Crystal Structure of wild-type CmoA from E.coli

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

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This is version 1.6 of the entry. See complete history


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: https://doi.org/10.1038/nature12180
  • Primary Citation of Related Structures:  

  • 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 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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA (cmo5U34)-methyltransferaseA,
B [auth G]
261Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
Gene Names: cmoA
EC: 2.1.1
Find proteins for C3T5M2 (Escherichia coli)
Explore C3T5M2 
Go to UniProtKB:  C3T5M2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC3T5M2
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • 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
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • 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
  • Version 1.6: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary