Escherichia coli cytidine deaminase provides a molecular model for ApoB RNA editing and a mechanism for RNA substrate recognition

J Mol Biol. 1998 Jan 30;275(4):695-714. doi: 10.1006/jmbi.1997.1506.


ApoB RNA-editing enzyme (APOBEC-1) is a cytidine deaminase. Molecular modeling and mutagenesis show that APOBEC-1 is related in quaternary and tertiary structure to Escherichia coli cytidine deaminase (ECCDA). Both enzymes form a homodimer with composite active sites constructed with contributions from each monomer. Significant gaps are present in the APOBEC-1 sequence, compared to ECCDA. The combined mass of the gaps (10 kDa) matches that for the minimal RNA substrate. Their location in ECCDA suggests how APOBEC-1 can be reshaped to accommodate an RNA substrate. In this model, the asymmetrical binding to one active site of a downstream U (equivalent to the deamination product) helps target the other active site for deamination of the upstream C substrate.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • APOBEC-1 Deaminase
  • Amino Acid Sequence
  • Apolipoproteins B / genetics*
  • Apolipoproteins B / metabolism
  • Binding Sites
  • Cytidine Deaminase / genetics
  • Cytidine Deaminase / metabolism*
  • Escherichia coli / enzymology*
  • Escherichia coli / genetics
  • Models, Molecular*
  • Molecular Sequence Data
  • RNA Editing*
  • RNA, Bacterial / metabolism*
  • Sequence Alignment
  • Sequence Homology, Amino Acid
  • Substrate Specificity


  • Apolipoproteins B
  • RNA, Bacterial
  • AICDA (activation-induced cytidine deaminase)
  • APOBEC-1 Deaminase
  • Cytidine Deaminase