Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 92.16 kDa 
• Atom Count: 5714 
• Residue Count: 692 
• Unique protein chains: 1

3RFA

X-ray structure of RlmN from Escherichia coli in complex with S-adenosylmethionine

• DOI: 10.2210/pdb3RFA/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-04-05 Released: 2011-05-11 
• Deposition Author(s): Boal, A.K., Grove, T.L., McLaughlin, M.I., Yennawar, N., Booker, S.J., Rosenzweig, A.C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.241 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 

Literature

Structural basis for methyl transfer by a radical SAM enzyme.

Boal, A.K., Grove, T.L., McLaughlin, M.I., Yennawar, N.H., Booker, S.J., Rosenzweig, A.C.

(2011) Science 332: 1089-1092

• PubMed: 21527678 
• DOI: 10.1126/science.1205358
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The radical S-adenosyl-L-methionine (SAM) enzymes RlmN and Cfr methylate 23S ribosomal RNA, modifying the C2 or C8 position of adenosine 2503. The methyl groups are installed by a two-step sequence involving initial methylation of a conserved Cys residue (RlmN Cys(355)) by SAM. Methyl transfer to the substrate requires reductive cleavage of a second equivalent of SAM. Crystal structures of RlmN and RlmN with SAM show that a single molecule of SAM coordinates the [4Fe-4S] cluster. Residue Cys(355) is S-methylated and located proximal to the SAM methyl group, suggesting the SAM that is involved in the initial methyl transfer binds at the same site. Thus, RlmN accomplishes its complex reaction with structural economy, harnessing the two most important reactivities of SAM within a single site.

---

Organizational Affiliation: 

Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Ribosomal RNA large subunit methyltransferase N	A, B	404	Escherichia coli K-12	Mutation(s): 0  Gene Names: rlmN, yfgB, b2517, JW2501 EC: 2.1.1.192
Find proteins for P36979 (Escherichia coli (strain K12)) Explore P36979  Go to UniProtKB:  P36979

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	A, B	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
SF4	A, B	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-VKOJMFJBAC

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SMC	A,B	L-PEPTIDE LINKING	C4 H9 N O2 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.241 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.18	α = 90
b = 55.621	β = 90
c = 252.179	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-04-05 
• Released Date: 2011-05-11 
Deposition Author(s): Boal, A.K., Grove, T.L., McLaughlin, M.I., Yennawar, N., Booker, S.J., Rosenzweig, A.C.

Revision History 

• Version 1.0: 2011-05-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance