Crystal structure of CmoB bound with Cx-SAM in P21212

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Determinants of the CmoB carboxymethyl transferase utilized for selective tRNA wobble modification.

Kim, J.Xiao, H.Koh, J.Wang, Y.Bonanno, J.B.Thomas, K.Babbitt, P.C.Brown, S.Lee, Y.S.Almo, S.C.

(2015) Nucleic Acids Res 43: 4602-4613

  • DOI: https://doi.org/10.1093/nar/gkv206
  • Primary Citation of Related Structures:  
    4QNU, 4QNV, 4QNX

  • PubMed Abstract: 

    Enzyme-mediated modifications at the wobble position of tRNAs are essential for the translation of the genetic code. We report the genetic, biochemical and structural characterization of CmoB, the enzyme that recognizes the unique metabolite carboxy-S-adenosine-L-methionine (Cx-SAM) and catalyzes a carboxymethyl transfer reaction resulting in formation of 5-oxyacetyluridine at the wobble position of tRNAs. CmoB is distinctive in that it is the only known member of the SAM-dependent methyltransferase (SDMT) superfamily that utilizes a naturally occurring SAM analog as the alkyl donor to fulfill a biologically meaningful function. Biochemical and genetic studies define the in vitro and in vivo selectivity for Cx-SAM as alkyl donor over the vastly more abundant SAM. Complementary high-resolution structures of the apo- and Cx-SAM bound CmoB reveal the determinants responsible for this remarkable discrimination. Together, these studies provide mechanistic insight into the enzymatic and non-enzymatic feature of this alkyl transfer reaction which affords the broadened specificity required for tRNAs to recognize multiple synonymous codons.

  • Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA (mo5U34)-methyltransferase
A, B, C, D, E
A, B, C, D, E, F, G, H
323Escherichia coli APEC O1Mutation(s): 0 
Gene Names: APECO1_921cmoBEcok1_17280
EC: 2.1.1
Find proteins for A1AC32 (Escherichia coli O1:K1 / APEC)
Explore A1AC32 
Go to UniProtKB:  A1AC32
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1AC32
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GEK

Download Ideal Coordinates CCD File 
I [auth A]
L [auth B]
N [auth C]
P [auth D]
R [auth E]
I [auth A],
L [auth B],
N [auth C],
P [auth D],
R [auth E],
T [auth F],
W [auth G],
Y [auth H]
(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
Query on PO4

Download Ideal Coordinates CCD File 
J [auth A]
K [auth A]
M [auth B]
O [auth C]
Q [auth D]
J [auth A],
K [auth A],
M [auth B],
O [auth C],
Q [auth D],
S [auth E],
U [auth F],
V [auth F],
X [auth G],
Z [auth H]
O4 P
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 184.803α = 90
b = 347.551β = 90
c = 59.415γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-17
    Type: Initial release
  • Version 1.1: 2015-04-22
    Changes: Database references
  • Version 1.2: 2015-06-10
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary