PDBsum entry 2ct8

Ligase/RNA

PDB id: 2ct8

Contents

Protein chains

465 a.a. *

DNA/RNA

Ligands

MSP ×2

Waters ×78

* Residue conservation analysis

PDB id:

2ct8

Name:

Ligase/RNA

Title:

Crystal structure of aquifex aeolicus methionyl-tRNA synthetase complexed with tRNA(met) and methionyl-adenylate anologue

Structure:

RNA (74-mer). Chain: c, d. Engineered: yes. Methionyl-tRNA synthetase. Chain: a, b. Synonym: methionine--tRNA ligase, metrs. Engineered: yes

Source:

Synthetic: yes. Aquifex aeolicus. Organism_taxid: 63363. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.70Å R-factor: 0.217 R-free: 0.272

Authors:

K.Nakanishi,Y.Ogiso,T.Nakama,S.Fukai,O.Nureki,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

K.Nakanishi et al. (2005). Structural basis for anticodon recognition by methionyl-tRNA synthetase. Nat Struct Biol, 12, 931-932. PubMed id: 16155581 DOI: 10.1038/nsmb988

Date:

23-May-05 Release date: 20-Sep-05

Protein chains

O67298  (SYM_AQUAE) -  Methionine--tRNA ligase from Aquifex aeolicus (strain VF5)

Seq: 497 a.a.

Struc: 465 a.a.

DNA/RNA chains

G-G-C-G-G-C-G-U-A-G-C-U-C-A-G-C-U-G-G-U-C-A-G-A-G-C-G-G-G-G-A-U-C-U-C-A-U-A-A- 74 bases

G-G-C-G-G-C-G-U-A-G-C-U-C-A-G-C-U-G-G-U-C-A-G-A-G-C-G-G-G-G-A-U-C-U-C-A-U-A-A- 74 bases

Enzyme reactions

• Enzyme class: E.C.6.1.1.10 - methionine--tRNA ligase.
• Reaction: tRNA(Met) + L-methionine + ATP = L-methionyl-tRNA(Met) + AMP + diphosphate

tRNA(Met) + L-methionine + ATP = L-methionyl-tRNA(Met) (Bound ligand (Het Group name = MSP) matches with 54.29% similarity) + AMP + diphosphate

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

reference

DOI no: 10.1038/nsmb988

Nat Struct Biol 12:931-932 (2005)

PubMed id: 16155581

Structural basis for anticodon recognition by methionyl-tRNA synthetase.

K.Nakanishi, Y.Ogiso, T.Nakama, S.Fukai, O.Nureki.

ABSTRACT

In the 2.7-A resolution crystal structure of methionyl-tRNA synthetase (MetRS) in complex with tRNA(Met) and a methionyl-adenylate analog, the tRNA anticodon loop is distorted to form a triple-base stack comprising C34, A35 and A38. A tryptophan residue stacks on C34 to extend the triple-base stack. In addition, C34 forms Watson-Crick-type hydrogen bonds with Arg357. This structure resolves the longstanding question of how MetRS specifically recognizes tRNA(Met).

Selected figure(s)

Figure 1.
Figure 1. The A. aeolicus MetRS−tRNA[m]^Met complex. Green, the Rossmann fold domain; cyan and dark blue, the CP1 and CP2 insertions, respectively; salmon, the MetRS-specific -strand insertion; red, the stem-contact-fold domain; pink, the -helix bundle domain; yellow, tRNA[m]^Met; stick model, MetSA.

Figure 2.
Figure 2. Recognition of the anticodon CAU of tRNA[m]^Met by MetRS. (a) Conformational change of A. aeolicus tRNA[m]^Met (yellow) upon binding MetRS, as compared with unbound yeast tRNA^Phe (blue). (b) Interaction between MetRS and the tRNA[m]^Met anticodon. Yellow, tRNA[m]^Met nucleotides; light purple, MetRS residues; dotted lines, hydrogen bonds; red, oxygen; blue, nitrogen.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2005, 12, 931-932) copyright 2005.