3OKX | pdb_00003okx

Crystal structure of YaeB-like protein from Rhodopseudomonas palustris


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
BSCOP2B SuperfamilyTrmO-like 8054396 3001753 SCOP2B (2022-06-29)
ASCOP2 FamilyTrmO-like 8054395 4003898 SCOP2 (2022-06-29)
ASCOP2 SuperfamilyTrmO-like 8054396 3001753 SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
BUPF0066e3okxB2 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: Alanine racemase-CF: UPF0066ECOD (1.6)
AUPF0066e3okxA1 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: Alanine racemase-CF: UPF0066ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
B2.40.30.70 Mainly Beta Beta Barrel Elongation Factor Tu (Ef-tu) domain 3CATH (4.3.0)
A2.40.30.70 Mainly Beta Beta Barrel Elongation Factor Tu (Ef-tu) domain 3CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, B
PF01980tRNA-methyltransferase O N-terminal domain (TrmO_N)tRNA-methyltransferase O N-terminal domainThis 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

InterPro: Protein Family Classification InterPro Database Homepage