Annotations: 4XRP

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	PNKP ligase-like	8045746	4004657	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	DNA ligase/mRNA capping enzyme catalytic domain	8091701	3000798	SCOP2 (2022-06-29)
E	SCOP2B Superfamily	DNA ligase/mRNA capping enzyme catalytic domain	8091701	3000798	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	AAA_33	e4xrpA2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_33	ECOD (1.6)
A	PNK3P	e4xrpA1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: PNK3P	ECOD (1.6)
D	AAA_33	e4xrpD1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_33	ECOD (1.6)
D	PNK3P	e4xrpD2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: PNK3P	ECOD (1.6)
B	PNKP_ligase	e4xrpB1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: PNKP_ligase	ECOD (1.6)
E	PNKP_ligase	e4xrpE1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: PNKP_ligase	ECOD (1.6)
C	EUF08395	e4xrpC1	A: a+b two layers	X: Glutamine synthetase-like	H: Methyltransferase type 12 N-terminal domain (From Topology)	T: Methyltransferase type 12 N-terminal domain	F: EUF08395	ECOD (1.6)
C	Methyltransf_11_6	e4xrpC2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_11_6	ECOD (1.6)
F	EUF08395	e4xrpF1	A: a+b two layers	X: Glutamine synthetase-like	H: Methyltransferase type 12 N-terminal domain (From Topology)	T: Methyltransferase type 12 N-terminal domain	F: EUF08395	ECOD (1.6)
F	Methyltransf_11_6	e4xrpF2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_11_6	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D	PF13671	AAA domain (AAA_33)	AAA domain	This family of domains contain only a P-loop motif, that is characteristic of the AAA superfamily. Many of the proteins in this family are just short fragments so there is no Walker B motif.	Domain
B, E	PF16542	PNKP adenylyltransferase domain, ligase domain (PNKP_ligase)	PNKP adenylyltransferase domain, ligase domain	PNKP_ligase is a classical ligase nucleotidyltransferase module of bacteria. PNKP (polynucleotide 5'-kinase/3'-phosphatase) is the end-healing and end-sealing component of an RNA-repair system present in diverse bacteria from ten different phyla. RNA ...	PNKP_ligase is a classical ligase nucleotidyltransferase module of bacteria. PNKP (polynucleotide 5'-kinase/3'-phosphatase) is the end-healing and end-sealing component of an RNA-repair system present in diverse bacteria from ten different phyla. RNA breakage by site-specific 'ribotoxins' is an ancient mechanism by which microbes respond to cellular stress and distinguish self from non-self. Ribotoxins are trans-esterifying endonucleases that generate 5'-OH and 2',3' cyclic phosphate termini. Repair of this type of RNA damage is feasible via sequential enzymatic end-healing and end-sealing steps [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D	Pnkp1	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding phosphoric ester hydrolase activity deoxynucleotide 3'-phosphatase activity hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity catalytic activity cation binding metal ion binding	-	-
B, E	Rnl	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding	-	-
C, F	Hen1	RNA methyltransferase activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid transferase activity methyltransferase activity catalytic activity O-methyltransferase activity cation binding ion binding binding metal ion binding small molecule binding	cellular metabolic process RNA metabolic process cellular nitrogen compound metabolic process primary metabolic process nucleic acid metabolic process macromolecule methylation nucleobase-containing compound metabolic process organic cyclic compound metabolic process RNA modification organic substance metabolic process heterocycle metabolic process methylation macromolecule modification nitrogen compound metabolic process cellular metabolic process RNA metabolic process cellular nitrogen compound metabolic process primary metabolic process nucleic acid metabolic process macromolecule methylation nucleobase-containing compound metabolic process organic cyclic compound metabolic process RNA modification organic substance metabolic process heterocycle metabolic process methylation macromolecule modification nitrogen compound metabolic process metabolic process cellular process macromolecule metabolic process RNA methylation cellular aromatic compound metabolic process regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process organic substance biosynthetic process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulatory ncRNA-mediated gene silencing regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D	IPR044493	Polynucleotide kinase PNKP, C-terminal phosphatase domain	Domain
A, D	IPR036412	HAD-like superfamily	Homologous Superfamily
A, D	IPR023214	HAD superfamily	Homologous Superfamily
A, D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B, E	IPR032380	Polynucleotide kinase-phosphatase, ligase domain	Domain
C, F	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
C, F	IPR026610	3'-RNA ribose 2'-O-methyltransferase, Hen1	Family

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.