4CKB | pdb_00004ckb

Vaccinia virus capping enzyme complexed with GTP and SAH

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)
D [auth E]	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8090818	3000118	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8090818	3000118	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	CYTH-like phosphatases	8090048	3001426	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8090055	3000118	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	Nucleic acid-binding proteins	8090052	3000135	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	DNA ligase/mRNA capping enzyme, catalytic domain	8090050	3000798	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8090055	3000118	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DNA ligase/mRNA capping enzyme, catalytic domain	8090050	3000798	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	CYTH-like phosphatases	8090048	3001426	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleic acid-binding proteins	8090052	3000135	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)
D [auth E]	tRNA-synt_1b	e4ckbE1	A: alpha bundles	X: jelly-roll	H: Double-stranded beta-helix	T: Double-stranded beta-helix	F: tRNA-synt_1b	ECOD (develop294)
B	tRNA-synt_1b	e4ckbB1	A: alpha bundles	X: jelly-roll	H: Double-stranded beta-helix	T: Double-stranded beta-helix	F: tRNA-synt_1b	ECOD (develop294)
C [auth D]	CBM_5_12	e4ckbD1	A: alpha bundles	X: DEATH domain	H: HTH	T: winged helix domain	F: CBM_5_12	ECOD (develop294)
A	CBM_5_12	e4ckbA1	A: alpha bundles	X: DEATH domain	H: HTH	T: winged helix domain	F: CBM_5_12	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth E]	3.40.50.11680	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Poxvirus mRNA capping enzyme, small subunit	CATH (4.3.0)
B	3.40.50.11680	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Poxvirus mRNA capping enzyme, small subunit	CATH (4.3.0)
C [auth D]	3.30.470.140	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
C [auth D]	3.20.100.20	Alpha Beta	Alpha-Beta Barrel	mRNA Triphosphatase Cet1	Chain A	CATH (4.3.0)
C [auth D]	2.40.50.830	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
C [auth D]	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
A	3.30.470.140	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
A	3.20.100.20	Alpha Beta	Alpha-Beta Barrel	mRNA Triphosphatase Cet1	Chain A	CATH (4.3.0)
A	2.40.50.830	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
A	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D [auth E]	PF03341	Poxvirus mRNA capping enzyme, small subunit (Pox_mRNA-cap)	Poxvirus mRNA capping enzyme, small subunit	-	Family
A, C [auth D]	PF21004	mRNA capping enzyme catalytic subunit, GTase, NTPase domain (MCEL_GT_NTPase)	mRNA capping enzyme catalytic subunit, GTase, NTPase domain	mRNA-capping enzyme catalytic subunit from Vaccinia virus (MCEL, also known as mRNA-capping enzyme D1 subunit) catalyses the hydrolysis of the 5' triphosphate end of the pre-mRNA, the capping of the resulting diphosphate RNA end with GMP and the meth ...	mRNA-capping enzyme catalytic subunit from Vaccinia virus (MCEL, also known as mRNA-capping enzyme D1 subunit) catalyses the hydrolysis of the 5' triphosphate end of the pre-mRNA, the capping of the resulting diphosphate RNA end with GMP and the methylation of the GpppN cap [1-3]. It consists of an N-terminal RNA triphosphatase (TPase)-guanylyltransferase (GTase) module, and a C-terminal guanine-N7-methyltransferase (MTase) module (Pfam:PF03291) [4]. The N-terminal module comprises a TPase domain (Pfam:PF10640), followed by the GTase at the C-terminal, which consists of the nucleotidyltransferase (NTPase, this entry) and OB fold (Pfam:PF21005) domains [3,4]. The TPase and GTase modules stabilize their active conformations and their contacts also clamp the NTase and OB fold.	Domain
A, C [auth D]	PF03291	mRNA (guanine-N(7))-methyltransferase domain (mRNA_G-N7_MeTrfase)	mRNA (guanine-N(7))-methyltransferase domain	This entry represents mRNA (guanine-N(7))-methyltransferase, which can either be found as a single domain protein, or as a domain within the mRNA-capping enzyme catalytic subunit. mRNA (guanine-N(7))-methyltransferase methylates the N7 position of th ...	This entry represents mRNA (guanine-N(7))-methyltransferase, which can either be found as a single domain protein, or as a domain within the mRNA-capping enzyme catalytic subunit. mRNA (guanine-N(7))-methyltransferase methylates the N7 position of the added guanosine to the 5'-cap structure of mRNAs. It binds RNA containing 5'-terminal GpppC [1-5]. Viral mRNA capping enzymes, meanwhile, are multidomain proteins that catalyse the first two reactions in the mRNA cap formation pathway [5]. They are heterodimers consisting of a large (catalytic) and small subunit.	Domain
A, C [auth D]	PF10640	mRNA capping enzyme catalytic subunit, RNA triphosphatase domain (MCEL_TPase)	mRNA capping enzyme catalytic subunit, RNA triphosphatase domain	mRNA-capping enzyme catalytic subunit from Vaccinia virus (MCEL, also known as mRNA-capping enzyme D1 subunit) catalyses the hydrolysis of the 5' triphosphate end of the pre-mRNA, the capping of the resulting diphosphate RNA end with GMP and the meth ...	mRNA-capping enzyme catalytic subunit from Vaccinia virus (MCEL, also known as mRNA-capping enzyme D1 subunit) catalyses the hydrolysis of the 5' triphosphate end of the pre-mRNA, the capping of the resulting diphosphate RNA end with GMP and the methylation of the GpppN cap [1-3]. It consists of an N-terminal RNA triphosphatase (TPase)-guanylyltransferase (GTase) module, and a C-terminal guanine-N7-methyltransferase (MTase) module (Pfam:PF03291) [4]. The N-terminal module comprises a TPase domain, represented in this entry, followed by the GTase at the C-terminal, which consists of the nucleotidyltransferase (NTPase, Pfam:PF21004) and OB fold (Pfam:PF21005) domains [4]. This domain catalyses the hydrolysis of the the 5' triphosphate end of the pre-mRNA.	Domain
A, C [auth D]	PF21005	mRNA-capping enzyme catalytic subunit, GTase, OB fold (OB_MCEL_GT)	mRNA-capping enzyme catalytic subunit, GTase, OB fold	mRNA-capping enzyme catalytic subunit from Vaccinia virus (MCEL, also known as mRNA-capping enzyme D1 subunit) catalyses the hydrolysis of the 5' triphosphate end of the pre-mRNA, the capping of the resulting diphosphate RNA end with GMP and the meth ...	mRNA-capping enzyme catalytic subunit from Vaccinia virus (MCEL, also known as mRNA-capping enzyme D1 subunit) catalyses the hydrolysis of the 5' triphosphate end of the pre-mRNA, the capping of the resulting diphosphate RNA end with GMP and the methylation of the GpppN cap [1,2]. It consists of an N-terminal RNA triphosphatase (TPase)-guanylyltransferase (GTase) module and a C-terminal guanine-N7-methyltransferase (MTase) module (Pfam:PF03291). The N-terminal module comprises a TPase domain (Pfam:PF10640), followed by the GTase at the C-terminal, which consists of the nucleotidyltransferase (NTPase, Pfam:PF21004) and OB fold (represented in this entry) domains [1]. This domain contains an essential motif (RxxK) for GTase activity.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D [auth E]	MRNA-CAPPING ENZYME REGULATORY SUBUNIT	RNA methyltransferase activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid transferase activity S-adenosylmethionine-dependent methyltransferase activity mRNA 5'-cap (guanine-N7-)-methyltransferase activity N-methyltransferase activity methyltransferase activity catalytic activity mRNA methyltransferase activity	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression DNA-templated transcription termination macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression DNA-templated transcription termination macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	virion component
A, C [auth D]	MRNA-CAPPING ENZYME CATALYTIC SUBUNIT	guanylyltransferase activity mRNA guanylyltransferase activity RNA guanylyltransferase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid transferase activity catalytic activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds polynucleotide 5'-phosphatase activity phosphatase activity hydrolase activity guanylyltransferase activity mRNA guanylyltransferase activity RNA guanylyltransferase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid transferase activity catalytic activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds polynucleotide 5'-phosphatase activity phosphatase activity hydrolase activity pyrophosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides inorganic triphosphate phosphatase activity RNA methyltransferase activity transferase activity, transferring one-carbon groups S-adenosylmethionine-dependent methyltransferase activity mRNA 5'-cap (guanine-N7-)-methyltransferase activity N-methyltransferase activity methyltransferase activity mRNA methyltransferase activity RNA binding binding nucleic acid binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding mRNA 5'-triphosphate monophosphatase activity cation binding metal ion binding	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression DNA-templated transcription termination macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression DNA-templated transcription termination macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	virion component

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D [auth E]	IPR005009	Poxvirus mRNA capping enzyme, small subunit	Family
B, D [auth E]	IPR043096	Poxvirus mRNA capping enzyme, small subunit superfamily	Homologous Superfamily
A, C [auth D]	IPR048425	mRNA capping enzyme catalytic subunit, GTase, NTPase domain	Domain
A, C [auth D]	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, C [auth D]	IPR019602	mRNA capping enzyme catalytic subunit, RNA triphosphatase domain, virus	Domain
A, C [auth D]	IPR046430	mRNA-capping enzyme catalytic subunit, RNA triphosphatase domain superfamily	Homologous Superfamily
A, C [auth D]	IPR046428	mRNA-capping enzyme catalytic subunit, OB fold domain superfamily	Homologous Superfamily
A, C [auth D]	IPR039753	mRNA cap guanine-N7 methyltransferase	Family
A, C [auth D]	IPR048426	mRNA-capping enzyme catalytic subunit, GTase, OB fold	Domain
A, C [auth D]	IPR046429	mRNA-capping enzyme catalytic subunit, nucleotidyltransferase domain superfamily	Homologous Superfamily
A, C [auth D]	IPR004971	mRNA (guanine-N(7))-methyltransferase domain	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.