1GZ0

23S RIBOSOMAL RNA G2251 2'O-METHYLTRANSFERASE RLMB

PDB DOI: https://doi.org/10.2210/pdb1GZ0/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2002-05-03 Released: 2002-10-17
Deposition Author(s): Michel, G., Cygler, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.279
R-Value Work: 0.231
R-Value Observed: 0.231

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The Structure of the Rlmb 23S Rrna Methyltransferase Reveals a New Methyltransferase Fold with a Unique Knot

Michel, G., Sauve, V., Larocque, R., Li, Y., Matte, A., Cygler, M.

(2002) Structure 10: 1303

PubMed: 12377117 Search on PubMed
DOI: https://doi.org/10.1016/s0969-2126(02)00852-3
Primary Citation of Related Structures:
1GZ0

PubMed Abstract:
In Escherichia coli, RlmB catalyzes the methylation of guanosine 2251, a modification conserved in the peptidyltransferase domain of 23S rRNA. The crystal structure of this 2'O-methyltransferase has been determined at 2.5 A resolution. RlmB consists of an N-terminal domain connected by a flexible extended linker to a catalytic C-terminal domain and forms a dimer in solution. The C-terminal domain displays a divergent methyltransferase fold with a unique knotted region, and lacks the classic AdoMet binding site features. The N-terminal domain is similar to ribosomal proteins L7 and L30, suggesting a role in 23S rRNA recognition. The conserved residues in this novel family of 2'O-methyltransferases cluster in the knotted region, suggesting the location of the catalytic and AdoMet binding sites.

Organizational Affiliation

Biotechnology Research Institute, National Research Council of Canada and Montreal Joint Centre for Structural Biology, Montreal, Quebec, Canada.

Macromolecule Content

Total Structure Weight: 223.56 kDa
Atom Count: 13,953
Modelled Residue Count: 1,807
Deposited Residue Count: 2,024
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE YJFH	A, B, C, D, E A, B, C, D, E, F, G, H	253	Escherichia coli	Mutation(s): 0 EC: 2.1.1
UniProt
Find proteins for P63177 (Escherichia coli (strain K12)) Explore P63177 Go to UniProtKB: P63177
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P63177
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.279
R-Value Work: 0.231
R-Value Observed: 0.231
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.478	α = 90
b = 132.288	β = 96.4
c = 90.71	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2002-10-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2002-10-17
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance

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.