PDBsum entry 2ztg

Ligase

PDB id: 2ztg

Contents

Protein chain

739 a.a. *

Ligands

A5A

Metals

_ZN ×2

Waters ×152

* Residue conservation analysis

PDB id:

2ztg

Name:

Ligase

Title:

Crystal structure of archaeoglobus fulgidus alanyl-tRNA synthetase lacking thE C-terminal dimerization domain in complex with ala-sa

Structure:

Alanyl-tRNA synthetase. Chain: a. Fragment: alars-deltac. Synonym: alanine-tRNA ligase, alars. Engineered: yes

Source:

Archaeoglobus fulgidus. Organism_taxid: 2234. Gene: af_2255, alas. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.20Å R-factor: 0.215 R-free: 0.264

Authors:

M.Naganuma,S.Sekine,R.Fukunaga,S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

M.Naganuma et al. (2009). Unique protein architecture of alanyl-tRNA synthetase for aminoacylation, editing, and dimerization. Proc Natl Acad Sci U S A, 106, 8489-8494. PubMed id: 19423669 DOI: 10.1073/pnas.0901572106

Date:

01-Oct-08 Release date: 30-Jun-09

Protein chain

O28029  (SYA_ARCFU) -  Alanine--tRNA ligase from Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)

Seq: 906 a.a.

Struc: 739 a.a.

Enzyme reactions

• Enzyme class: E.C.6.1.1.7 - alanine--tRNA ligase.
• Reaction: tRNA(Ala) + L-alanine + ATP = L-alanyl-tRNA(Ala) + AMP + diphosphate

tRNA(Ala) + L-alanine + ATP = L-alanyl-tRNA(Ala) (Bound ligand (Het Group name = A5A) matches with 59.38% similarity) + AMP + diphosphate

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

reference

DOI no: 10.1073/pnas.0901572106

Proc Natl Acad Sci U S A 106:8489-8494 (2009)

PubMed id: 19423669

Unique protein architecture of alanyl-tRNA synthetase for aminoacylation, editing, and dimerization.

M.Naganuma, S.I.Sekine, R.Fukunaga, S.Yokoyama.

ABSTRACT

Alanyl-tRNA synthetase (AlaRS) specifically recognizes the major identity determinant, the G3:U70 base pair, in the acceptor stem of tRNA(Ala) by both the tRNA-recognition and editing domains. In this study, we solved the crystal structures of 2 halves of Archaeoglobus fulgidus AlaRS: AlaRS-DeltaC, comprising the aminoacylation, tRNA-recognition, and editing domains, and AlaRS-C, comprising the dimerization domain. The aminoacylation/tRNA-recognition domains contain an insertion incompatible with the class-specific tRNA-binding mode. The editing domain is fixed tightly via hydrophobic interactions to the aminoacylation/tRNA-recognition domains, on the side opposite from that in threonyl-tRNA synthetase. A groove formed between the aminoacylation/tRNA-recognition domains and the editing domain appears to be an alternative tRNA-binding site, which might be used for the aminoacylation and/or editing reactions. Actually, the amino acid residues required for the G3:U70 recognition are mapped in this groove. The dimerization domain consists of helical and globular subdomains. The helical subdomain mediates dimerization by forming a helix-loop-helix zipper. The globular subdomain, which is important for the aminoacylation and editing activities, has a positively-charged face suitable for tRNA binding.

Selected figure(s)

Figure 2.
The aminoacylation and tRNA-recognition domains. (A) The aminoacylation and tRNA-recognition domains of A. fulgidus AlaRS, colored as in Fig. 1B, are shown. (B) The A. aeolicus AlaRS-N structure, shown in the same orientation. The 2 regions missing in A. fulgidus (InsB/E1 and InsB/E2) are colored brown, and Mid2 is shown in gold.

Figure 6.
A model of the full-length AlaRS dimer. Two copies of AlaRS-ΔC, which are correlated by the crystallographic 2-fold axis, and an AlaRS-C dimer, are shown. The N termini of AlaRS-C were placed near the C termini of AlaRS-ΔC. The model was colored as in Fig. 1.

Figures were selected by an automated process.