Biological Assembly 1  

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

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 39.98 kDa 
• Atom Count: 2458 
• Modelled Residue Count: 283 
• Deposited Residue Count: 347 
• Unique protein chains: 1

3TKA

crystal structure and solution saxs of methyltransferase rsmh from E.coli

• PDB DOI: 10.2210/pdb3TKA/pdb

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


• Deposited: 2011-08-25 Released: 2012-05-30 
• Deposition Author(s): Gao, Z.Q., Wei, Y., Zhang, H., Dong, Y.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.234 
• R-Value Work: 0.184 
• R-Value Observed: 0.187 

Literature

Crystal and solution structures of methyltransferase RsmH provide basis for methylation of C1402 in 16S rRNA.

Wei, Y., Zhang, H., Gao, Z.Q., Wang, W.J., Shtykova, E.V., Xu, J.H., Liu, Q.S., Dong, Y.H.

(2012) J Struct Biol 179: 29-40

• PubMed: 22561317 
• DOI: 10.1016/j.jsb.2012.04.011
• Primary Citation of Related Structures:  
  3TKA


• PubMed Abstract: 
  

RsmH is a specific AdoMet-dependent methyltransferase (MTase) responsible for N(4)-methylation of C1402 in 16S rRNA and conserved in almost all species of bacteria. The methylcytidine interacts with the P-site codon of the mRNA and increases ribosomal decoding fidelity. In this study, high resolution crystal structure (2.25Å) of Escherichia coli RsmH in complex with AdoMet and cytidine (the putative rRNA binding site) was determined. The structural analysis demonstrated that the complex consists of two distinct but structurally related domains: the typical MTase domain and the putative substrate recognition and binding domain. A deep pocket was found in the conserved AdoMet binding domain. It was also found that the cytidine bound far from AdoMet with the distance of 25.9Å. It indicates that the complex is not in a catalytically active state, and structural rearrangement of RsmH or the nucleotides neighboring C1402 may be necessary to trigger catalysis. Although there is only one molecule in the asymmetric unit of the crystals, RsmH can form a compact dimer across a crystallographic twofold axis. Further analysis of RsmH by small-angle X-ray scattering (SAXS) also revealed the dimer in solution, but with a more flexible conformation than that in crystal, likely resulting from the absence of the substrate. It implies that an active status of RsmH in vivo is achieved by a formation of the dimeric architecture. In general, crystal and solution structural analysis provides new information on the mechanism of the methylation of the fine-tuning ribosomal decoding center by the RsmH.

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Organizational Affiliation: 

School of Life Sciences, University of Science and Technology of China, Hefei 230027, People's Republic of China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal RNA small subunit methyltransferase H	A	347	Escherichia coli K-12	Mutation(s): 0  Gene Names: rsmH, mraW, yabC, b0082, JW0080 EC: 2.1.1.199
UniProt
Find proteins for P60390 (Escherichia coli (strain K12)) Explore P60390  Go to UniProtKB:  P60390

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	B [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
CTN	C [auth A]	4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE C9 H13 N3 O5 UHDGCWIWMRVCDJ-XVFCMESISA-N
PG4	I [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.234 
• R-Value Work: 0.184 
• R-Value Observed: 0.187 
• Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.66	α = 90
b = 85.66	β = 90
c = 107.059	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-08-25 
• Released Date: 2012-05-30 
Deposition Author(s): Gao, Z.Q., Wei, Y., Zhang, H., Dong, Y.H.

Revision History  

• Version 1.0: 2012-05-30
  Type: Initial release
  
• Version 1.1: 2013-07-10
  Changes: Database references
• Version 1.2: 2017-11-08
  Changes: Refinement description