1.92 Angstrom Zinc-Free APOBEC3F Catalytic Domain Crystal Structure

Shaban, Nadine M.; Shi, Ke; Li, Ming; Aihara, Hideki; Harris, Reuben S.

doi:10.1016/j.jmb.2016.04.026

Title: 1.92 Angstrom Zinc-Free APOBEC3F Catalytic Domain Crystal Structure

Journal Article · Sat Apr 30 00:00:00 EDT 2016 · Journal of Molecular Biology

DOI:https://doi.org/10.1016/j.jmb.2016.04.026· OSTI ID:1255304

Shaban, Nadine M. ^[1]; Shi, Ke ^[1]; Li, Ming ^[1]; Aihara, Hideki ^[1]; Harris, Reuben S. ^[1]

Univ. of Minnesota, Minneapolis, MN (United States)

The APOBEC3 family of DNA cytosine deaminases is capable of restricting the replication of HIV-1 and other pathogens. Here, we report a 1.92 Å resolution crystal structure of the Vif-binding and catalytic domain of APOBEC3F (A3F). This structure is distinct from the previously published APOBEC and phylogenetically related deaminase structures, as it is the first without zinc in the active site. We determined an additional structure containing zinc in the same crystal form that allows direct comparison with the zinc-free structure. In the absence of zinc, the conserved active site residues that normally participate in zinc coordination show unique conformations, including a 90 degree rotation of His249 and disulfide bond formation between Cys280 and Cys283. We found that zinc coordination is influenced by pH, and treating the protein at low pH in crystallization buffer is sufficient to remove zinc. Zinc coordination and catalytic activity are reconstituted with the addition of zinc only in a reduced environment likely due to the two active site cysteines readily forming a disulfide bond when not coordinating zinc. We show that the enzyme is active in the presence of zinc and cobalt but not with other divalent metals. Furthermore, these results unexpectedly demonstrate that zinc is not required for the structural integrity of A3F and suggest that metal coordination may be a strategy for regulating the activity of A3F and related deaminases.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: USDOE; NIH NIGMS; NIH-ORIP HEI

Grant/Contract Number:: AC02-06CH11357; GM095558; GM109770; P41 GM103403; S10 RR029205

OSTI ID:: 1255304

Alternate ID(s):: OSTI ID: 1425518

Journal Information:: Journal of Molecular Biology, Vol. 428, Issue 11; ISSN 0022-2836

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: ENGLISH

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Cited by: 27 works

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59 BASIC BIOLOGICAL SCIENCES
cytosine deaminase
zinc-free and zinc-bound APOBEC3 structures
HIV-1 restriction factor
APOBEC3 regulation
X-ray crystallography

Title: 1.92 Angstrom Zinc-Free APOBEC3F Catalytic Domain Crystal Structure

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