2B56

Structural Basis for UTP Specificity of RNA Editing TUTases From Trypanosoma Brucei

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2b56a2	All alpha proteins	PAP/OAS1 substrate-binding domain	PAP/OAS1 substrate-binding domain	RNA editing terminal uridyl transferase 2, RET2, domain 2	RNA editing terminal uridyl transferase 2, TUTase 2, RET2	(Trypanosoma brucei ) [TaxId: 5691 ],	SCOPe (2.08)
A	d2b56a1	Alpha and beta proteins (a+b)	Nucleotidyltransferase	Nucleotidyltransferase	RNA editing terminal uridyl transferase 2, RET2, catalytic domain	RNA editing terminal uridyl transferase 2, TUTase 2, RET2	(Trypanosoma brucei ) [TaxId: 5691 ],	SCOPe (2.08)

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	8037640	3000941	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleotidyltransferase-like	8037642	3000129	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	PAP_assoc	e2b56A1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: PAP/OAS1 substrate-binding domain	F: PAP_assoc	ECOD (1.6)
A	EUF08330	e2b56A2	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: EUF08330	ECOD (1.6)
A	NT_PAP_TUTase	e2b56A3	A: a+b three layers	X: Nucleotidyltransferase-like	H: Nucleotidyltransferase (From Topology)	T: Nucleotidyltransferase	F: NT_PAP_TUTase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.1410.10	Mainly Alpha	Orthogonal Bundle	Poly(a)-polymerase, middle domain		CATH (4.3.0)
A	3.30.460.50	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (4.3.0)
A	3.30.70.1970	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF03828	Cid1 family poly A polymerase (PAP_assoc)	Cid1 family poly A polymerase	-	Family
A	PF18528	RNA editing 3' terminal uridylyl transferase 2 middle domain (Ret2_MD)	RNA editing 3' terminal uridylyl transferase 2 middle domain	Post-transcriptional RNA editing in Trypanosomatids (pathogenic protozoa) is catalyzed by a large multiprotein complex, the editosome. A key editosome enzyme, RNA editing terminal uridylyl transferase 2 (TUTase 2; RET2) catalyzes the uridylate additi ...	Post-transcriptional RNA editing in Trypanosomatids (pathogenic protozoa) is catalyzed by a large multiprotein complex, the editosome. A key editosome enzyme, RNA editing terminal uridylyl transferase 2 (TUTase 2; RET2) catalyzes the uridylate addition reaction. RET2 structure consists of three domains: the N-terminal domain (NTD), the middle domain (MD) and the C-terminal domain (CTD). This MD domain is mainly composed of six helices and a four-stranded antiparallel beta-sheet. structural comparison reveals that the fold of this MD is topologically similar to the binding domains of several RNA-binding proteins such as the RNA-binding domain of the U1A spliceosomal protein, the RRM domain of the human La protein and the CTD of an archaeal CCA-adding enzyme. The CTD of the archaeal CCA-adding enzyme has been shown to bind double-stranded tRNA stem substrate through the alpha-helices regions. Hence it is suggested that this domain might be an RNA-binding domain [1].	Domain
A	PF22600	Poly(A) RNA polymerase, mitochondrial-like, central palm domain (MTPAP-like_central)	Poly(A) RNA polymerase, mitochondrial-like, central palm domain	This domain is found in human Poly(A) RNA polymerase, mitochondrial (MTPAP) and similar proteins from eukaryotes. MTPAP is a noncanonical polymerase that creates the 3' poly(A) tail of mitochondrial transcripts. It contains three domains: a N-termina ...	This domain is found in human Poly(A) RNA polymerase, mitochondrial (MTPAP) and similar proteins from eukaryotes. MTPAP is a noncanonical polymerase that creates the 3' poly(A) tail of mitochondrial transcripts. It contains three domains: a N-terminal domain RL (Pfam:PF17797) and the canonical palm (this entry) and fingers domains. This domain shows a five -stranded beta-sheet with the three catalytic aspartic acid residues located on its surface [6], together with several alpha- helices, forming an alpha-beta configuration.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	RNA editing complex protein MP57	RNA binding binding organic cyclic compound binding nucleic acid binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding uridylyltransferase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid transferase activity RNA uridylyltransferase activity catalytic activity RNA binding binding organic cyclic compound binding nucleic acid binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding uridylyltransferase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid transferase activity RNA uridylyltransferase activity catalytic activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups cation binding ion binding metal ion binding	cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA processing mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA processing mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process RNA processing RNA 3' uridylation RNA 3'-end processing	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle mitochondrial protein-containing complex protein-containing complex catalytic complex mRNA editing complex mitochondrial mRNA editing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR043519	Nucleotidyltransferase superfamily	Homologous Superfamily
A	IPR002058	PAP/25A-associated	Domain
A	IPR041060	RNA editing 3' terminal uridylyl transferase 2 middle 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.