PDBsum entry: 1mb2

Ligase

PDB id: 1mb2

Contents

Protein chains

(+ 0 more) 326 a.a. *

Ligands

TRP ×6

* Residue conservation analysis

PDB id:

1mb2

Name:

Ligase

Title:

Crystal structure of tryptophanyl-tRNA synthetase complexed with tryptophan in an open conformation

Structure:

Tryptophan-tRNA ligase. Chain: a, b, c, d, e, f. Synonym: tryptophanyl-tRNA synthetase. Engineered: yes

Source:

Geobacillus stearothermophilus. Organism_taxid: 1422. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Tetramer (from PQS)

Resolution:

2.70Å R-factor: 0.220 R-free: 0.254

Authors:

P.Retailleau,X.Huang,Y.Yin,M.Hu,V.Weinreb,P.Vachette, C.Vonrhein,G.Bricogne,P.Roversi,V.Ilyin,C.W.Carter Jr.

Key ref:

P.Retailleau et al. (2003). Interconversion of ATP binding and conformational free energies by tryptophanyl-tRNA synthetase: structures of ATP bound to open and closed, pre-transition-state conformations. J Mol Biol, 325, 39-63. PubMed id: 12473451 DOI: 10.1016/S0022-2836(02)01156-7

Date:

02-Aug-02 Release date: 07-Jan-03

Protein chains

P00953  (SYW_GEOSE) -  Tryptophanyl-tRNA synthetase

Seq: 328 a.a.

Struc: 326 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

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

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

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

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: translation (3 terms)
• Biochemical function: nucleotide binding (5 terms)

reference

DOI no: 10.1016/S0022-2836(02)01156-7

J Mol Biol 325:39-63 (2003)

PubMed id: 12473451

Interconversion of ATP binding and conformational free energies by tryptophanyl-tRNA synthetase: structures of ATP bound to open and closed, pre-transition-state conformations.

P.Retailleau, X.Huang, Y.Yin, M.Hu, V.Weinreb, P.Vachette, C.Vonrhein, G.Bricogne, P.Roversi, V.Ilyin, C.W.Carter.

ABSTRACT

Binding ATP to tryptophanyl-tRNA synthetase (TrpRS) in a catalytically competent configuration for amino acid activation destabilizes the enzyme structure prior to forming the transition state. This conclusion follows from monitoring the titration of TrpRS with ATP by small angle solution X-ray scattering, enzyme activity, and crystal structures. ATP induces a significantly smaller radius of gyration at pH=7 with a transition midpoint at approximately 8mM. A non-reciprocal dependence of Trp and ATP dissociation constants on concentrations of the second substrate show that Trp binding enhances affinity over the same concentration range ( approximately 5mM) that induces the more compact conformation. Two distinct TrpRS:ATP structures have been solved, a high-affinity complex grown with 1mM ATP and a low-affinity complex grown at 10mM ATP. The former is isomorphous with unliganded TrpRS and the Trp complex from monoclinic crystals. Reacting groups of the two individually-bound substrates are separated by 6.7A. Although it lacks tryptophan, the low-affinity complex has a closed conformation similar to that observed in the presence of both ATP and Trp analogs such as indolmycin, and resembles a complex previously postulated to form in the closely-related TyrRS upon induced-fit active-site assembly, just prior to catalysis. Titration of TrpRS with ATP therefore successively produces structurally distinct high- and low-affinity ATP-bound states. The higher quality X-ray data for the closed ATP complex (2.2A) provide new structural details likely related to catalysis, including an extension of the KMSKS loop that engages the second lysine and serine residues, K195 and S196, with the alpha and gamma-phosphates; interactions of the K111 side-chain with the gamma-phosphate; and a water molecule bridging the consensus sequence residue T15 to the beta-phosphate. Induced-fit therefore strengthens active-site interactions with ATP, substantially intensifying the interaction of the KMSKS loop with the leaving PP(i) group. Formation of this conformation in the absence of a Trp analog implies that ATP is a key allosteric effector for TrpRS. The implies that Gibbs binding free energy is stored in an unfavorable protein conformation and can then be recovered for useful purposes, including catalysis in the case of TrpRS.

Selected figure(s)

Figure 6.
Figure 6. The structure of the closed, pre-TS TrpRS binary ATP complex compared with the open ATP complex and the closed, product complex containing Trp-5'AMP. Adenine nucleotide ligands are colored green for ATP and red for tryptophanyl-5'AMP. The figure illustrates the differences in R[g] of the three TrpRS conformational states, as well as the domain rearrangements within the monomer. The two closed states can be differentiated relative to the internal orthonormal coordinate system; the product complex fully reveals the axis on the lower right.

Figure 11.
Figure 11. Final 2.2 Å electron density map contoured at 1.5s showing the ATP-binding site in the closed, pre-TS conformation. The green ball corresponds to the model of the putative Mg2+.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 325, 39-63) copyright 2003.

Figures were selected by an automated process.