3TTD

Crystal structure of E. coli HypF with AMP-CPP and carbamoyl phosphate

Summary for 3TTD

• Entry DOI: 10.2210/pdb3ttd/pdb
• Related: 3TSP 3TSQ 3TSU 3TTC 3TTF
• Descriptor: Transcriptional regulatory protein, ZINC ION, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: zn finger, nucleotide binding, hydrogenase maturation factor, hype, transferase
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 71445.88

Authors

Petkun, S.,Shi, R.,Li, Y.,Cygler, M. (deposition date: 2011-09-14, release date: 2011-12-28, Last modification date: 2024-02-28)

Primary citation

Petkun, S.,Shi, R.,Li, Y.,Asinas, A.,Munger, C.,Zhang, L.,Waclawek, M.,Soboh, B.,Sawers, R.G.,Cygler, M.
Structure of Hydrogenase Maturation Protein HypF with Reaction Intermediates Shows Two Active Sites.
Structure, 19:1773-1783, 2011

PubMed Abstract: [NiFe]-hydrogenases are multimeric proteins. The large subunit contains the NiFe(CN)(2)CO bimetallic active center and the small subunit contains Fe-S clusters. Biosynthesis and assembly of the NiFe(CN)(2)CO active center requires six Hyp accessory proteins. The synthesis of the CN(-) ligands is catalyzed by the combined actions of HypF and HypE using carbamoylphosphate as a substrate. We report the structure of Escherichia coli HypF(92-750) lacking the N-terminal acylphosphatase domain. HypF(92-750) comprises the novel Zn-finger domain, the nucleotide-binding YrdC-like domain, and the Kae1-like universal domain, also binding a nucleotide and a Zn(2+) ion. The two nucleotide-binding sites are sequestered in an internal cavity, facing each other and separated by ∼14 Å. The YrdC-like domain converts carbamoyl moiety to a carbamoyl adenylate intermediate, which is channeled to the Kae1-like domain. Mutations within either nucleotide-binding site compromise hydrogenase maturation but do not affect the carbamoylphosphate phosphatase activity.

PubMed: 22153500
DOI: 10.1016/j.str.2011.09.023

Experimental method

X-RAY DIFFRACTION (2.2 Å)