PDBsum entry 3w3s

Ligase/RNA

PDB id: 3w3s

Contents

Protein chain

527 a.a.

DNA/RNA

Ligands

SSA

SO4 ×8

Metals

_ZN

_PT ×15

PDB id:

3w3s

Name:

Ligase/RNA

Title:

Crystal structure of a. Aeolicus trnasec in complex with m. Kandleri serrs

Structure:

Type-2 serine--tRNA ligase. Chain: a. Synonym: seryl-tRNA synthetase, serrs, seryl-tRNA(ser/sec) synthetase. Engineered: yes. Mutation: yes. Selenocysteine tRNA. Chain: b. Engineered: yes

Source:

Methanopyrus kandleri. Organism_taxid: 190192. Strain: av19. Gene: sers. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Aquifex aeolicus vf5. Organism_taxid: 224324.

Resolution:

3.10Å R-factor: 0.206 R-free: 0.260

Authors:

Y.Itoh,S.Sekine,S.Yokoyama

Key ref:

Y.Itoh et al. (2013). Tertiary structure of bacterial selenocysteine tRNA. Nucleic Acids Res, 41, 6729-6738. PubMed id: 23649835 DOI: 10.1093/nar/gkt321

Date:

27-Dec-12 Release date: 13-Feb-13

Protein chain

Q8TVD2  (SYS2_METKA) -  Type-2 serine--tRNA ligase from Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)

Seq: 527 a.a.

Struc: 527 a.a.*

* PDB and UniProt seqs differ at 11 residue positions (black crosses)

DNA/RNA chain

G-G-G-A-G-A-G-G-U-U-G-G-C-C-G-G-C-U-G-G-U-G-C-C-G-C-C-C-C-G-G-G-A-C-U-U-C-A-A- 98 bases

Enzyme reactions

• Enzyme class: E.C.6.1.1.11 - serine--tRNA ligase.
• Reaction:
  1. tRNA(Ser) + L-serine + ATP = L-seryl-tRNA(Ser) + AMP + diphosphate + H⁺
  2. tRNA(Sec) + L-serine + ATP = L-seryl-tRNA(Sec) + AMP + diphosphate + H⁺

tRNA(Ser) + L-serine + ATP = L-seryl-tRNA(Ser) (Bound ligand (Het Group name = SSA) matches with 57.58% similarity) + AMP + diphosphate + H(+)

tRNA(Sec) + L-serine + ATP = L-seryl-tRNA(Sec) (Bound ligand (Het Group name = SSA) matches with 57.58% similarity) + AMP + diphosphate + H(+)

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

reference

DOI no: 10.1093/nar/gkt321

Nucleic Acids Res 41:6729-6738 (2013)

PubMed id: 23649835

Tertiary structure of bacterial selenocysteine tRNA.

Y.Itoh, S.Sekine, S.Suetsugu, S.Yokoyama.

ABSTRACT

Selenocysteine (Sec) is translationally incorporated into proteins in response to the UGA codon. The tRNA specific to Sec (tRNA(Sec)) is first ligated with serine by seryl-tRNA synthetase (SerRS). In the present study, we determined the 3.1 Å crystal structure of the tRNA(Sec) from the bacterium Aquifex aeolicus, in complex with the heterologous SerRS from the archaeon Methanopyrus kandleri. The bacterial tRNA(Sec) assumes the L-shaped structure, from which the long extra arm protrudes. Although the D-arm conformation and the extra-arm orientation are similar to those of eukaryal/archaeal tRNA(Sec)s, A. aeolicus tRNA(Sec) has unique base triples, G14:C21:U8 and C15:G20a:G48, which occupy the positions corresponding to the U8:A14 and R15:Y48 tertiary base pairs of canonical tRNAs. Methanopyrus kandleri SerRS exhibited serine ligation activity toward A. aeolicus tRNA(Sec) in vitro. The SerRS N-terminal domain interacts with the extra-arm stem and the outer corner of tRNA(Sec). Similar interactions exist in the reported tRNA(Ser) and SerRS complex structure from the bacterium Thermus thermophilus. Although the catalytic C-terminal domain of M. kandleri SerRS lacks interactions with A. aeolicus tRNA(Sec) in the present complex structure, the conformational flexibility of SerRS is likely to allow the CCA terminal region of tRNA(Sec) to enter the SerRS catalytic site.