PDBsum entry: 2zue

Ligase/RNA

PDB-id: 2zue

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PROCHECK

Protein chain

628 a.a. *

DNA/RNA

Ligands

ANP

Metal ions

_MG

Waters ×362

* Residue conservation analysis

Tools

Clefts Calculation

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PDB id:

2zue

Name:

Ligase/RNA

Title:

Crystal structure of pyrococcus horikoshii arginyl-tRNA synthetase complexed with tRNA(arg) and an atp analog (anp)

Structure:

Arginyl-tRNA synthetase. Chain: a. Synonym: arginine--tRNA ligase, argrs. Engineered: yes. tRNA-arg. Chain: b. Engineered: yes

Source:

Pyrococcus horikoshii. Organism_taxid: 53953. Gene: args, ph1478. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes. Other_details: this tRNA occurs from pyrococcus horikoshii, in vitro transcription

UniProt:

O59147 (SYR_PYRHO)

Seq:

Struc:

Seq:

Struc:

Seq:

629 a.a.

Struc:

628 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

Enzyme class:

E.C.6.1.1.19   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

ATP + L-arginine + tRNA(Arg) = AMP + diphosphate + L-arginyl-tRNA(Arg) (see diagram below)

Resolution:

2.00Å

R-factor:

0.213

R-free:

0.253

Authors:

M.Konno,T.Sumida,E.Uchikawa,Y.Mori,T.Yanagisawa,S.Sekine, S.Yokoyama

Key ref:

M.Konno et al. (2009). Modeling of tRNA-assisted mechanism of Arg activation based on a structure of Arg-tRNA synthetase, tRNA, and an ATP analog (ANP).. Febs J, 276, 4763-4779. [PubMed id: 19656186] [DOI: 10.1111/j.1742-4658.2009.07178.x]

Date:

16-Oct-08

Release date:

18-Aug-09

Related entries:

2zuf
the same protein complexed with tRNA(arg)

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Key reference

DOI no: 10.1111/j.1742-4658.2009.07178.x

Febs J 276:4763-4779 (2009)

PubMed id: 19656186

Modeling of tRNA-assisted mechanism of Arg activation based on a structure of Arg-tRNA synthetase, tRNA, and an ATP analog (ANP).

M.Konno, T.Sumida, E.Uchikawa, Y.Mori, T.Yanagisawa, S.Sekine, S.Yokoyama.

ABSTRACT

The ATP-pyrophosphate exchange reaction catalyzed by Arg-tRNA, Gln-tRNA and Glu-tRNA synthetases requires the assistance of the cognate tRNA. tRNA also assists Arg-tRNA synthetase in catalyzing the pyrophosphorolysis of synthetic Arg-AMP at low pH. The mechanism by which the 3'-end A76, and in particular its hydroxyl group, of the cognate tRNA is involved with the exchange reaction catalyzed by those enzymes has yet to be established. We determined a crystal structure of a complex of Arg-tRNA synthetase from Pyrococcus horikoshii, tRNA(Arg)(CCU) and an ATP analog with Rfactor = 0.213 (Rfree = 0.253) at 2.0 A resolution. On the basis of newly obtained structural information about the position of ATP bound on the enzyme, we constructed a structural model for a mechanism in which the formation of a hydrogen bond between the 2'-OH group of A76 of tRNA and the carboxyl group of Arg induces both formation of Arg-AMP (Arg + ATP --> Arg-AMP + pyrophosphate) and pyrophosphorolysis of Arg-AMP (Arg-AMP + pyrophosphate --> Arg + ATP) at low pH. Furthermore, we obtained a structural model of the molecular mechanism for the Arg-tRNA synthetase-catalyzed deacylation of Arg-tRNA (Arg-tRNA + AMP --> Arg-AMP + tRNA at high pH), in which the deacylation of aminoacyl-tRNA bound on Arg-tRNA synthetase and Glu-tRNA synthetase is catalyzed by a quite similar mechanism, whereby the proton-donating group (-NH-C+(NH2)2 or -COOH) of Arg and Glu assists the aminoacyl transfer from the 2'-OH group of tRNA to the phosphate group of AMP at high pH.