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

Abstract

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 zincmore » 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.« less

Authors:
 [1];  [1];  [1];  [1];  [1]
  1. Univ. of Minnesota, Minneapolis, MN (United States)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE; NIH NIGMS; NIH-ORIP HEI
OSTI Identifier:
1255304
Alternate Identifier(s):
OSTI ID: 1425518
Grant/Contract Number:  
AC02-06CH11357; GM095558; GM109770; P41 GM103403; S10 RR029205
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Molecular Biology
Additional Journal Information:
Journal Volume: 428; Journal Issue: 11; Journal ID: ISSN 0022-2836
Publisher:
Elsevier
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES; cytosine deaminase; zinc-free and zinc-bound APOBEC3 structures; HIV-1 restriction factor; APOBEC3 regulation; X-ray crystallography

Citation Formats

Shaban, Nadine M., Shi, Ke, Li, Ming, Aihara, Hideki, and Harris, Reuben S. 1.92 Angstrom Zinc-Free APOBEC3F Catalytic Domain Crystal Structure. United States: N. p., 2016. Web. doi:10.1016/j.jmb.2016.04.026.
Shaban, Nadine M., Shi, Ke, Li, Ming, Aihara, Hideki, & Harris, Reuben S. 1.92 Angstrom Zinc-Free APOBEC3F Catalytic Domain Crystal Structure. United States. doi:10.1016/j.jmb.2016.04.026.
Shaban, Nadine M., Shi, Ke, Li, Ming, Aihara, Hideki, and Harris, Reuben S. Sat . "1.92 Angstrom Zinc-Free APOBEC3F Catalytic Domain Crystal Structure". United States. doi:10.1016/j.jmb.2016.04.026. https://www.osti.gov/servlets/purl/1255304.
@article{osti_1255304,
title = {1.92 Angstrom Zinc-Free APOBEC3F Catalytic Domain Crystal Structure},
author = {Shaban, Nadine M. and Shi, Ke and Li, Ming and Aihara, Hideki and Harris, Reuben S.},
abstractNote = {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.},
doi = {10.1016/j.jmb.2016.04.026},
journal = {Journal of Molecular Biology},
number = 11,
volume = 428,
place = {United States},
year = {2016},
month = {4}
}

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Works referencing / citing this record:

Mechanism of Enhanced HIV Restriction by Virion Coencapsidated Cytidine Deaminases APOBEC3F and APOBEC3G
journal, November 2016

  • Ara, Anjuman; Love, Robin P.; Follack, Tyson B.
  • Journal of Virology, Vol. 91, Issue 3
  • DOI: 10.1128/jvi.02230-16