1P16 | pdb_00001p16

Structure of an mRNA capping enzyme bound to the phosphorylated carboxyl-terminal domain of RNA polymerase II

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d1p16b1	All beta proteins	OB-fold	Nucleic acid-binding proteins	DNA ligase/mRNA capping enzyme postcatalytic domain	mRNA capping enzyme alpha subunit	(Candida albicans ) [TaxId: 5476 ],	SCOPe (2.08)
B	d1p16b2	Alpha and beta proteins (a+b)	ATP-grasp	DNA ligase/mRNA capping enzyme, catalytic domain	mRNA capping enzyme	mRNA capping enzyme alpha subunit	(Candida albicans ) [TaxId: 5476 ],	SCOPe (2.08)
B	d1p16b3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Candida albicans ) [TaxId: 5476 ],	SCOPe (2.08)
A	d1p16a1	All beta proteins	OB-fold	Nucleic acid-binding proteins	DNA ligase/mRNA capping enzyme postcatalytic domain	mRNA capping enzyme alpha subunit	(Candida albicans ) [TaxId: 5476 ],	SCOPe (2.08)
A	d1p16a2	Alpha and beta proteins (a+b)	ATP-grasp	DNA ligase/mRNA capping enzyme, catalytic domain	mRNA capping enzyme	mRNA capping enzyme alpha subunit	(Candida albicans ) [TaxId: 5476 ],	SCOPe (2.08)
A	d1p16a3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Candida albicans ) [TaxId: 5476 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	DNA ligase/mRNA capping enzyme, catalytic domain	8034540	3000798	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleic acid-binding proteins	8034539	3000135	SCOP2B (2022-06-29)
A	SCOP2 Family	DNA ligase/mRNA capping enzyme postcatalytic domain-like	8022159	4001931	SCOP2 (2022-06-29)
A	SCOP2 Family	mRNA capping enzyme guanylyltransferase domain-like	8022160	4002077	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleic acid-binding proteins	8034539	3000135	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	DNA ligase/mRNA capping enzyme, catalytic domain	8034540	3000798	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	Stap_Strp_toxin	e1p16B1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Stap_Strp_toxin	ECOD (v294.1)
B	LRR_6,LRR_RI_capping	e1p16B2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: LRR_6,LRR_RI_capping	ECOD (v294.1)
A	mRNA_cap_C	e1p16A1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding protein	T: Nucleic acid-binding protein	F: mRNA_cap_C	ECOD (v294.1)
A	mRNA_cap_enzyme	e1p16A2	A: beta duplicates or obligate multimers	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: mRNA_cap_enzyme	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.470.30	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
B	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
A	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
A	3.30.470.30	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	phosphorylated peptide from C-terminal of RNA polymerase II	-	-	-
A, B	mRNA capping enzyme alpha subunit	RNA polymerase binding protein binding binding RNA polymerase II complex binding RNA polymerase II C-terminal domain binding RNA polymerase core enzyme binding enzyme binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding RNA polymerase binding protein binding binding RNA polymerase II complex binding RNA polymerase II C-terminal domain binding RNA polymerase core enzyme binding enzyme 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 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 guanyl nucleotide binding GTP binding guanyl ribonucleotide binding	RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process tRNA processing metabolic process cellular process RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process tRNA processing metabolic process cellular process macromolecule metabolic process RNA processing 7-methylguanosine mRNA capping 7-methylguanosine RNA capping RNA capping mRNA processing mRNA metabolic process RNA 5'-end processing regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II regulation of biological process biological regulation regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process regulation of gene expression positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process	membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle mRNA capping enzyme complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001339	mRNA capping enzyme, adenylation domain	Domain
A, B	IPR051029	mRNA_Capping_Enz/RNA_Phosphat	Unknown
A, B	IPR017075	mRNA capping enzyme, alpha subunit	Family
A, B	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A, B	IPR013846	mRNA capping enzyme, C-terminal domain	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C, D	SEP	Parent Component: SER RESID: AA0037 PSI-MOD : O-phospho-L-serine MOD:00046
A, B	MSE	Parent Component: MET RESID: AA0037

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.