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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.

Type

Journal article

Publication Date

1998

Volume

275

Pages

695 - 714

Keywords

Amino Acid Sequence Apolipoproteins B/*genetics/metabolism Binding Sites Cytidine Deaminase/genetics/*metabolism Escherichia coli/*enzymology/genetics *Models, Molecular Molecular Sequence Data *RNA Editing RNA, Bacterial/*metabolism Sequence Alignment Sequence Homology, Amino Acid Substrate Specificity Support, Non-U.S. Gov't