4X4N | pdb_00004x4n

Crystal structure of the A.fulgidus CCA-adding enzyme in complex with a G70A arginyl-tRNA minihelix

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	PAP/OAS1 substrate-binding domain-like	8040432	3000941	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PAP/Archaeal CCA-adding enzyme C-terminal domain-like	8040438	3001147	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleotidyltransferase-like	8040434	3000129	SCOP2B (2022-06-29)
D [auth C]	SCOP2B Superfamily	PAP/OAS1 substrate-binding domain-like	8040432	3000941	SCOP2B (2022-06-29)
D [auth C]	SCOP2B Superfamily	Nucleotidyltransferase-like	8040434	3000129	SCOP2B (2022-06-29)
D [auth C]	SCOP2B Superfamily	PAP/Archaeal CCA-adding enzyme C-terminal domain-like	8040438	3001147	SCOP2B (2022-06-29)
F [auth E]	SCOP2B Superfamily	PAP/Archaeal CCA-adding enzyme C-terminal domain-like	8040438	3001147	SCOP2B (2022-06-29)
F [auth E]	SCOP2B Superfamily	Nucleotidyltransferase-like	8040434	3000129	SCOP2B (2022-06-29)
F [auth E]	SCOP2B Superfamily	PAP/OAS1 substrate-binding domain-like	8040432	3000941	SCOP2B (2022-06-29)
G [auth F]	SCOP2B Superfamily	PAP/Archaeal CCA-adding enzyme C-terminal domain-like	8040438	3001147	SCOP2B (2022-06-29)
G [auth F]	SCOP2B Superfamily	Nucleotidyltransferase-like	8040434	3000129	SCOP2B (2022-06-29)
G [auth F]	SCOP2B Superfamily	PAP/OAS1 substrate-binding domain-like	8040432	3000941	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	tRNA_NucTransf2	e4x4nA1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: PAP/OAS1 substrate-binding domain	F: tRNA_NucTransf2	ECOD (1.6)
A	PRK13300	e4x4nA2	A: a+b two layers	X: Alpha-beta plaits	H: PAP/Archaeal CCA-adding enzyme, C-terminal domain (From Topology)	T: PAP/Archaeal CCA-adding enzyme, C-terminal domain	F: PRK13300	ECOD (1.6)
A	NTP_transf_2	e4x4nA3	A: a+b three layers	X: Nucleotidyltransferase-like	H: Nucleotidyltransferase (From Topology)	T: Nucleotidyltransferase	F: NTP_transf_2	ECOD (1.6)
D [auth C]	tRNA_NucTransf2	e4x4nC3	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: PAP/OAS1 substrate-binding domain	F: tRNA_NucTransf2	ECOD (1.6)
D [auth C]	PRK13300	e4x4nC1	A: a+b two layers	X: Alpha-beta plaits	H: PAP/Archaeal CCA-adding enzyme, C-terminal domain (From Topology)	T: PAP/Archaeal CCA-adding enzyme, C-terminal domain	F: PRK13300	ECOD (1.6)
D [auth C]	NTP_transf_2	e4x4nC2	A: a+b three layers	X: Nucleotidyltransferase-like	H: Nucleotidyltransferase (From Topology)	T: Nucleotidyltransferase	F: NTP_transf_2	ECOD (1.6)
F [auth E]	tRNA_NucTransf2	e4x4nE1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: PAP/OAS1 substrate-binding domain	F: tRNA_NucTransf2	ECOD (1.6)
F [auth E]	PRK13300	e4x4nE2	A: a+b two layers	X: Alpha-beta plaits	H: PAP/Archaeal CCA-adding enzyme, C-terminal domain (From Topology)	T: PAP/Archaeal CCA-adding enzyme, C-terminal domain	F: PRK13300	ECOD (1.6)
F [auth E]	NTP_transf_2	e4x4nE3	A: a+b three layers	X: Nucleotidyltransferase-like	H: Nucleotidyltransferase (From Topology)	T: Nucleotidyltransferase	F: NTP_transf_2	ECOD (1.6)
G [auth F]	tRNA_NucTransf2	e4x4nF1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: PAP/OAS1 substrate-binding domain	F: tRNA_NucTransf2	ECOD (1.6)
G [auth F]	PRK13300	e4x4nF3	A: a+b two layers	X: Alpha-beta plaits	H: PAP/Archaeal CCA-adding enzyme, C-terminal domain (From Topology)	T: PAP/Archaeal CCA-adding enzyme, C-terminal domain	F: PRK13300	ECOD (1.6)
G [auth F]	NTP_transf_2	e4x4nF2	A: a+b three layers	X: Nucleotidyltransferase-like	H: Nucleotidyltransferase (From Topology)	T: Nucleotidyltransferase	F: NTP_transf_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.1410.30	Mainly Alpha	Orthogonal Bundle	Poly(a)-polymerase, middle domain	CCA tRNA nucleotidyltransferase, domain 2	CATH (4.3.0)
A	3.30.460.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (4.3.0)
A	3.30.70.590	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Poly(A) polymerase predicted RNA binding domain	CATH (4.3.0)
A	3.30.70.1550	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Archaeal tRNA CCA-adding enzyme catalytic domain	CATH (4.3.0)
D [auth C]	1.10.1410.30	Mainly Alpha	Orthogonal Bundle	Poly(a)-polymerase, middle domain	CCA tRNA nucleotidyltransferase, domain 2	CATH (4.3.0)
D [auth C]	3.30.460.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (4.3.0)
D [auth C]	3.30.70.590	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Poly(A) polymerase predicted RNA binding domain	CATH (4.3.0)
D [auth C]	3.30.70.1550	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Archaeal tRNA CCA-adding enzyme catalytic domain	CATH (4.3.0)
F [auth E]	1.10.1410.30	Mainly Alpha	Orthogonal Bundle	Poly(a)-polymerase, middle domain	CCA tRNA nucleotidyltransferase, domain 2	CATH (4.3.0)
F [auth E]	3.30.460.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (4.3.0)
F [auth E]	3.30.70.590	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Poly(A) polymerase predicted RNA binding domain	CATH (4.3.0)
F [auth E]	3.30.70.1550	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Archaeal tRNA CCA-adding enzyme catalytic domain	CATH (4.3.0)
G [auth F]	1.10.1410.30	Mainly Alpha	Orthogonal Bundle	Poly(a)-polymerase, middle domain	CCA tRNA nucleotidyltransferase, domain 2	CATH (4.3.0)
G [auth F]	3.30.460.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (4.3.0)
G [auth F]	3.30.70.590	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Poly(A) polymerase predicted RNA binding domain	CATH (4.3.0)
G [auth F]	3.30.70.1550	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Archaeal tRNA CCA-adding enzyme catalytic domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D [auth C], F [auth E], G [auth F]	PF21133	CCA-adding enzyme, C-terminal domain (CAA_C)	CCA-adding enzyme, C-terminal domain	Archaeal CCA-adding enzyme builds and repairs the 3'-end of tRNA [1-4]. This is the C-terminal domain (tail) of CCA-adding enzyme, which serves as a ruler to ensure that only tRNAs and tRNA-like transcripts are substrates for the enzyme and also cont ...	Archaeal CCA-adding enzyme builds and repairs the 3'-end of tRNA [1-4]. This is the C-terminal domain (tail) of CCA-adding enzyme, which serves as a ruler to ensure that only tRNAs and tRNA-like transcripts are substrates for the enzyme and also contributes to the discrimination between stable and unstable RNA substrates [4].	Domain
A, D [auth C], F [auth E], G [auth F]	PF01909	Nucleotidyltransferase domain (NTP_transf_2)	Nucleotidyltransferase domain	Members of this family belong to a large family of nucleotidyltransferases [1]. This family includes kanamycin nucleotidyltransferase (KNTase) which is a plasmid-coded enzyme responsible for some types of bacterial resistance to aminoglycosides. KNTa ...	Members of this family belong to a large family of nucleotidyltransferases [1]. This family includes kanamycin nucleotidyltransferase (KNTase) which is a plasmid-coded enzyme responsible for some types of bacterial resistance to aminoglycosides. KNTase in-activates antibiotics by catalysing the addition of a nucleotidyl group onto the drug.	Domain
A, D [auth C], F [auth E], G [auth F]	PF09249	tRNA nucleotidyltransferase, second domain (tRNA_NucTransf2)	tRNA nucleotidyltransferase, second domain	Members of this family adopt a structure consisting of a five helical bundle core. They are predominantly found in Archaeal tRNA nucleotidyltransferase, following the catalytic nucleotidyltransferase domain [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D [auth C], F [auth E], G [auth F]	CCA-adding enzyme	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding cytidylyltransferase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA transferase activity nucleotidyltransferase activity catalytic activity CCA tRNA nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups CCACCA tRNA nucleotidyltransferase activity RNA binding tRNA binding nucleic acid binding	nucleobase-containing compound metabolic process RNA metabolic process metabolic process cellular process primary metabolic process macromolecule metabolic process RNA repair nucleic acid metabolic process catabolic process macromolecule catabolic process nucleobase-containing compound catabolic process tRNA metabolic process tRNA surveillance nucleic acid catabolic process nucleobase-containing compound metabolic process RNA metabolic process metabolic process cellular process primary metabolic process macromolecule metabolic process RNA repair nucleic acid metabolic process catabolic process macromolecule catabolic process nucleobase-containing compound catabolic process tRNA metabolic process tRNA surveillance nucleic acid catabolic process RNA surveillance tRNA decay RNA catabolic process tRNA 3'-terminal CCA addition gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process tRNA processing RNA 3'-end processing RNA processing tRNA 3'-end processing	-
B [auth G], C [auth B], E [auth D]	G70A tRNA minihelix	-	-	-
H [auth I]	RNA (5'-D(PCPG)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D [auth C], F [auth E], G [auth F]	IPR011068	Nucleotidyltransferase, class I-like, C-terminal	Homologous Superfamily
A, D [auth C], F [auth E], G [auth F]	IPR006116	2-5OAS/ClassI-CCAase, nucleotidyltransferase domain	Domain
A, D [auth C], F [auth E], G [auth F]	IPR048833	CCA-adding enzyme, C-terminal domain	Domain
A, D [auth C], F [auth E], G [auth F]	IPR042090	tRNA nucleotidyltransferase, domain 2	Homologous Superfamily
A, D [auth C], F [auth E], G [auth F]	IPR043519	Nucleotidyltransferase superfamily	Homologous Superfamily
A, D [auth C], F [auth E], G [auth F]	IPR015329	tRNA nucleotidyltransferase, substrate binding	Domain
A, D [auth C], F [auth E], G [auth F]	IPR002934	Polymerase, nucleotidyl transferase domain	Domain
A, D [auth C], F [auth E], G [auth F]	IPR008229	tRNA nucleotidyltransferase, archaea	Family

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.