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

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 f...

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Bibliographic Details
Published in:Journal of molecular biology 1998-01, Vol.275 (4), p.695-714
Main Authors: Navaratnam, N, Fujino, T, Bayliss, J, Jarmuz, A, How, A, Richardson, N, Somasekaram, A, Bhattacharya, S, Carter, C, Scott, J
Format: Article
Language:English
Subjects:
Amino Acid Sequence
APOBEC-1 Deaminase
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
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Summary: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.
ISSN:0022-2836
DOI:10.1006/jmbi.1997.1506