1D8H | pdb_00001d8h

X-RAY CRYSTAL STRUCTURE OF YEAST RNA TRIPHOSPHATASE IN COMPLEX WITH SULFATE AND MANGANESE IONS.

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1d8ha_	Alpha and beta proteins (a+b)	CYTH-like phosphatases	CYTH-like phosphatases	mRNA triphosphatase CET1	mRNA triphosphatase CET1	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d1d8hb_	Alpha and beta proteins (a+b)	CYTH-like phosphatases	CYTH-like phosphatases	mRNA triphosphatase CET1	mRNA triphosphatase CET1	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d1d8hc_	Alpha and beta proteins (a+b)	CYTH-like phosphatases	CYTH-like phosphatases	mRNA triphosphatase CET1	mRNA triphosphatase CET1	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	CYTH-like phosphatases	8035719	3001426	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	CYTH-like phosphatases	8035719	3001426	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	CYTH-like phosphatases	8035719	3001426	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	mRNA_triPase	e1d8hA1	A: a+b complex topology	X: mRNA triphosphatase CET1-related (From Topology)	H: mRNA triphosphatase CET1-related (From Topology)	T: mRNA triphosphatase CET1-related	F: mRNA_triPase	ECOD (1.6)
B	mRNA_triPase	e1d8hB1	A: a+b complex topology	X: mRNA triphosphatase CET1-related (From Topology)	H: mRNA triphosphatase CET1-related (From Topology)	T: mRNA triphosphatase CET1-related	F: mRNA_triPase	ECOD (1.6)
C	mRNA_triPase	e1d8hC1	A: a+b complex topology	X: mRNA triphosphatase CET1-related (From Topology)	H: mRNA triphosphatase CET1-related (From Topology)	T: mRNA triphosphatase CET1-related	F: mRNA_triPase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.20.100.10	Alpha Beta	Alpha-Beta Barrel	mRNA Triphosphatase Cet1	Chain A	CATH (4.3.0)
B	3.20.100.10	Alpha Beta	Alpha-Beta Barrel	mRNA Triphosphatase Cet1	Chain A	CATH (4.3.0)
C	3.20.100.10	Alpha Beta	Alpha-Beta Barrel	mRNA Triphosphatase Cet1	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF02940	mRNA capping enzyme, beta chain (mRNA_triPase)	mRNA capping enzyme, beta chain	The beta chain of mRNA capping enzyme has triphosphatase activity. The function of the capping enzyme also depends on the guanylyltransferase activity conferred by the alpha chain (see Pfam:PF01331)	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	mRNA TRIPHOSPHATASE CET1	phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds polynucleotide 5'-phosphatase activity phosphatase activity hydrolase activity catalytic activity pyrophosphatase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides mRNA 5'-triphosphate monophosphatase activity	protein localization regulation of localization regulation of biological process cellular localization regulation of cellular process regulation of protein localization positive regulation of protein localization to nucleus biological regulation positive regulation of biological process regulation of protein localization to nucleus protein localization to nucleus localization regulation of cellular localization cellular macromolecule localization macromolecule localization protein localization regulation of localization regulation of biological process cellular localization regulation of cellular process regulation of protein localization positive regulation of protein localization to nucleus biological regulation positive regulation of biological process regulation of protein localization to nucleus protein localization to nucleus localization regulation of cellular localization cellular macromolecule localization macromolecule localization protein localization to organelle positive regulation of protein localization cellular process positive regulation of cellular process transcription elongation by RNA polymerase II positive regulation of DNA-templated transcription positive regulation of transcription elongation by RNA polymerase II RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process positive regulation of metabolic process regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of DNA-templated transcription, elongation positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II regulation of DNA-templated transcription elongation positive regulation of nucleobase-containing compound metabolic process regulation of transcription elongation by RNA polymerase II primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression positive regulation of transcription by RNA polymerase II macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression DNA-templated transcription elongation biosynthetic process positive regulation of RNA biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process 7-methylguanosine mRNA capping 7-methylguanosine RNA capping RNA capping mRNA processing mRNA metabolic process RNA 5'-end processing RNA processing	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, C	IPR040343	RNA 5'-triphosphatase Cet1/Ctl1	Family
A, B, C	IPR004206	mRNA triphosphatase Cet1-like	Domain
A, B, C	IPR037009	mRNA triphosphatase Cet1-like superfamily	Homologous Superfamily
A, B, C	IPR033469	CYTH-like domain superfamily	Homologous Superfamily

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	polynucleotide 5'-phosphatase M-CSA #486	RNA triphosphatase is an essential mRNA processing enzyme that catalyses the first step in cap formation. Capping entails three enzymatic reactions in which the 5' triphosphate end of pre-mRNA is hydrolysed to a 5' diphosphate by RNA triphosphatase, then capped with GMP by RNA guanylyltransferase, and methylated by RNA methyltransferase. Each of the capping activities is essential for cell growth. Yeast RNA triphosphatase forms a heteromeric complex with the yeast RNA guanylyltransferase . The binding serves two purposes, firstly, the interaction stimulates guanylyltransferase activity by enhancing the affinity of RNA guanylyltransferase for GTP. Secondly the tethering facilitates the recruitment of the triphosphatase to the RNA polymerase II elongation complex. The structure reveals a novel active site fold, a topologically closed trisphosphate tunnel formed from an eight stranded beta barrel.	Defined by 6 residues: GLU:A-67 [auth A-305]GLU:A-69 [auth A-307]ARG:A-155 [auth A-393]LYS:A-171 [auth A-409]LYS:A-218 [auth A-456]GLU:A-258 [auth A-496] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 3.1.3.33 (PDB Primary Data) Search M-CSA Motif + EC 3.1.3.33 EC: 3.6.1.74 (UniProt) Search M-CSA Motif + EC 3.6.1.74

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.