RCSB PDB - 4IWN: Crystal structure of a putative methyltransferase CmoA in complex with a novel SAM derivative

 4IWN

Crystal structure of a putative methyltransferase CmoA in complex with a novel SAM derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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Literature

S-Adenosyl-S-carboxymethyl-L-homocysteine: a novel cofactor found in the putative tRNA-modifying enzyme CmoA.

Byrne, R.T.Whelan, F.Aller, P.Bird, L.E.Dowle, A.Lobley, C.M.Reddivari, Y.Nettleship, J.E.Owens, R.J.Antson, A.A.Waterman, D.G.

(2013) Acta Crystallogr D Biol Crystallogr 69: 1090-1098

  • DOI: https://doi.org/10.1107/S0907444913004939
  • Primary Citation of Related Structures:  
    4IWN

  • PubMed Abstract: 

    Uridine at position 34 of bacterial transfer RNAs is commonly modified to uridine-5-oxyacetic acid (cmo(5)U) to increase the decoding capacity. The protein CmoA is involved in the formation of cmo(5)U and was annotated as an S-adenosyl-L-methionine-dependent (SAM-dependent) methyltransferase on the basis of its sequence homology to other SAM-containing enzymes. However, both the crystal structure of Escherichia coli CmoA at 1.73 Å resolution and mass spectrometry demonstrate that it contains a novel cofactor, S-adenosyl-S-carboxymethyl-L-homocysteine (SCM-SAH), in which the donor methyl group is substituted by a carboxymethyl group. The carboxyl moiety forms a salt-bridge interaction with Arg199 that is conserved in a large group of CmoA-related proteins but is not conserved in other SAM-containing enzymes. This raises the possibility that a number of enzymes that have previously been annotated as SAM-dependent are in fact SCM-SAH-dependent. Indeed, inspection of electron density for one such enzyme with known X-ray structure, PDB entry 1im8, suggests that the active site contains SCM-SAH and not SAM.


  • Organizational Affiliation

    York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington YO10 5DD, England.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA (cmo5U34)-methyltransferase
A, B
229Escherichia coliMutation(s): 0 
Gene Names: cmoAyecOb1870JW1859
EC: 2.1.1 (PDB Primary Data), 2.1.3 (UniProt)
UniProt
Find proteins for P76290 (Escherichia coli (strain K12))
Explore P76290 
Go to UniProtKB:  P76290
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP76290
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.12α = 90
b = 91.38β = 90
c = 70.64γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
GDAdata collection
XSCALEdata scaling
MrBUMPphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GEKClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-29
    Type: Initial release
  • Version 1.1: 2013-06-05
    Changes: Database references
  • Version 1.2: 2013-06-19
    Changes: Non-polymer description
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary