1R5T

The Crystal Structure of Cytidine Deaminase CDD1, an Orphan C to U editase from Yeast

Summary for 1R5T

• Entry DOI: 10.2210/pdb1r5t/pdb
• Related: 1AF2 1JTK
• Descriptor: Cytidine deaminase, ZINC ION (3 entities in total)
• Functional Keywords: zinc dependent deaminase, rna editing, apobec-1 related protein, hydrolase
• Biological source: Saccharomyces cerevisiae (baker's yeast)
• Total number of polymer chains: 4
• Total formula weight: 62469.82

Authors

Xie, K.,Sowden, M.P.,Dance, G.S.C.,Torelli, A.T.,Smith, H.C.,Wedekind, J.E. (deposition date: 2003-10-13, release date: 2004-05-25, Last modification date: 2024-02-14)

Primary citation

Xie, K.,Sowden, M.P.,Dance, G.S.,Torelli, A.T.,Smith, H.C.,Wedekind, J.E.
The structure of a yeast RNA-editing deaminase provides insight into the fold and function of activation-induced deaminase and APOBEC-1.
Proc.Natl.Acad.Sci.Usa, 101:8114-8119, 2004

PubMed Abstract: Activation-induced deaminase (AID) uses base deamination for class-switch recombination and somatic hypermutation and is related to the mammalian RNA-editing enzyme apolipoprotein B editing catalytic subunit 1 (APOBEC-1). CDD1 is a yeast ortholog of APOBEC-1 that exhibits cytidine deaminase and RNA-editing activity. Here, we present the crystal structure of CDD1 at 2.0-A resolution and its use in comparative modeling of APOBEC-1 and AID. The models explain dimerization and the need for trans-acting loops that contribute to active site formation. Substrate selectivity appears to be regulated by a central active site "flap" whose size and flexibility accommodate large substrates in contrast to deaminases of pyrimidine metabolism that bind only small nucleosides or free bases. Most importantly, the results suggested both AID and APOBEC-1 are equally likely to bind single-stranded DNA or RNA, which has implications for the identification of natural AID targets.

PubMed: 15148397
DOI: 10.1073/pnas.0400493101

Experimental method

X-RAY DIFFRACTION (2 Å)