2B3T | pdb_00002b3t

Structure of complex between E. coli translation termination factor RF1 and the PrmC methyltransferase

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)
B	d2b3tb1	Multi-domain proteins (alpha and beta)	Release factor	Release factor	Release factor	Peptide chain release factor 1, RF1	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2b3ta_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	N5-glutamine methyltransferase, HemK	N5-glutamine methyltransferase, HemK	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	PCRF domain-like	8020399	4002864	SCOP2 (2022-06-29)
B	SCOP2 Family	Peptidyl-tRNA hydrolase domain	8054406	4002570	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	RNA-binding domain, RBD	8054405	3000110	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Peptidyl-tRNA hydrolase domain-like	8054407	3001421	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Release factor N-terminal domain-like	8032779	3001827	SCOP2 (2022-06-29)
A	SCOP2 Family	N5-glutamine methyltransferase, HemK	8025223	4000538	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8037602	3000118	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	PCRF_N	e2b3tB8	A: alpha bundles	X: Release factor (Pfam 00472) N-terminal alpha helical domain (From Topology)	H: Release factor (Pfam 00472) N-terminal alpha helical domain (From Topology)	T: Release factor (Pfam 00472) N-terminal alpha helical domain	F: PCRF_N	ECOD (1.6)
B	PCRF_C	e2b3tB5	A: a+b two layers	X: Alpha-beta plaits	H: Ferredoxin-like domain in release factor (From Topology)	T: Ferredoxin-like domain in release factor	F: PCRF_C	ECOD (1.6)
B	RF-1_N	e2b3tB7	A: a+b two layers	X: dsRBD-like	H: Peptidyl-tRNA hydrolase domain-like (From Topology)	T: Peptidyl-tRNA hydrolase domain-like	F: RF-1_N	ECOD (1.6)
B	RF-1_C	e2b3tB6	A: a+b two layers	X: dsRBD-like	H: Peptidyl-tRNA hydrolase domain-like (From Topology)	T: Peptidyl-tRNA hydrolase domain-like	F: RF-1_C	ECOD (1.6)
A	PRK09328	e2b3tA2	A: alpha arrays	X: SP1917-like (From Topology)	H: SP1917-like (From Topology)	T: SP1917-like	F: PRK09328	ECOD (1.6)
A	Methyltransf_11_2	e2b3tA3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_11_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	6.10.140.1980	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
B	3.30.70.1660	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
B	3.30.160.20	Alpha Beta	2-Layer Sandwich	Double Stranded RNA Binding Domain		CATH (4.3.0)
A	1.10.8.10	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	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	PF03462	PCRF domain (PCRF)	PCRF domain	This domain is found in peptide chain release factors.	Domain
B	PF00472	RF-1 domain (RF-1)	RF-1 domain	This domain is found in peptide chain release factors such as RF-1 (Swiss:P07011) and RF-2 (Swiss:P07012), and a number of smaller proteins of unknown function such as Swiss:P40711. This domain contains the peptidyl-tRNA hydrolase activity. The domai ...	This domain is found in peptide chain release factors such as RF-1 (Swiss:P07011) and RF-2 (Swiss:P07012), and a number of smaller proteins of unknown function such as Swiss:P40711. This domain contains the peptidyl-tRNA hydrolase activity. The domain contains a highly conserved motif GGQ, where the glutamine is thought to coordinate the water that mediates the hydrolysis.	Domain
A	PF17827	PrmC N-terminal domain (PrmC_N)	PrmC N-terminal domain	This entry corresponds to the N-terminal alpha helical domain of the HemK protein. HemK is a methyltransferase enzyme that carries out the methylation of the N5 nitrogen of the glutamine found in the conserved GGQ motif of class-1 release factors [3] ...	This entry corresponds to the N-terminal alpha helical domain of the HemK protein. HemK is a methyltransferase enzyme that carries out the methylation of the N5 nitrogen of the glutamine found in the conserved GGQ motif of class-1 release factors [3].	Domain
A	PF05175	Methyltransferase small domain (MTS)	Methyltransferase small domain	This domain is found in ribosomal RNA small subunit methyltransferase C (eg Swiss:P44453) as well as other methyltransferases (eg Swiss:Q53742).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Peptide chain release factor 1	translation release factor activity, codon specific translation factor activity translation release factor activity translation termination factor activity ribonucleoprotein complex binding protein-containing complex binding binding ribosome binding	cellular component disassembly protein-containing complex organization protein-containing complex disassembly primary metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process cellular component organization biosynthetic process cellular process metabolic process translational termination cellular component organization or biogenesis cellular component disassembly protein-containing complex organization protein-containing complex disassembly primary metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process cellular component organization biosynthetic process cellular process metabolic process translational termination cellular component organization or biogenesis protein metabolic process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol
A	Protein methyltransferase hemK	catalytic activity, acting on a protein transferase activity, transferring one-carbon groups N-methyltransferase activity protein methyltransferase activity protein-glutamine N-methyltransferase activity transferase activity methyltransferase activity catalytic activity S-adenosylmethionine-dependent methyltransferase activity binding nucleic acid binding peptide chain release factor N(5)-glutamine methyltransferase activity	protein methylation primary metabolic process macromolecule methylation protein alkylation methylation macromolecule modification peptidyl-glutamine methylation metabolic process cellular process protein metabolic process macromolecule metabolic process protein modification process regulation of biosynthetic process regulation of biological process protein methylation primary metabolic process macromolecule methylation protein alkylation methylation macromolecule modification peptidyl-glutamine methylation metabolic process cellular process protein metabolic process macromolecule metabolic process protein modification process regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process cellular component disassembly protein-containing complex organization protein-containing complex disassembly translation protein biosynthetic process cellular component organization translational termination cellular component organization or biogenesis	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR050057	Prokaryotic/Mitochondrial Release Factor	Family
B	IPR004373	Peptide chain release factor 1	Family
B	IPR000352	Peptide chain release factor class I	Domain
B	IPR045853	Peptide chain release factor class I superfamily	Homologous Superfamily
B	IPR005139	Peptide chain release factor	Domain
A	IPR040758	Release factor glutamine methyltransferase, N-terminal domain	Domain
A	IPR019874	Release factor glutamine methyltransferase	Family
A	IPR002052	DNA methylase, N-6 adenine-specific, conserved site	Conserved Site
A	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A	IPR007848	Methyltransferase small domain	Domain
A	IPR004556	Methyltransferase HemK-like	Family
A	IPR050320	Protein N5-glutamine methyltransferase	Family

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.