2C5U

T4 RNA Ligase (Rnl1) Crystal Structure

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	SCOP2 Family	Rnl1-like	8045001	4004248	SCOP2 (2022-06-29)
A	SCOP2 Family	Rnl1 C-terminal domain-like	8054022	4007625	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	DNA ligase/mRNA capping enzyme, catalytic domain	8054021	3000798	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Rnl1 C-terminal domain-like	8054023	3002266	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Rnl1 C-terminal domain-like	8054023	3002266	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DNA ligase/mRNA capping enzyme, catalytic domain	8054021	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	rnlA	e2c5uA2	A: alpha arrays	X: T4 RNA ligase (From Homology)	H: T4 RNA ligase	T: T4 RNA ligase (Rnl1) C-terminal domain	F: rnlA	ECOD (1.6)
A	RNA_lig_T4_1	e2c5uA1	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: RNA_lig_T4_1	ECOD (1.6)
B	rnlA	e2c5uB2	A: alpha arrays	X: T4 RNA ligase (From Homology)	H: T4 RNA ligase	T: T4 RNA ligase (Rnl1) C-terminal domain	F: rnlA	ECOD (1.6)
B	RNA_lig_T4_1	e2c5uB1	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: RNA_lig_T4_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.3550.20	Mainly Alpha	Orthogonal Bundle	eoxyguanosinetriphosphate triphosphohydrolase fold		CATH (4.3.0)
B	1.10.3550.20	Mainly Alpha	Orthogonal Bundle	eoxyguanosinetriphosphate triphosphohydrolase fold		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF20819	T4 RNA ligase 1, C-terminal domain (T4_Rnl1_C)	T4 RNA ligase 1, C-terminal domain	This domain is found at the C-terminal end of T4 RNA ligase 1 (Rnl1) from Bacteriophage T4 and similar proteins from tailed bacteriophages. Rnl1 is involved in countering a host defense mechanism by repairing tRNA. The C-terminal domain shows an all ...	This domain is found at the C-terminal end of T4 RNA ligase 1 (Rnl1) from Bacteriophage T4 and similar proteins from tailed bacteriophages. Rnl1 is involved in countering a host defense mechanism by repairing tRNA. The C-terminal domain shows an all alpha-helical fold and has a charge distribution and architecture for helix-nucleic acid groove interaction compatible with tRNA binding. It confers specificity for the repair of tRNAs with breaks in the anticodon loop [1,2].	Domain
A, B	PF09511	RNA ligase (RNA_lig_T4_1)	RNA ligase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	RNA LIGASE	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 ligase activity, forming phosphoric ester bonds RNA ligase (ATP) activity catalytic activity, acting on RNA RNA ligase activity catalytic activity, acting on a nucleic acid catalytic activity ligase activity cation binding metal ion binding	virion assembly viral tail assembly virus tail fiber assembly viral process viral life cycle nucleobase-containing compound metabolic process RNA metabolic process metabolic process cellular process primary metabolic process macromolecule metabolic process RNA repair nucleic acid metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR012648	T4 RNA ligase 1	Family
A, B	IPR049042	T4 RNA ligase 1, C-terminal domain	Domain
A, B	IPR019039	T4 RNA ligase 1-like, 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.