4QNU

Crystal structure of CmoB bound with Cx-SAM in P21212


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.221 

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:  

  • 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
tRNA (mo5U34)-methyltransferase
A, B, C, D, E, F, G, H
323Escherichia coli O1:K1 / APECMutation(s): 0 
Gene Names: cmoB
EC: 2.5.1.-
Find proteins for A1AC32 (Escherichia coli O1:K1 / APEC)
Go to UniProtKB:  A1AC32
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GEK
Query on GEK

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
(2S)-4-[{[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}(carboxylatomethyl)sulfonio]-2-ammoniobutanoate
CARBOXY-S-ADENOSYLMETHIONINE
C16 H22 N6 O7 S
VFFTYSZNZJBRBG-HEOPWLPUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.221 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 184.803α = 90.00
b = 347.551β = 90.00
c = 59.415γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
CBASSdata collection
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-17
    Type: Initial release
  • Version 1.1: 2015-04-22
    Type: Database references
  • Version 1.2: 2015-06-10
    Type: Database references