PDBsum entry 2a4m

Ligase

PDB id: 2a4m

Contents

Protein chains

331 a.a. *

Ligands

TRP

Waters ×1191

* Residue conservation analysis

PDB id:

2a4m

Name:

Ligase

Title:

Structure of trprs ii bound to atp

Structure:

Tryptophanyl-tRNA synthetase ii. Chain: a, b, c. Synonym: tryptophan--tRNA ligase ii, trprs ii. Engineered: yes

Source:

Deinococcus radiodurans. Organism_taxid: 1299. Gene: trps2, trpsii. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PDB file)

Resolution:

2.30Å R-factor: 0.230 R-free: 0.270

Authors:

M.R.Buddha,B.R.Crane

Key ref:

M.R.Buddha and B.R.Crane (2005). Structures of tryptophanyl-tRNA synthetase II from Deinococcus radiodurans bound to ATP and tryptophan. Insight into subunit cooperativity and domain motions linked to catalysis. J Biol Chem, 280, 31965-31973. PubMed id: 15998643 DOI: 10.1074/jbc.M501568200

Date:

29-Jun-05 Release date: 02-Aug-05

Protein chains

Q9RVD6  (SYW2_DEIRA) -  Tryptophan--tRNA ligase 2 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 351 a.a.

Struc: 331 a.a.

Enzyme reactions

• Enzyme class: E.C.6.1.1.2 - tryptophan--tRNA ligase.
• Reaction: tRNA(Trp) + L-tryptophan + ATP = L-tryptophyl-tRNA(Trp) + AMP + diphosphate + H⁺

tRNA(Trp) + L-tryptophan (Bound ligand (Het Group name = TRP) corresponds exactly) + ATP = L-tryptophyl-tRNA(Trp) + AMP + diphosphate + H(+)

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

reference

DOI no: 10.1074/jbc.M501568200

J Biol Chem 280:31965-31973 (2005)

PubMed id: 15998643

Structures of tryptophanyl-tRNA synthetase II from Deinococcus radiodurans bound to ATP and tryptophan. Insight into subunit cooperativity and domain motions linked to catalysis.

M.R.Buddha, B.R.Crane.

ABSTRACT

An auxiliary tryptophanyl tRNA synthetase (drTrpRS II) that interacts with nitric-oxide synthase in the radiation-resistant bacterium Deinococcus radiodurans charges tRNA with tryptophan and 4-nitrotryptophan, a specific nitration product of nitric-oxide synthase. Crystal structures of drTrpRS II, empty of ligands or bound to either Trp or ATP, reveal that drTrpRS II has an overall structure similar to standard bacterial TrpRSs but undergoes smaller amplitude motions of the helical tRNA anti-codon binding (TAB) domain on binding substrates. TAB domain loop conformations that more closely resemble those of human TrpRS than those of Bacillus stearothermophilus TrpRS (bsTrpRS) indicate different modes of tRNA recognition by subclasses of bacterial TrpRSs. A compact state of drTrpRS II binds ATP, from which only minimal TAB domain movement is necessary to bring nucleotide in contact with Trp. However, the signature KMSKS loop of class I synthetases does not completely engage the ATP phosphates, and the adenine ring is not well ordered in the absence of Trp. Thus, progression of the KMSKS loop to a high energy conformation that stages acyl-adenylation requires binding of both substrates. In an asymmetric drTrpRS II dimer, the closed subunit binds ATP, whereas the open subunit binds Trp. A crystallographically symmetric dimer binds no ligands. Half-site reactivity for Trp binding is confirmed by thermodynamic measurements and explained by an asymmetric shift of the dimer interface toward the occupied active site. Upon Trp binding, Asp68 propagates structural changes between subunits by switching its hydrogen bonding partner from dimer interface residue Tyr139 to active site residue Arg30. Since TrpRS IIs are resistant to inhibitors of standard TrpRSs, and pathogens contain drTrpRS II homologs, the structure of drTrpRS II provides a framework for the design of potentially useful antibiotics.

Selected figure(s)

Figure 1.
FIG. 1. A, ribbon diagram of the drTrpRS II asymmetric dimer that binds ATP. Each subunit has an RF catalytic domain (B in cyan and C in dark blue) and a TAB domain (B in violet and C in red). ATP binds only the B subunit, which has a more closed conformation than the C subunit. B, ribbon diagram of drTrpRS II asymmetric dimer colored as in A with L-tryptophan bound in the more "open" C subunit (Protein Data Bank code 1YI8 [PDB] ). C, superposition of drTrpRS II with bsTrpRS in the open and closed conformations (Protein Data Bank codes 1D2R [PDB] and 1I6M, respectively). Only equivalent secondary structure elements in the respective RF domains were superimposed. D, superposition of drTrpRS II with human TrpRS (hTrpRS; Protein Data Bank code 1Q5T [PDB] ).

Figure 6.
FIG. 6. A, ATP recognition by bsTrpRS and drTrpRS II. A, ATP binding site of bsTrpRS in the open conformation (Protein Data Bank code 1MAW [PDB] ). B, ATP binding site of drTrpRS II with F[o] - F[c] electron density map (red, 3.5; , green, 2.5 ) calculated with Mg-ATP removed from F[c]. C, active site of bsTrpRS in closed pretransition state with ATP bound (Protein Data Bank code 1M83 [PDB] ). In both bsTrpRS and drTrpRS II, magnesium is solely coordinated by the phosphates of ATP.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 31965-31973) copyright 2005.

Figures were selected by an automated process.