3TY9 | pdb_00003ty9

Crystal Structure of C. Thermocellum PNKP Ligase Domain AMP-Adenylate

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)
B	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)
D	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	e3ty9A2	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	PNKP_ligase	e3ty9B2	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	e3ty9C2	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)
D	PNKP_ligase	e3ty9D2	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)

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)
B	3.30.470.30	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	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)
D	3.30.470.30	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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, B, C, D	Polynucleotide 2',3'-cyclic phosphate phosphodiesterase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase	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 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	-	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR004843	Calcineurin-like phosphoesterase domain, ApaH type	Domain
A, B, C, D	IPR024028	Polynucleotide kinase-phosphatase, bacterial	Family
A, B, C, D	IPR041780	PrpE-like, metallophosphatase domain	Domain
A, B, C, D	IPR029052	Metallo-dependent phosphatase-like	Homologous Superfamily
A, B, C, D	IPR032380	Polynucleotide kinase-phosphatase, ligase domain	Domain
A, B, C, D	IPR006186	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase	Domain
A, B, C, D	IPR050126	Diadenosine polyphosphate hydrolase	Family
A, B, C, D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	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.