PDBsum entry 5erg

Transferase

PDB id: 5erg

Contents

Protein chains

340 a.a.

324 a.a.

Ligands

SAM

Waters ×199

PDB id:

5erg

Name:

Transferase

Title:

Crystal structure of the two-subunit tRNA m1a58 methyltransferase trm6-trm61 in complex with sam

Structure:

tRNA (adenine(58)-n(1))-methyltransferase non-catalytic subunit trm6. Chain: a. Synonym: general control non-derepressible protein 10,protein gcd10, tRNA(m1a58)-methyltransferase subunit trm6,tRNA(m1a58)mtase subunit trm6. Engineered: yes. tRNA (adenine(58)-n(1))-methyltransferase catalytic subunit trm61.

Source:

Saccharomyces cerevisiae (strain atcc 204508 / s288c). Baker's yeast. Organism_taxid: 559292. Strain: atcc 204508 / s288c. Gene: gcd10, tif33, trm6, ynl062c, n2422. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: gcd14, trm61, yjl125c, j0710.

Resolution:

2.20Å R-factor: 0.186 R-free: 0.214

Authors:

Y.Zhu,M.Wang,C.Wang,X.Fan,X.Jiang,M.Teng,X.Li

Key ref:

M.Wang et al. (2016). Crystal structure of the two-subunit tRNA m(1)A58 methyltransferase TRM6-TRM61 from Saccharomyces cerevisiae. Sci Rep, 6, 32562. PubMed id: 27582183

Date:

14-Nov-15 Release date: 14-Sep-16

Protein chain

P41814  (TRM6_YEAST) -  tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 478 a.a.

Struc: 340 a.a.

Protein chain

P46959  (TRM61_YEAST) -  tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRM61 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 383 a.a.

Struc: 324 a.a.

Enzyme reactions

• Enzyme class 1: Chain A: E.C.?
• Enzyme class 2: Chain B: E.C.2.1.1.220 - tRNA (adenine(58)-N(1))-methyltransferase.
• Reaction: adenosine₅₈ in tRNA + S-adenosyl-L-methionine = N₁- methyladenosine₅₈ in tRNA + S-adenosyl-L-homocysteine + H⁺

adenosine(58) in tRNA + S-adenosyl-L-methionine (Bound ligand (Het Group name = SAM) corresponds exactly) = N(1)- methyladenosine(58) in tRNA + S-adenosyl-L-homocysteine + H(+)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

Sci Rep 6:32562 (2016)

PubMed id: 27582183

Crystal structure of the two-subunit tRNA m(1)A58 methyltransferase TRM6-TRM61 from Saccharomyces cerevisiae.

M.Wang, Y.Zhu, C.Wang, X.Fan, X.Jiang, M.Ebrahimi, Z.Qiao, L.Niu, M.Teng, X.Li.

ABSTRACT

The N(1) methylation of adenine at position 58 (m(1)A58) of tRNA is an important post-transcriptional modification, which is vital for maintaining the stability of the initiator methionine tRNAi(Met). In eukaryotes, this modification is performed by the TRM6-TRM61 holoenzyme. To understand the molecular mechanism that underlies the cooperation of TRM6 and TRM61 in the methyl transfer reaction, we determined the crystal structure of TRM6-TRM61 holoenzyme from Saccharomyces cerevisiae in the presence and absence of its methyl donor S-Adenosyl-L-methionine (SAM). In the structures, two TRM6-TRM61 heterodimers assemble as a heterotetramer. Both TRM6 and TRM61 subunits comprise an N-terminal β-barrel domain linked to a C-terminal Rossmann-fold domain. TRM61 functions as the catalytic subunit, containing a methyl donor (SAM) binding pocket. TRM6 diverges from TRM61, lacking the conserved motifs used for binding SAM. However, TRM6 cooperates with TRM61 forming an L-shaped tRNA binding regions. Collectively, our results provide a structural basis for better understanding the m(1)A58 modification of tRNA occurred in Saccharomyces cerevisiae.