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Hydrogenase Maturation Protein HypF

  1. Miroslaw Cygler1,2,
  2. Svetlana Petkun2

Published Online: 23 SEP 2013

DOI: 10.1002/9781119951438.eibc2167

Encyclopedia of Inorganic and Bioinorganic Chemistry

Encyclopedia of Inorganic and Bioinorganic Chemistry

How to Cite

Cygler, M. and Petkun, S. 2013. Hydrogenase Maturation Protein HypF. Encyclopedia of Inorganic and Bioinorganic Chemistry. 1–11.

Author Information

  1. 1

    University of Saskatchewan, Saskatoon, Saskatchewan, Canada

  2. 2

    McGill University, Montreal, Quebec, Canada

Publication History

  1. Published Online: 23 SEP 2013

Abstract

HypF is an accessory protein for assembling the NiFe(CN)2CO active center of [NiFe]-hydrogenases. HypF together with HypE catalyzes the synthesis of the CN- ligands using carbamoylphosphate as the initial substrate. HypF comprises four domains: the acylphosphatase domain, the Zn finger domain, the YrdC-like domain with a nucleotide-binding site and the Kae1-like “universal domain” with a second nucleotide-binding site coordinated by a metal. The YrdC- and Kae1-like domains are juxtaposed with their nucleotide-binding sites facing each other and sequestered in an internal cavity. The distance between the two sites is approximately 14 Å. The carbamoylphosphate is hydrolyzed to carbamate within the acylphosphatase domain, which then likely migrates through a tunnel in the YrdC-like domain toward the ATP molecule bound within this domain's nucleotide-binding site. The end of the tunnel is near the α-phosphate of ATP where the carbamate is converted to carbamoyl adenylate intermediate. This intermediate presumably diffuses across the cavity to the nucleotide-binding site in Kae1-like domain where the transfer of CN moiety to the C-terminal cysteine of HypE finally occurs. While the structure discloses the architecture of the various active sites, the details of each catalytic step require further investigations.

3D Structure

  • original image

    Ribbon representation of the CsHypF (PDB code 3VTH). The ACP domain is colored yellow, the Zn finger domain is colored green, the YrdC-like domain is colored magenta, and the Kae1-like domain is colored cyan. The Zn atoms are orange spheres, Fe is gray, Mg is red, and SO4 is orange–red (in ACP domain). The nucleotides are depicted in their binding sites within the YrdC- and Kae1-like domains. This and subsequent structural figures were prepared using PyMOL Molecular Graphics System. (Schrödinger, LLC, www.pymol.org).

Keywords:

  • hydrogenase maturation;
  • hydrogenase accessory protein;
  • acylphosphatase activity;
  • nucleotide-binding site;
  • reaction mechanism;
  • substrate tunneling