6X0A

X-ray structure of a chimeric ParDE toxin-antitoxin complex from Mesorhizobium opportunistum

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF05016	e6x0aA1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: PF05016	ECOD (1.6)
B	PF05016	e6x0aB1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: PF05016	ECOD (1.6)
C	PF05016	e6x0aC1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: PF05016	ECOD (1.6)
D	PF05016	e6x0aD1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: PF05016	ECOD (1.6)
E	PF05016	e6x0aE1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: PF05016	ECOD (1.6)
F	PF05016	e6x0aF1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: PF05016	ECOD (1.6)
G	PF05016	e6x0aG1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: PF05016	ECOD (1.6)
H	PF05016	e6x0aH1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: PF05016	ECOD (1.6)
I	PF05016	e6x0aI1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: PF05016	ECOD (1.6)
J	PF05016	e6x0aJ1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: PF05016	ECOD (1.6)
K	PF05016	e6x0aK1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: PF05016	ECOD (1.6)
L	PF05016	e6x0aL1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: PF05016	ECOD (1.6)
M	PF05016	e6x0aM1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: PF05016	ECOD (1.6)
N	PF05016	e6x0aN1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: PF05016	ECOD (1.6)
O	PF05016	e6x0aO1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: PF05016	ECOD (1.6)
P	PF05016	e6x0aP1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: PF05016	ECOD (1.6)
Q	PF05016	e6x0aQ1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: PF05016	ECOD (1.6)
R	PF05016	e6x0aR1	A: a+b two layers	X: RelE-like	H: RelE-like (From Topology)	T: RelE-like	F: PF05016	ECOD (1.6)
AA [auth i]	PF03693	e6x0ai1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: PF03693	ECOD (1.6)
BA [auth j]	PF03693	e6x0aj1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: PF03693	ECOD (1.6)
CA [auth k]	PF03693	e6x0ak1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: PF03693	ECOD (1.6)
DA [auth l]	PF03693	e6x0al1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: PF03693	ECOD (1.6)
EA [auth m]	PF03693	e6x0am1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: PF03693	ECOD (1.6)
FA [auth n]	PF03693	e6x0an1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: PF03693	ECOD (1.6)
GA [auth o]	PF03693	e6x0ao1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: PF03693	ECOD (1.6)
HA [auth p]	PF03693	e6x0ap1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: PF03693	ECOD (1.6)
IA [auth q]	PF03693	e6x0aq1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: PF03693	ECOD (1.6)
JA [auth r]	PF03693	e6x0ar1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: PF03693	ECOD (1.6)
S [auth a]	PF03693	e6x0aa1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: PF03693	ECOD (1.6)
T [auth b]	PF03693	e6x0ab1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: PF03693	ECOD (1.6)
U [auth c]	PF03693	e6x0ac1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: PF03693	ECOD (1.6)
V [auth d]	PF03693	e6x0ad1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: PF03693	ECOD (1.6)
W [auth e]	PF03693	e6x0ae1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: PF03693	ECOD (1.6)
X [auth f]	PF03693	e6x0af1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: PF03693	ECOD (1.6)
Y [auth g]	PF03693	e6x0ag1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: PF03693	ECOD (1.6)
Z [auth h]	PF03693	e6x0ah1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: PF03693	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	PF05016	ParE toxin of type II toxin-antitoxin system, parDE (ParE_toxin)	ParE toxin of type II toxin-antitoxin system, parDE	ParE is the toxin family of a type II toxin-antitoxin family. It is toxic towards DNA gyrase, but is neutralised by the antitoxin ParD. The family also encompasses RelE/ParE described in [2].	Domain
AA [auth i], BA [auth j], CA [auth k], DA [auth l], EA [auth m], AA [auth i], BA [auth j], CA [auth k], DA [auth l], EA [auth m], FA [auth n], GA [auth o], HA [auth p], IA [auth q], JA [auth r], S [auth a], T [auth b], U [auth c], V [auth d], W [auth e], X [auth f], Y [auth g], Z [auth h]	PF03693	Bacterial antitoxin of ParD toxin-antitoxin type II system and RHH (ParD_antitoxin)	Bacterial antitoxin of ParD toxin-antitoxin type II system and RHH	ParD is the antitoxin of a bacterial toxin-antitoxin gene pair. The cognate toxin is ParE in, Pfam:PF05016. The family contains several related antitoxins from Cyanobacteria, Proteobacteria and Actinobacteria. Antitoxins of this class carry an N-ter ...	ParD is the antitoxin of a bacterial toxin-antitoxin gene pair. The cognate toxin is ParE in, Pfam:PF05016. The family contains several related antitoxins from Cyanobacteria, Proteobacteria and Actinobacteria. Antitoxins of this class carry an N-terminal ribbon-helix-helix domain, RHH, that is highly conserved across all type II bacterial antitoxins, which dimerises with the RHH domain of a second VapB molecule. A hinge section follows the RHH, with an additional pair of flexible alpha helices at the C-terminus. This C-terminus is the toxin-binding region of the dimer, and so is specific to the cognate toxin, whereas the RHH domain has the specific function of lying across the RNA-binding groove of the toxin dimer and inactivating the active-site - a more general function of all type II antitoxins.	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, H, I, J, K, L, M, N, O, P, Q, R	Plasmid stabilization system	-	-	-
AA [auth i], BA [auth j], CA [auth k], DA [auth l], EA [auth m], AA [auth i], BA [auth j], CA [auth k], DA [auth l], EA [auth m], FA [auth n], GA [auth o], HA [auth p], IA [auth q], JA [auth r], S [auth a], T [auth b], U [auth c], V [auth d], W [auth e], X [auth f], Y [auth g], Z [auth h]	Putative addiction module antidote protein, CopG/Arc/MetJ family chimera	-	regulation of cellular process cellular biosynthetic 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 organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of cellular process cellular biosynthetic 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 organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process cellular metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process cellular 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, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	IPR007712	Toxin-antitoxin system, RelE/ParE toxin family	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	IPR035093	Toxin-antitoxin system, RelE/ParE toxin domain superfamily	Homologous Superfamily
AA [auth i], BA [auth j], CA [auth k], DA [auth l], EA [auth m], AA [auth i], BA [auth j], CA [auth k], DA [auth l], EA [auth m], FA [auth n], GA [auth o], HA [auth p], IA [auth q], JA [auth r], S [auth a], T [auth b], U [auth c], V [auth d], W [auth e], X [auth f], Y [auth g], Z [auth h]	IPR022789	Antitoxin ParD	Family
AA [auth i], BA [auth j], CA [auth k], DA [auth l], EA [auth m], AA [auth i], BA [auth j], CA [auth k], DA [auth l], EA [auth m], FA [auth n], GA [auth o], HA [auth p], IA [auth q], JA [auth r], S [auth a], T [auth b], U [auth c], V [auth d], W [auth e], X [auth f], Y [auth g], Z [auth h]	IPR038296	Antitoxin ParD superfamily	Homologous Superfamily
AA [auth i], BA [auth j], CA [auth k], DA [auth l], EA [auth m], AA [auth i], BA [auth j], CA [auth k], DA [auth l], EA [auth m], FA [auth n], GA [auth o], HA [auth p], IA [auth q], JA [auth r], S [auth a], T [auth b], U [auth c], V [auth d], W [auth e], X [auth f], Y [auth g], Z [auth h]	IPR010985	Ribbon-helix-helix	Homologous Superfamily
AA [auth i], BA [auth j], CA [auth k], DA [auth l], EA [auth m], AA [auth i], BA [auth j], CA [auth k], DA [auth l], EA [auth m], FA [auth n], GA [auth o], HA [auth p], IA [auth q], JA [auth r], S [auth a], T [auth b], U [auth c], V [auth d], W [auth e], X [auth f], Y [auth g], Z [auth h]	IPR022789	Antitoxin ParD	Family
AA [auth i], BA [auth j], CA [auth k], DA [auth l], EA [auth m], AA [auth i], BA [auth j], CA [auth k], DA [auth l], EA [auth m], FA [auth n], GA [auth o], HA [auth p], IA [auth q], JA [auth r], S [auth a], T [auth b], U [auth c], V [auth d], W [auth e], X [auth f], Y [auth g], Z [auth h]	IPR038296	Antitoxin ParD superfamily	Homologous Superfamily
AA [auth i], BA [auth j], CA [auth k], DA [auth l], EA [auth m], AA [auth i], BA [auth j], CA [auth k], DA [auth l], EA [auth m], FA [auth n], GA [auth o], HA [auth p], IA [auth q], JA [auth r], S [auth a], T [auth b], U [auth c], V [auth d], W [auth e], X [auth f], Y [auth g], Z [auth h]	IPR010985	Ribbon-helix-helix	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 R01GM133198.

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6X0A

X-ray structure of a chimeric ParDE toxin-antitoxin complex from Mesorhizobium opportunistum

External Resource: Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage