PDBsum entry 2i4l

Ligase

PDB id: 2i4l

Contents

Protein chains

439 a.a. *

Waters ×623

* Residue conservation analysis

PDB id:

2i4l

Name:

Ligase

Title:

Rhodopseudomonas palustris prolyl-tRNA synthetase

Structure:

Proline-tRNA ligase. Chain: a, b, c. Engineered: yes

Source:

Rhodopseudomonas palustris. Organism_taxid: 1076. Strain: cga009-atcc baa-98. Gene: pros,rpa2928. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PDB file)

Resolution:

2.00Å R-factor: 0.192 R-free: 0.221

Authors:

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

Key ref:

T.Crepin et al. (2006). Structures of two bacterial prolyl-tRNA synthetases with and without a cis-editing domain. Structure, 14, 1511-1525. PubMed id: 17027500 DOI: 10.1016/j.str.2006.08.007

Date:

22-Aug-06 Release date: 24-Oct-06

Protein chains

Q6N5P6  (SYP_RHOPA) -  Proline--tRNA ligase from Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)

Seq: 438 a.a.

Struc: 439 a.a.

Enzyme reactions

• Enzyme class: E.C.6.1.1.15 - proline--tRNA ligase.
• Reaction: tRNA(Pro) + L-proline + ATP = L-prolyl-tRNA(Pro) + AMP + diphosphate

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

reference

DOI no: 10.1016/j.str.2006.08.007

Structure 14:1511-1525 (2006)

PubMed id: 17027500

Structures of two bacterial prolyl-tRNA synthetases with and without a cis-editing domain.

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

ABSTRACT

Prolyl-tRNA synthetases (ProRSs) are unique among synthetases in that they have diverse architectures, notably the variable presence of a cis-editing domain homologous to the freestanding deacylase proteins YbaK and ProX. Here, we describe crystal structures of two bacterial ProRSs from the pathogen Enterococcus faecalis, which possesses an editing domain, and from Rhodopseudomonas palustris, which does not. We compare the overall structure and binding mode of ATP and prolyl-adenylate with those of the archael/eukaryote-type ProRS from Thermus thermophilus. Although structurally more homologous to YbaK, which preferentially hydrolyzes Cys-tRNA(Pro), the editing domain of E. faecalis ProRS possesses key elements similar to ProX, with which it shares the activity of hydrolyzing Ala-tRNA(Pro). The structures give insight into the complex evolution of ProRSs, the mechanism of editing, and structural differences between prokaryotic- and eukaryotic-type ProRSs that can be exploited for antibiotic design.

Selected figure(s)

Figure 3.
Figure 3. Interactions of ProRSs with ATP
(A–C) Active sites of (A) R. palustris, (B) E. faecalis, and (C) T. thermophilus ProRS with bound ATP (predominantly pink molecule), showing hydrogen bonds with key interacting residues. The insertion domains are in magenta (in [A] and [B]), and the eukaryote/archae-type-specific C-terminal domain is in yellow (in [C]). Note the functionally equivalent roles of Glu218 in PrsRp and PrsEf with the conserved carboxy terminus (Tyr477) in PrsTt. In each case, the proline-binding loop is in the open conformation.

Figure 4.
Figure 4. Interactions of ProRSs with the Prolyl-Adenylate Analog, ProAMS
(A–C) ProAMS (predominantly gray molecule) bound in the active sites of (A) R. palustris, (B) E. faecalis, and (C) T. thermophilus ProRS, showing key hydrogen bonds to the proline and sulfate moieties. Class II synthetase conserved motifs 1, 2, and 3 are shown in green, cyan, and red, respectively, and the TXE loop is shown in gold. On the proline-binding loop (violet), which is in the closed conformation, hydrophobic residues Ile202, Met202, and Phe205 play equivalent roles in PrsRp, PrsEf, and PrsTt, respectively.

The above figures are reprinted by permission from Cell Press: Structure (2006, 14, 1511-1525) copyright 2006.

Figures were selected by an automated process.