3CES

Crystal Structure of E.coli MnmG (GidA), a Highly-Conserved tRNA Modifying Enzyme

PDB DOI: https://doi.org/10.2210/pdb3CES/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-02-29 Released: 2009-03-03
Deposition Author(s): Shi, R., Matte, A., Cygler, M., Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free: 0.238
R-Value Work: 0.201
R-Value Observed: 0.203

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structure-function analysis of Escherichia coli MnmG (GidA), a highly conserved tRNA-modifying enzyme.

Shi, R., Villarroya, M., Ruiz-Partida, R., Li, Y., Proteau, A., Prado, S., Moukadiri, I., Benitez-Paez, A., Lomas, R., Wagner, J., Matte, A., Velazquez-Campoy, A., Armengod, M.E., Cygler, M.

(2009) J Bacteriol 191: 7614-7619

PubMed: 19801413 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1128/JB.00650-09
Primary Citation of Related Structures:
3CES, 3G05

PubMed Abstract:
The MnmE-MnmG complex is involved in tRNA modification. We have determined the crystal structure of Escherichia coli MnmG at 2.4-A resolution, mutated highly conserved residues with putative roles in flavin adenine dinucleotide (FAD) or tRNA binding and MnmE interaction, and analyzed the effects of these mutations in vivo and in vitro. Limited trypsinolysis of MnmG suggests significant conformational changes upon FAD binding.

Organizational Affiliation

Department of Biochemistry, McGill University, Montreal, Quebec, Canada.

Macromolecule Content

Total Structure Weight: 288.2 kDa
Atom Count: 15,980
Modelled Residue Count: 2,073
Deposited Residue Count: 2,604
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA uridine 5-carboxymethylaminomethyl modification enzyme gidA	A, B, C, D	651	Escherichia coli	Mutation(s): 0 Gene Names: gidA
UniProt
Find proteins for P0A6U3 (Escherichia coli (strain K12)) Explore P0A6U3 Go to UniProtKB: P0A6U3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A6U3
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free: 0.238
R-Value Work: 0.201
R-Value Observed: 0.203
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.904	α = 90
b = 144.326	β = 106.63
c = 147.745	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-03-03

Deposition Author(s):

Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)

Revision History (Full details and data files)

Version 1.0: 2009-03-03
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2024-02-21
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.