4DRF

Crystal Structure of Bacterial Pnkp-C/Hen1-N Heterodimer

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)
A	SCOP2B Superfamily	DNA ligase/mRNA capping enzyme, catalytic domain	8045735	3000798	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DNA ligase/mRNA capping enzyme, catalytic domain	8045735	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	PNKP_ligase	e4drfA2	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	PNKP_ligase	e4drfC2	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)
B	Hen1_L	e4drfB1	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: Hen1_L	ECOD (1.6)
D	Hen1_L	e4drfD1	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: Hen1_L	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.470.30	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
A	6.10.140.1010	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
C	3.30.470.30	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
C	6.10.140.1010	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
B	3.30.1610.20	Alpha Beta	2-Layer Sandwich	c-terminal autoproteolytic domain of nucleoporin nup98	Hen1, N-terminal domain	CATH (4.3.0)
D	3.30.1610.20	Alpha Beta	2-Layer Sandwich	c-terminal autoproteolytic domain of nucleoporin nup98	Hen1, N-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	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
B, D	PF12623	RNA repair, ligase-Pnkp-associating, region of Hen1 (Hen1_L)	RNA repair, ligase-Pnkp-associating, region of Hen1	This domain is the N-terminal region of the bacterial Hen1 protein. This protein forms stable hetero-tetramer with Pnkp. The hetero-tetramer was able to repair transfer RNAs cleaved by ribotoxins in vitro [1]. This domain provides the ligase activit ...	This domain is the N-terminal region of the bacterial Hen1 protein. This protein forms stable hetero-tetramer with Pnkp. The hetero-tetramer was able to repair transfer RNAs cleaved by ribotoxins in vitro [1]. This domain provides the ligase activity of the hetero-tetramer.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	Metallophosphoesterase	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 hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity catalytic activity guanyl nucleotide binding GTP binding guanyl ribonucleotide binding cation binding metal ion binding	-	intracellular anatomical structure cytoplasm cellular anatomical entity
B, D	Methyltransferase type 12	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 identical protein binding 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 identical protein binding protein binding	RNA metabolic process primary metabolic process nucleic acid metabolic process macromolecule methylation nucleobase-containing compound metabolic process RNA modification methylation macromolecule modification metabolic process macromolecule metabolic process RNA methylation regulation of cellular process cellular biosynthetic process negative regulation of biological process RNA metabolic process primary metabolic process nucleic acid metabolic process macromolecule methylation nucleobase-containing compound metabolic process RNA modification methylation macromolecule modification metabolic process macromolecule metabolic process RNA methylation regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process cellular metabolic 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 cellular process regulation of metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR004843	Calcineurin-like phosphoesterase domain, ApaH type	Domain
A, C	IPR024028	Polynucleotide kinase-phosphatase, bacterial	Family
A, C	IPR041780	PrpE-like, metallophosphatase domain	Domain
A, C	IPR029052	Metallo-dependent phosphatase-like	Homologous Superfamily
A, C	IPR032380	Polynucleotide kinase-phosphatase, ligase domain	Domain
A, C	IPR006186	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase	Domain
A, C	IPR050126	Diadenosine polyphosphate hydrolase	Family
A, C	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B, D	IPR024026	3'-RNA ribose 2'-O-methyltransferase, Hen1, bacterial	Family
B, D	IPR013217	Methyltransferase type 12	Domain
B, D	IPR038546	Hen1, N-terminal domain superfamily	Homologous Superfamily
B, D	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
B, D	IPR026610	3'-RNA ribose 2'-O-methyltransferase, Hen1	Family
B, D	IPR024740	Hen1, 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.