PDBsum entry: 2ztg

Ligase

PDB-id: 2ztg

Contents

Description

Header details

Header records

References

PROCHECK

Protein chain

739 a.a. *

Ligands

A5A

Metal ions

_ZN ×2

Waters ×152

* Residue conservation analysis

Tools

Clefts Calculation

• 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.

UniProt:

()

• Enzyme class: E.C.6.1.1.7 [IntEnz] [ExPASy] [KEGG] [BRENDA]
• Reaction: ATP + L-alanine + tRNA(Ala) = AMP + diphosphate + L-alanyl-tRNA(Ala) (see diagram below)
• Resolution: 2.20Å
• R-factor: 0.215
• R-free: 0.264
• Authors: M.Naganuma,S.Sekine,R.Fukunaga,S.Yokoyama
• 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
• Related entries: Ar_001000589.1 related db: targetdb

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Procheck

Clefts

Surface

Key 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.