PDBsum entry 1v4p

Ligase

PDB id: 1v4p

Contents

Protein chains

151 a.a. *

Metals

_ZN ×3

Waters ×599

* Residue conservation analysis

PDB id:

1v4p

Name:

Ligase

Title:

Crystal structure of alanyl-tRNA synthetase from pyrococcus horikoshii ot3

Structure:

Alanyl-tRNA synthetase. Chain: a, b, c. Engineered: yes

Source:

Pyrococcus horikoshii. Organism_taxid: 53953. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.45Å R-factor: 0.206 R-free: 0.227

Authors:

J.Ishijima,K.Yutani,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

J.Ishijima et al. (2006). Crystal structure of alanyl-tRNA synthetase editing-domain homolog (PH0574) from a hyperthermophile, Pyrococcus horikoshii OT3 at 1.45 A resolution. Proteins, 62, 1133-1137. PubMed id: 16374837 DOI: 10.1002/prot.20760

Date:

14-Nov-03 Release date: 23-Nov-04

Protein chains

O58307  (ALAXS_PYRHO) -  Alanyl-tRNA editing protein AlaX-S from Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)

Seq: 157 a.a.

Struc: 151 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

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

reference

DOI no: 10.1002/prot.20760

Proteins 62:1133-1137 (2006)

PubMed id: 16374837

Crystal structure of alanyl-tRNA synthetase editing-domain homolog (PH0574) from a hyperthermophile, Pyrococcus horikoshii OT3 at 1.45 A resolution.

J.Ishijima, Y.Uchida, C.Kuroishi, C.Tuzuki, N.Takahashi, N.Okazaki, K.Yutani, M.Miyano.

ABSTRACT

No abstract given.

Selected figure(s)

Figure 1.
Figure 1. Multiple alignment of the editing domain of AlaRS and ThrRS enzymes. Residues involved in coordination of the zinc ion (red) and highly conserved residues (yellow) are indicated. The secondary structure elements in the crystal structure of PH0574 (above) and ecThrRS (below) are shown in the alignment. GenBank accession numbers given in parentheses are PH0574 (NP_142539), mbAlaX (ZP_00296079), pfAlaRS (NP_577999), ecAlaRS (NP_417177), saThrRS (NP_646443, PDB ID: 1NYR), ecThrRS (NP_416234, PDB ID: 1QF6).

Figure 2.
Figure 2. (A) Ribbon diagram of PH0574, which consists of a large (green) domain and a small (orange) domain. The Zn^2+ ion is located between the two domains. (B) Close-up view of the Zn^2+ ion binding site. A strong peak in the anomalous difference Fourier map was observed only at the zinc position. Many water molecules were observed around the Zn^2+ ion, although none of these are involved in coordination. The anomalous difference Fourier map contoured at 20 (orange) and 2F[o] - F[c] map contoured at 2 (blue) are shown. (C) Zinc ion coordinate diagram. The coordination of the Zn^2+ ion is mediated by the conserved histidine and cysteine residues both in PH0574 (green) and in saThrRS (blue, parentheses, PDB ID: 1NYR). (D) Structure of the putative active site drawn with a van der Waals surface with charge. The cavity accommodates an acyl serine.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2006, 62, 1133-1137) copyright 2006.

Author's comment

The structural and functional report of the same protein, PH0574 as AlaX was published independently by Sogabe et al., and they confirmed the tRNA editing function experimentally.
Sokabe M, Okada A, Yao M, Nakashima T, Tanaka I (2005). Molecular basis of alanine discrimination in editing site. Proc. Natl. Acad. Sci. USA, 102, 11669-11674. [PubMed: 16087889]
PDB entries: 1wnu and 1wxo.