PDBsum entry 1hc7

Aminoacyl-tRNA synthetase

PDB id: 1hc7

Contents

Protein chains

464 a.a. *

Metals

_ZN ×4

Waters ×738

* Residue conservation analysis

References listed in PDB file

Key reference

Title

A succession of substrate induced conformational changes ensures the amino acid specificity of thermus thermophilus prolyl-Trna synthetase: comparison with histidyl-Trna synthetase.

Authors

A.Yaremchuk, M.Tukalo, M.Grøtli, S.Cusack.

Ref.

J Mol Biol, 2001, 309, 989. [DOI no: 10.1006/jmbi.2001.4712]

PubMed id

11399074

Abstract

We describe the recognition by Thermus thermophilus prolyl-tRNA synthetase (ProRSTT) of proline, ATP and prolyl-adenylate and the sequential conformational changes occurring when the substrates bind and the activated intermediate is formed. Proline and ATP binding cause respectively conformational changes in the proline binding loop and motif 2 loop. However formation of the activated intermediate is necessary for the final conformational ordering of a ten residue peptide ("ordering loop") close to the active site which would appear to be essential for functional tRNA 3' end binding. These induced fit conformational changes ensure that the enzyme is highly specific for proline activation and aminoacylation. We also present new structures of apo and AMP bound histidyl-tRNA synthetase (HisRS) from T. thermophilus which we compare to our previous structures of the histidine and histidyl-adenylate bound enzyme. Qualitatively, similar results to those observed with T. thermophilus prolyl-tRNA synthetase are found. However histidine binding is sufficient to induce the co-operative ordering of the topologically equivalent histidine binding loop and ordering loop. These two examples contrast with most other class II aminoacyl-tRNA synthetases whose pocket for the cognate amino acid side-chain is largely preformed. T. thermophilus prolyl-tRNA synthetase appears to be the second class II aminoacyl-tRNA synthetase, after HisRS, to use a positively charged amino acid instead of a divalent cation to catalyse the amino acid activation reaction.

Figure 2.
Figure 2. The prolyl-adenylate complex. (a) Unbiased positive difference electron density for the prolyl-adenylate analogue in the active site of ProRSTT contoured at 3.0 sigma after refinement of the structure without inclusion of the substrate in the model. (b) Hydrogen bond interactions (red dotted lines) of the prolyl-adenylate in the active site of ProRSTT. Class II synthetase conserved features, the TXE loop (gold), motif 2 (outlined in blue) and motif 3 (outlined in red) are shown.

Figure 5.
Figure 5. Induced fit recognition of histidine by HisRSTT. The histidine bound conformation of the histidine-1 loop is purple with white side-chains; that of the unbound form is pink with green side-chains. The histidine substrate is in yellow. Hydrogen bonds stabilising the position of the bound histidine and the catalytic Arg259 are shown as dotted red lines.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 309, 989-0) copyright 2001.

Secondary reference #1

Title

Crystal structure of a eukaryote/archaeon-Like protyl-Trna synthetase and its complex with trnapro(cgg).

Authors

A.Yaremchuk, S.Cusack, M.Tukalo.

Ref.

EMBO J, 2000, 19, 4745-4758. [DOI no: 10.1093/emboj/19.17.4745]

PubMed id

10970866

Figure 3.
Figure 3 Ribbon diagrams of single subunits of representatives of each of the five class IIa tRNA synthetases. All have the class II catalytic domain aligned in the same orientation with motifs 1, 2 and 3 shown in green, cyan and red, respectively. All except SerRS (top right) have the class IIa anticodon-binding domain (purple). System-specific domains are shown in yellow.

Figure 7.
Figure 7 Final 2F[o] – F[c] map of the anticodon loop of tRNA^Pro(CGG) contoured at 1.5 .

The above figures are reproduced from the cited reference which is an Open Access publication published by Macmillan Publishers Ltd

Secondary reference #2

Title

Crystallization and preliminary X-Ray diffraction analysis of thermus thermophilus prolyl-Trna synthetase.

Authors

A.Yaremchuk, S.Cusack, M.Tukalo.

Ref.

Acta Crystallogr D Biol Crystallogr, 2000, 56, 195-196.

PubMed id

10666603

Secondary reference #3

Title

Improved crystals of thermus thermophilus prolyl-Trna synthetase complexed with cognate tRNA obtained by crystallization from precipitate.

Authors

A.Yaremchuk, I.Kriklivyi, S.Cusack, M.Tukalo.

Ref.

Acta Crystallogr D Biol Crystallogr, 2000, 56, 197-199. [DOI no: 10.1107/S0907444999015504]

PubMed id

10666604

Figure 1.
Figure 1 (a) Superposition of the C^ trace of subunit A of the prolyl-tRNA synthetase dimer in form 1 and form 2 crystals showing the slight rotation of the anticodon-binding domain. (b) Crystal contact between subunit B of the ProRSTT dimer and the anticodon-binding domain of a crystal symmetry-related subunit A (denoted A'). A' is related to A by the crystal symmetry -y, -x, ½ - z in space group 96. This figure was obtained after superposition of subunit B from the two crystal forms. The anticodon-binding domain from subunit A' is grey for form 1 and black for form 2. In both crystal forms, the crystal contact involves the same regions but the residue interactions are different in detail (see text).

The above figure is reproduced from the cited reference with permission from the IUCr

Secondary reference #4

Title

Trna(pro) anticodon recognition by thermus thermophilus prolyl-Trna synthetase.

Authors

S.Cusack, A.Yaremchuk, I.Krikliviy, M.Tukalo.

Ref.

Structure, 1998, 6, 101-108. [DOI no: 10.1016/S0969-2126(98)00011-2]

PubMed id

9493271

Figure 1.
Figure 1. Anticodon stem-loop sequences of two T. thermophilus tRNA^Pro iso-acceptors. *Indicates a base modification.

The above figure is reproduced from the cited reference with permission from Cell Press