PDBsum entry 2zr3

Ligase

PDB id: 2zr3

Contents

Protein chains

448 a.a. *

Waters ×30

* Residue conservation analysis

PDB id:

2zr3

Name:

Ligase

Title:

Crystal structure of seryl-tRNA synthetase from pyrococcus horikoshii

Structure:

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

Source:

Pyrococcus horikoshii. Organism_taxid: 70601. Strain: ot3. Gene: ph0710. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

3.00Å R-factor: 0.190 R-free: 0.258

Authors:

Y.Itoh,S.Sekine,S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

Y.Itoh et al. (2008). Crystallographic and mutational studies of seryl-tRNA synthetase from the archaeon Pyrococcus horikoshii. Rna Biol, 5, 169-177. PubMed id: 18818520

Date:

22-Aug-08 Release date: 09-Sep-08

Supersedes:

2dq2

Protein chains

O58441  (SYS_PYRHO) -  Serine--tRNA ligase from Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)

Seq: 455 a.a.

Struc: 448 a.a.

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⁺

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

reference

Rna Biol 5:169-177 (2008)

PubMed id: 18818520

Crystallographic and mutational studies of seryl-tRNA synthetase from the archaeon Pyrococcus horikoshii.

Y.Itoh, S.Sekine, C.Kuroishi, T.Terada, M.Shirouzu, S.Kuramitsu, S.Yokoyama.

ABSTRACT

Seryl-tRNA synthetase (SerRS) catalyzes the ligation of serine to the 3'-end of serine tRNA (tRNA(Ser)), which is typical of the type-2 tRNAs characterized by a long extra arm. The SerRSs are divided into two types, the archaeal/eukaryal and bacterial types. In this study, we solved the crystal structures of the SerRS from the archaeon Pyrococcus horikoshii bound with 5'-O-[N-(L-seryl)-sulfamoyl]-adenosine at 2.6 A and with ATP at 2.8 A, as well as in the apo form at 3.0 A. P. horikoshii SerRS recognizes the seryl and adenylate moieties in a manner similar to those of the bacterial and mitochondrial SerRSs from Thermus thermophilus and Bos taurus, respectively, but different from that of the unusual SerRS from the methanogenic archaeon Methanosarcina barkeri. P. horikoshii SerRS efficiently aminoacylated not only P. horikoshii tRNA(Ser) but also bacterial tRNA(Ser)s from T. thermophilus and Escherichia coli. Models of P. horikoshii SerRS bound with the T. thermophilus and P. horikoshii tRNA(Ser)s suggested that the helical domain of P. horikoshii SerRS is involved in the extra arm binding. This region of P. horikoshii SerRS has additional basic residues as compared with T. thermophilus SerRS, and a Trp residue specific to the archaeal/eukaryal SerRSs. Mutational analyses revealed that the basic and Trp residues are important for tRNA aminoacylation. P. horikoshii SerRS has the archaea-specific insertion, which collaborates with the core domain to form a basic channel leading to the active site. Two sulfate ions are bound to the channel, suggesting that the tRNA 3' region might bind to the channel.