2HNK

Crystal structure of SAM-dependent O-methyltransferase from pathogenic bacterium Leptospira interrogans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of SAM-dependent O-methyltransferase from pathogenic bacterium Leptospira interrogans.

Hou, X.Wang, Y.Zhou, Z.Bao, S.Lin, Y.Gong, W.

(2007) J.Struct.Biol. 159: 523-528

  • DOI: 10.1016/j.jsb.2007.04.007

  • PubMed Abstract: 
  • The S-adenosylmethionine (SAM)-dependent O-methyltransferase from Leptospira interrogans (LiOMT) expressed by gene LA0415 belongs to the Methyltransf_3 family (Pfam PF01596). In this family all of the five bacterial homologues with known function are ...

    The S-adenosylmethionine (SAM)-dependent O-methyltransferase from Leptospira interrogans (LiOMT) expressed by gene LA0415 belongs to the Methyltransf_3 family (Pfam PF01596). In this family all of the five bacterial homologues with known function are reported as SAM-dependent O-methylstransferases involved in antibiotic production. The crystal structure of LiOMT in complex with S-adenosylhomocysteine reported here is the first bacterial protein structure in this family. The LiOMT structure shows a conserved SAM-binding region and a probable metal-dependent catalytic site. The molecules of LiOMT generate homodimers by N-terminal swapping, which assists the pre-organization of the substrate-binding site. Based on the sequence and structural analysis, it is implied by the catalytic and substrate-binding site that the substrate of LiOMT is a phenolic derivative, which probably has a large ring-shaped moiety.


    Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, PR China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SAM-dependent O-methyltransferase
A, B, C
239Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai (strain 56601)Mutation(s): 0 
Find proteins for Q8F8Y3 (Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai (strain 56601))
Go to UniProtKB:  Q8F8Y3
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
SAH
Query on SAH

Download SDF File 
Download CCD File 
A, B, C
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A, B, C
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.213 
  • Space Group: P 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 157.810α = 90.00
b = 60.331β = 90.00
c = 138.232γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-09-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-18
    Type: Refinement description