Crystal structure of E. coli HypF with ATP and Carbamoyl phosphate

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.158 

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Structure of Hydrogenase Maturation Protein HypF with Reaction Intermediates Shows Two Active Sites.

Petkun, S.Shi, R.Li, Y.Asinas, A.Munger, C.Zhang, L.Waclawek, M.Soboh, B.Sawers, R.G.Cygler, M.

(2011) Structure 19: 1773-1783

  • DOI: https://doi.org/10.1016/j.str.2011.09.023
  • Primary Citation of Related Structures:  
    3TSP, 3TSQ, 3TSU, 3TTC, 3TTD, 3TTF

  • 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.

  • Organizational Affiliation

    Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulatory protein658Escherichia coli O157:H7Mutation(s): 0 
Gene Names: ECs3568hypFECs_3568
EC: 2.1.3 (PDB Primary Data), 6.2 (UniProt)
Find proteins for A0A0H3JHT3 (Escherichia coli O157:H7)
Explore A0A0H3JHT3 
Go to UniProtKB:  A0A0H3JHT3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3JHT3
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.158 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.53α = 90
b = 78.287β = 90
c = 200.815γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
MxDCdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-28
    Type: Initial release