4GEK

Crystal Structure of wild-type CmoA from E.coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structure-guided discovery of the metabolite carboxy-SAM that modulates tRNA function

Kim, J.Xiao, H.Bonanno, J.B.Kalyanaraman, C.Brown, S.Tang, X.Al-Obaidi, N.F.Patskovsky, Y.Babbitt, P.C.Jacobson, M.P.Lee, Y.-S.Almo, S.C.

(2013) Nature 498: 123-126

  • DOI: 10.1038/nature12180
  • Primary Citation of Related Structures:  
    4GEK

  • PubMed Abstract: 
  • The identification of novel metabolites and the characterization of their biological functions are major challenges in biology. X-ray crystallography can reveal unanticipated ligands that persist through purification and crystallization. These advent ...

    The identification of novel metabolites and the characterization of their biological functions are major challenges in biology. X-ray crystallography can reveal unanticipated ligands that persist through purification and crystallization. These adventitious protein-ligand complexes provide insights into new activities, pathways and regulatory mechanisms. We describe a new metabolite, carboxy-S-adenosyl-l-methionine (Cx-SAM), its biosynthetic pathway and its role in transfer RNA modification. The structure of CmoA, a member of the SAM-dependent methyltransferase superfamily, revealed a ligand consistent with Cx-SAM in the catalytic site. Mechanistic analyses showed an unprecedented role for prephenate as the carboxyl donor and the involvement of a unique ylide intermediate as the carboxyl acceptor in the CmoA-mediated conversion of SAM to Cx-SAM. A second member of the SAM-dependent methyltransferase superfamily, CmoB, recognizes Cx-SAM and acts as a carboxymethyltransferase to convert 5-hydroxyuridine into 5-oxyacetyl uridine at the wobble position of multiple tRNAs in Gram-negative bacteria, resulting in expanded codon-recognition properties. CmoA and CmoB represent the first documented synthase and transferase for Cx-SAM. These findings reveal new functional diversity in the SAM-dependent methyltransferase superfamily and expand the metabolic and biological contributions of SAM-based biochemistry. These discoveries highlight the value of structural genomics approaches in identifying ligands within the context of their physiologically relevant macromolecular binding partners, and in revealing their functions.


    Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA. jungwook.kim@einstein.yu.edu



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
tRNA (cmo5U34)-methyltransferaseAG261Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
Gene Names: cmoA
EC: 2.1.1 (PDB Primary Data), 2.1.3 (UniProt)
Find proteins for C3T5M2 (Escherichia coli)
Explore C3T5M2 
Go to UniProtKB:  C3T5M2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GEK
Query on GEK

Download Ideal Coordinates CCD File 
A, G
(2S)-4-[{[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}(carboxylatomethyl)sulfonio] -2-ammoniobutanoate
C16 H22 N6 O7 S
VFFTYSZNZJBRBG-HEOPWLPUSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
A, G
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.314α = 90
b = 78.677β = 90
c = 92.372γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
MOLREPphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-10
    Type: Initial release
  • Version 1.1: 2013-05-15
    Changes: Database references
  • Version 1.2: 2013-05-29
    Changes: Database references
  • Version 1.3: 2013-06-12
    Changes: Database references, Structure summary
  • Version 1.4: 2013-06-19
    Changes: Non-polymer description
  • Version 1.5: 2017-11-15
    Changes: Refinement description