3KGD | pdb_00003kgd

Crystal structure of E. coli RNA 3' cyclase

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	SCOP2B Superfamily	EPT/RTPC-like	8035758	3001530	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RNA 3'-terminal phosphate cyclase, RPTC, insert domain	8044394	3000413	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	EPT/RTPC-like	8035758	3001530	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RNA 3'-terminal phosphate cyclase, RPTC, insert domain	8044394	3000413	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	EPT/RTPC-like	8035758	3001530	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	EPT/RTPC-like	8035758	3001530	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	EPT/RTPC-like	8035758	3001530	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	EPT/RTPC-like	8035758	3001530	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RNA 3'-terminal phosphate cyclase, RPTC, insert domain	8044394	3000413	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	EPT/RTPC-like	8035758	3001530	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RNA 3'-terminal phosphate cyclase, RPTC, insert domain	8044394	3000413	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	EPT/RTPC-like	8035758	3001530	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	RTC	e3kgdD1	A: a+b two layers	X: IF3-like	H: EPT/RTPC-like (From Topology)	T: EPT/RTPC-like	F: RTC	ECOD (1.6)
D	RTC_insert	e3kgdD2	A: a+b three layers	X: Thioredoxin-like	H: RNA 3'-terminal phosphate cyclase, RPTC, insert domain (From Topology)	T: RNA 3'-terminal phosphate cyclase, RPTC, insert domain	F: RTC_insert	ECOD (1.6)
C	RTC	e3kgdC1	A: a+b two layers	X: IF3-like	H: EPT/RTPC-like (From Topology)	T: EPT/RTPC-like	F: RTC	ECOD (1.6)
C	RTC_insert	e3kgdC2	A: a+b three layers	X: Thioredoxin-like	H: RNA 3'-terminal phosphate cyclase, RPTC, insert domain (From Topology)	T: RNA 3'-terminal phosphate cyclase, RPTC, insert domain	F: RTC_insert	ECOD (1.6)
B	RTC	e3kgdB1	A: a+b two layers	X: IF3-like	H: EPT/RTPC-like (From Topology)	T: EPT/RTPC-like	F: RTC	ECOD (1.6)
B	RTC_insert	e3kgdB2	A: a+b three layers	X: Thioredoxin-like	H: RNA 3'-terminal phosphate cyclase, RPTC, insert domain (From Topology)	T: RNA 3'-terminal phosphate cyclase, RPTC, insert domain	F: RTC_insert	ECOD (1.6)
A	RTC	e3kgdA1	A: a+b two layers	X: IF3-like	H: EPT/RTPC-like (From Topology)	T: EPT/RTPC-like	F: RTC	ECOD (1.6)
A	RTC_insert	e3kgdA2	A: a+b three layers	X: Thioredoxin-like	H: RNA 3'-terminal phosphate cyclase, RPTC, insert domain (From Topology)	T: RNA 3'-terminal phosphate cyclase, RPTC, insert domain	F: RTC_insert	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.65.10.20	Alpha Beta	Alpha-beta prism	UDP-n-acetylglucosamine1-carboxyvinyl-transferase	Chain	CATH (4.3.0)
D	3.30.360.20	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
C	3.65.10.20	Alpha Beta	Alpha-beta prism	UDP-n-acetylglucosamine1-carboxyvinyl-transferase	Chain	CATH (4.3.0)
C	3.30.360.20	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
B	3.65.10.20	Alpha Beta	Alpha-beta prism	UDP-n-acetylglucosamine1-carboxyvinyl-transferase	Chain	CATH (4.3.0)
B	3.30.360.20	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
A	3.65.10.20	Alpha Beta	Alpha-beta prism	UDP-n-acetylglucosamine1-carboxyvinyl-transferase	Chain	CATH (4.3.0)
A	3.30.360.20	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF05189	RNA 3'-terminal phosphate cyclase (RTC), insert domain (RTC_insert)	RNA 3'-terminal phosphate cyclase (RTC), insert domain	RNA cyclases are a family of RNA-modifying enzymes that are conserved in all cellular organisms. They catalyse the ATP-dependent conversion of the 3'-phosphate to the 2',3'-cyclic phosphodiester at the end of RNA, in a reaction involving formation o ...	RNA cyclases are a family of RNA-modifying enzymes that are conserved in all cellular organisms. They catalyse the ATP-dependent conversion of the 3'-phosphate to the 2',3'-cyclic phosphodiester at the end of RNA, in a reaction involving formation of the covalent AMP-cyclase intermediate [1]. The structure of RTC demonstrates that RTCs are comprised two domain. The larger domain contains an insert domain of approximately 100 amino acids [1].	Domain
A, B, C, D	PF01137	RNA 3'-terminal phosphate cyclase (RTC)	RNA 3'-terminal phosphate cyclase	RNA cyclases are a family of RNA-modifying enzymes that are conserved in all cellular organisms. They catalyse the ATP-dependent conversion of the 3'-phosphate to the 2',3'-cyclic phosphodiester at the end of RNA, in a reaction involving formation o ...	RNA cyclases are a family of RNA-modifying enzymes that are conserved in all cellular organisms. They catalyse the ATP-dependent conversion of the 3'-phosphate to the 2',3'-cyclic phosphodiester at the end of RNA, in a reaction involving formation of the covalent AMP-cyclase intermediate [1]. The structure of RTC demonstrates that RTCs are comprised two domain. The larger domain contains an insert domain of approximately 100 amino acids [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	RNA 3'-terminal phosphate cyclase	ligase activity, forming phosphoric ester bonds catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid cyclase activity catalytic activity RNA-3'-phosphate cyclase activity ligase activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding ligase activity, forming phosphoric ester bonds catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid cyclase activity catalytic activity RNA-3'-phosphate cyclase activity ligase activity 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	RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process metabolic process cellular process RNA processing macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR013792	RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta	Homologous Superfamily
A, B, C, D	IPR023797	RNA 3'-terminal phosphate cyclase domain	Domain
A, B, C, D	IPR000228	RNA 3'-terminal phosphate cyclase	Family
A, B, C, D	IPR020719	RNA 3'-terminal phosphate cyclase-like, conserved site	Conserved Site
A, B, C, D	IPR017770	RNA 3'-terminal phosphate cyclase type 1	Family
A, B, C, D	IPR037136	RNA 3'-terminal phosphate cyclase domain superfamily	Homologous Superfamily
A, B, C, D	IPR013791	RNA 3'-terminal phosphate cyclase, insert domain	Domain
A, B, C, D	IPR036553	RNA 3'-terminal phosphate cyclase, insert domain superfamily	Homologous Superfamily

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.