNA catabolic process	-
E, F	RelJ (Antitoxin Rv3357)	DNA binding binding nucleic acid binding	regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound 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 primary metabolic process regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound 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 primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, I, J, M A, B, I, J, M, N	IPR006442	Type II toxin-antitoxin system, antitoxin Phd/YefM	Family
A, B, I, J, M A, B, I, J, M, N	IPR051405	phD/YefM antitoxin	Family
A, B, I, J, M A, B, I, J, M, N	IPR036165	YefM-like superfamily	Homologous Superfamily
C, D, G, H, K C, D, G, H, K, L, O, P	IPR009614	Toxin YoeB	Family
C, D, G, H, K C, D, G, H, K, L, O, P	IPR035093	Toxin-antitoxin system, RelE/ParE toxin domain superfamily	Homologous Superfamily
E, F	IPR006442	Type II toxin-antitoxin system, antitoxin Phd/YefM	Family
E, F	IPR051405	phD/YefM antitoxin	Family
E, F	IPR036165	YefM-like superfamily	Homologous Superfamily