2FRX | pdb_00002frx

Crystal structure of YebU, a m5C RNA methyltransferase from E.coli

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	Methyltranf_PUA_1	e2frxB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: Methyltranf_PUA_1	ECOD (1.6)
B	yebU	e2frxB3	A: a+b two layers	X: Cystatin-like	H: Pre-PUA domain (From Topology)	T: Pre-PUA domain	F: yebU	ECOD (1.6)
B	Methyltr_RsmB-F_1	e2frxB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltr_RsmB-F_1	ECOD (1.6)
C	Methyltranf_PUA_1	e2frxC1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: Methyltranf_PUA_1	ECOD (1.6)
C	yebU	e2frxC3	A: a+b two layers	X: Cystatin-like	H: Pre-PUA domain (From Topology)	T: Pre-PUA domain	F: yebU	ECOD (1.6)
C	Methyltr_RsmB-F_1	e2frxC2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltr_RsmB-F_1	ECOD (1.6)
D	Methyltranf_PUA_1	e2frxD4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: Methyltranf_PUA_1	ECOD (1.6)
D	yebU	e2frxD3	A: a+b two layers	X: Cystatin-like	H: Pre-PUA domain (From Topology)	T: Pre-PUA domain	F: yebU	ECOD (1.6)
D	Methyltr_RsmB-F_1	e2frxD2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltr_RsmB-F_1	ECOD (1.6)
A	Methyltranf_PUA_1	e2frxA4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: Methyltranf_PUA_1	ECOD (1.6)
A	yebU	e2frxA3	A: a+b two layers	X: Cystatin-like	H: Pre-PUA domain (From Topology)	T: Pre-PUA domain	F: yebU	ECOD (1.6)
A	Methyltr_RsmB-F_1	e2frxA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltr_RsmB-F_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
B	3.10.450.720	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
C	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
C	3.10.450.720	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
D	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
D	3.10.450.720	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	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)
A	3.10.450.720	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF13636	RNA-binding PUA-like domain of methyltransferase RsmF (Methyltranf_PUA)	RNA-binding PUA-like domain of methyltransferase RsmF	-	Family
A, B, C, D	PF17125	N-terminal domain of 16S rRNA methyltransferase RsmF (Methyltr_RsmF_N)	N-terminal domain of 16S rRNA methyltransferase RsmF	This is the N-terminal domain of the RsmF methyl transferase. RsmF is a multi-site-specific methyltransferase that is responsible for the synthesis of three modifications on cytidines in 16S ribosomal RNA. The N-terminus is critical for stabilising t ...	This is the N-terminal domain of the RsmF methyl transferase. RsmF is a multi-site-specific methyltransferase that is responsible for the synthesis of three modifications on cytidines in 16S ribosomal RNA. The N-terminus is critical for stabilising the catalytic core of the enzyme [1]. It has a ferredoxin-like fold.	Domain
A, B, C, D	PF01189	16S rRNA methyltransferase RsmB/F (Methyltr_RsmB-F)	16S rRNA methyltransferase RsmB/F	This is the catalytic core of this SAM-dependent 16S ribosomal methyltransferase RsmB/F enzyme [1,2]. There is a catalytic cysteine residue at 180 in UniProtKB:Q5SII2, with another highly conserved cysteine at residue 230. It methylates the C(5) posi ...	This is the catalytic core of this SAM-dependent 16S ribosomal methyltransferase RsmB/F enzyme [1,2]. There is a catalytic cysteine residue at 180 in UniProtKB:Q5SII2, with another highly conserved cysteine at residue 230. It methylates the C(5) position of cytosine 2870 (m5C2870) in 25S rRNA [1,2].	Domain
A, B, C, D	PF21150	Ribosomal RNA small subunit methyltransferase F, pre-PUA domain (YebU_pre-PUA_dom)	Ribosomal RNA small subunit methyltransferase F, pre-PUA domain	This domain is found in Ribosomal RNA small subunit methyltransferase F from Escherichia coli (YebU) and similar proteins mainly from proteobacteria. YebU requires S-adenosyl-l-methionine (SAM) to specifically methylate the cytosine at position 1407 ...	This domain is found in Ribosomal RNA small subunit methyltransferase F from Escherichia coli (YebU) and similar proteins mainly from proteobacteria. YebU requires S-adenosyl-l-methionine (SAM) to specifically methylate the cytosine at position 1407 of assembled 30 S rRNA subunits. This proteins is organized into two distinct structural domains: the N-terminal MTase domain (catalytic domain), which can be divided in Pfam:PF17125 and Pfam:PF01189, and the C-terminal, also consisting of two subdomains. This entry represents the first of these subdomains, which is found N-terminal to the PUA- like domain (Pfam:PF13636). The pre-PUA domain has six beta-strands that form a central sheet in an anti-parallel fashion, and three alpha-helices packing against the edges of the sheet [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Hypothetical protein yebU	RNA methyltransferase activity rRNA methyltransferase activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid transferase activity catalytic activity, acting on a rRNA S-adenosylmethionine-dependent methyltransferase activity C-methyltransferase activity methyltransferase activity catalytic activity rRNA (cytosine) methyltransferase activity rRNA (cytosine-C5-)-methyltransferase activity RNA binding RNA methyltransferase activity rRNA methyltransferase activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid transferase activity catalytic activity, acting on a rRNA S-adenosylmethionine-dependent methyltransferase activity C-methyltransferase activity methyltransferase activity catalytic activity rRNA (cytosine) methyltransferase activity rRNA (cytosine-C5-)-methyltransferase activity RNA binding binding nucleic acid binding	ribonucleoprotein complex biogenesis rRNA methylation RNA metabolic process rRNA processing rRNA modification nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process cellular component organization or biogenesis RNA processing rRNA metabolic process primary metabolic process ribonucleoprotein complex biogenesis rRNA methylation RNA metabolic process rRNA processing rRNA modification nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process cellular component organization or biogenesis RNA processing rRNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process macromolecule methylation RNA modification biosynthetic process methylation macromolecule modification metabolic process cellular process macromolecule metabolic process rRNA base methylation RNA methylation	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR018314	RsmB/NOL1/NOP2-like, conserved site	Conserved Site
A, B, C, D	IPR001678	SAM-dependent methyltransferase RsmB-F/NOP2-type domain	Domain
A, B, C, D	IPR048457	Ribosomal RNA small subunit methyltransferase F, pre-PUA domain	Domain
A, B, C, D	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, B, C, D	IPR023267	RNA (C5-cytosine) methyltransferase	Family
A, B, C, D	IPR011023	Nop2p	Domain
A, B, C, D	IPR031341	Ribosomal RNA small subunit methyltransferase F, N-terminal	Domain
A, B, C, D	IPR049560	SAM-dependent methyltransferase RsmB-F/NOP2-type, catalytic core	Domain
A, B, C, D	IPR027391	rRNA small subunit methyltransferase F, RNA-binding PUA-like domain	Domain
A, B, C, D	IPR023545	rRNA small subunit methyltransferase F	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.