2I4O | pdb_00002i4o

Rhodopseudomonas palustris prolyl-tRNA synthetase in complex with ATP

PDB DOI: https://doi.org/10.2210/pdb2I4O/pdb

Classification: LIGASE
Organism(s): Rhodopseudomonas palustris
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2006-08-22 Released: 2006-10-24
Deposition Author(s): Crepin, T., Yaremchuk, A., Tukalo, M., Cusack, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.261 (Depositor), 0.255 (DCC)
R-Value Work:
0.197 (Depositor), 0.192 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structures of Two Bacterial Prolyl-tRNA Synthetases with and without a cis-Editing Domain.

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

(2006) Structure 14: 1511-1525

PubMed: 17027500 Search on PubMed
DOI: https://doi.org/10.1016/j.str.2006.08.007
Primary Citation Related Structures:
2I4L, 2I4M, 2I4N, 2I4O, 2J3L, 2J3M

PubMed 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.

Organizational Affiliation

European Molecular Biology Laboratory, Grenoble Outstation, 6 rue Jules Horowitz, BP 181, F-38042 Grenoble Cedex 9, France.

Macromolecule Content

Total Structure Weight: 156.35 kDa
Atom Count: 10,865
Modeled Residue Count: 1,323
Deposited Residue Count: 1,374
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proline-tRNA ligase	A, B, C	458	Rhodopseudomonas palustris	Mutation(s): 0 Gene Names: proS, RPA2928 EC: 6.1.1.15
UniProt
Find proteins for Q6N5P6 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6N5P6 Go to UniProtKB: Q6N5P6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6N5P6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C]	G [auth A], K [auth B], N [auth C]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain N [auth C] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain N [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain M [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C]	D [auth A] E [auth A] F [auth A] H [auth B] I [auth B] D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], L [auth C], M [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.261 (Depositor), 0.255 (DCC)
R-Value Work: 0.197 (Depositor), 0.192 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.2	α = 90
b = 211.21	β = 90
c = 148.21	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MxCuBE	data collection
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-10-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-10-24
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.3: 2024-02-21
Changes: Data collection, Database references, Derived calculations
Version 1.4: 2024-04-03
Changes: Refinement description