Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 32.25 kDa 
• Atom Count: 2282 
• Modelled Residue Count: 260 
• Deposited Residue Count: 281 
• Unique protein chains: 1

3LCU

Crystal Structure of Antibiotic related Methyltransferase

• PDB DOI: 10.2210/pdb3LCU/pdb

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


• Deposited: 2010-01-11 Released: 2010-06-02 
• Deposition Author(s): Sivaraman, J., Husain, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.259 
• R-Value Work: 0.205 
• R-Value Observed: 0.205 

Literature

Structural basis for the methylation of G1405 in 16S rRNA by aminoglycoside resistance methyltransferase Sgm from an antibiotic producer: a diversity of active sites in m7G methyltransferases.

Husain, N., Tkaczuk, K.L., Tulsidas, S.R., Kaminska, K.H., Cubrilo, S., Maravic-Vlahovicek, G., Bujnicki, J.M., Sivaraman, J.

(2010) Nucleic Acids Res 

• PubMed: 20194115 
• DOI: 10.1093/nar/gkq122
• Primary Citation of Related Structures:  
  3LCU, 3LCV


• PubMed Abstract: 
  

Sgm (Sisomicin-gentamicin methyltransferase) from antibiotic-producing bacterium Micromonospora zionensis is an enzyme that confers resistance to aminoglycosides like gentamicin and sisomicin by specifically methylating G1405 in bacterial 16S rRNA. Sgm belongs to the aminoglycoside resistance methyltransferase (Arm) family of enzymes that have been recently found to spread by horizontal gene transfer among disease-causing bacteria. Structural characterization of Arm enzymes is the key to understand their mechanism of action and to develop inhibitors that would block their activity. Here we report the structure of Sgm in complex with cofactors S-adenosylmethionine (AdoMet) and S-adenosylhomocysteine (AdoHcy) at 2.0 and 2.1 A resolution, respectively, and results of mutagenesis and rRNA footprinting, and protein-substrate docking. We propose the mechanism of methylation of G1405 by Sgm and compare it with other m(7)G methyltransferases, revealing a surprising diversity of active sites and binding modes for the same basic reaction of RNA modification. This analysis can serve as a stepping stone towards developing drugs that would specifically block the activity of Arm methyltransferases and thereby re-sensitize pathogenic bacteria to aminoglycoside antibiotics.

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Organizational Affiliation: 

Department of Biological Sciences, 14 Science drive 4, National University of Singapore, Singapore.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sisomicin-gentamicin resistance methylase Sgm	A	281	Micromonospora zionensis	Mutation(s): 0  Gene Names: sgm EC: 2.1.1.179
UniProt
Find proteins for Q7M0R2 (Micromonospora zionensis) Explore Q7M0R2  Go to UniProtKB:  Q7M0R2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	B [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Binding Affinity Annotations
ID	Source	Binding Affinity
SAH	Binding MOAD:  3LCU	Kd: 3.00e+5 (nM) from 1 assay(s)
	PDBBind:  3LCU	Kd: 3.00e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.259 
• R-Value Work: 0.205 
• R-Value Observed: 0.205 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.087	α = 90
b = 68.891	β = 93.47
c = 52.201	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-01-11 
• Released Date: 2010-06-02 
Deposition Author(s): Sivaraman, J., Husain, N.

Revision History  

• Version 1.0: 2010-06-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description