1XQB | pdb_00001xqb

X-Ray Structure Of YaeB from Haemophilus influenzae. Northeast Structural Genomics Research Consortium (NESGC)target IR47.

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	d1xqba_	Multi-domain proteins (alpha and beta)	YaeB-like	YaeB-like	YaeB-like	Hypothetical protein HI0510	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)
B	d1xqbb_	Multi-domain proteins (alpha and beta)	YaeB-like	YaeB-like	YaeB-like	Hypothetical protein HI0510	(Haemophilus influenzae ) [TaxId: 727 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	TrmO-like	8031746	4003898	SCOP2 (2022-06-29)
A	SCOP2 Family	TrmO C-terminal domain-like	8054393	4007639	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	TrmO-like	8044124	3001753	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RelE-like	8054394	3000741	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	TrmO-like	8044124	3001753	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	UPF0066	e1xqbA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: UPF0066	ECOD (1.6)
A	KOG2942_like	e1xqbA2	A: a+b two layers	X: RelE-like	H: YaeB-like (From Topology)	T: YaeB-like	F: KOG2942_like	ECOD (1.6)
B	UPF0066	e1xqbB3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: UPF0066	ECOD (1.6)
B	KOG2942_like	e1xqbB4	A: a+b two layers	X: RelE-like	H: YaeB-like (From Topology)	T: YaeB-like	F: KOG2942_like	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.30.70	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
A	3.30.2310.10	Alpha Beta	2-Layer Sandwich	YaeB-like fold	YaeB-like	CATH (4.3.0)
B	2.40.30.70	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
B	3.30.2310.10	Alpha Beta	2-Layer Sandwich	YaeB-like fold	YaeB-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF18389	TrmO C-terminal domain (TrmO_C)	TrmO C-terminal domain	This domain is found at the C-terminus of TrmO tRNA methyltransferase proteins. This domain has a RelE fold.	Domain
A, B	PF01980	tRNA-methyltransferase O N-terminal domain (TrmO_N)	tRNA-methyltransferase O N-terminal domain	This family includes members such as TrmO (tRNA-methyltransferase O) also known as YaeB, which contains a single-sheeted beta-barrel structure. TrmO is an AdoMet-dependent methyltransferase responsible for m6t6A formation [1]. Its human homolog, is r ...	This family includes members such as TrmO (tRNA-methyltransferase O) also known as YaeB, which contains a single-sheeted beta-barrel structure. TrmO is an AdoMet-dependent methyltransferase responsible for m6t6A formation [1]. Its human homolog, is responsible for formation of m6t6A37 in cytoplasmic tRNASer. Lack of TrmO decreases attenuation activity of the thr operon, indicating that N6 methylation of m6t6A37 ensures efficient decoding of ACY codons [2]. In bacteria and eukaryotes, TrmO has a C-terminal domain containing the conserved DPRxxY motif. Where the Asp194 and Arg196 in this motif of E. coli TrmO are necessary for N6-methylation. However, no archaeal YaeB has a C-terminal domain containing the DPRxxY motif that is conserved in bacterial and mammalian TrmO homologs [1]. This entry represents the N-terminal domain of TrmO.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Hypothetical UPF0066 protein HI0510	tRNA methyltransferase activity RNA methyltransferase activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA transferase activity S-adenosylmethionine-dependent methyltransferase activity tRNA (L-threonylcarbamoyladenosine(37)-C2) methyltransferase activity tRNA (adenine) methyltransferase activity methyltransferase activity catalytic activity RNA binding binding tRNA methyltransferase activity RNA methyltransferase activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA transferase activity S-adenosylmethionine-dependent methyltransferase activity tRNA (L-threonylcarbamoyladenosine(37)-C2) methyltransferase activity tRNA (adenine) methyltransferase activity methyltransferase activity catalytic activity RNA binding binding tRNA binding nucleic acid binding	RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process tRNA processing RNA processing tRNA modification primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process macromolecule methylation tRNA metabolic process RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process tRNA processing RNA processing tRNA modification primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process macromolecule methylation tRNA metabolic process RNA modification biosynthetic process methylation macromolecule modification metabolic process cellular process macromolecule metabolic process RNA methylation tRNA methylation	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036414	YaeB, N-terminal domain superfamily	Homologous Superfamily
A, B	IPR023368	Uncharacterised protein family UPF0066, conserved site	Conserved Site
A, B	IPR040372	YaeB-like	Family
A, B	IPR023370	TrmO-like, N-terminal domain	Domain
A, B	IPR041369	TrmO, C-terminal	Domain
A, B	IPR036413	YaeB-like 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.