4QNU

Crystal structure of CmoB bound with Cx-SAM in P21212

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

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: 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- ...

    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 Department of Physiology & Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461, USA steve.almo@einstein.yu.edu.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
tRNA (mo5U34)-methyltransferaseA, B, C, D, E, F, G, H323Escherichia coli APEC O1Mutation(s): 0 
Gene Names: APECO1_921, cmoB, Ecok1_17280
EC: 2.1.1 (PDB Primary Data), 2.5.1 (UniProt)
Find proteins for A1AC32 (Escherichia coli O1:K1 / APEC)
Explore A1AC32 
Go to UniProtKB:  A1AC32
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
MOLREPphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • 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