3VYT

Crystal structure of the HypC-HypD-HypE complex (form I inward)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 

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This is version 1.2 of the entry. See complete history


Literature

Crystal structures of the HypCD complex and the HypCDE ternary complex: transient intermediate complexes during [NiFe] hydrogenase maturation

Watanabe, S.Matsumi, R.Atomi, H.Imanaka, T.Miki, K.

(2012) Structure 20: 2124-2137

  • DOI: https://doi.org/10.1016/j.str.2012.09.018
  • Primary Citation of Related Structures:  
    3VYR, 3VYS, 3VYT, 3VYU

  • PubMed Abstract: 

    [NiFe] hydrogenase maturation represents one of the most dynamic and sophisticated processes in metallocenter assembly. The Fe(CN)(2)CO moiety of [NiFe] hydrogenases is assembled via unknown transient interactions among specific maturation proteins HypC (metallochaperone), HypD (redox protein), and HypE (cyanide synthesis/donor). Here, we report the structures of the HypC-HypD and HypC-HypD-HypE complexes, providing a view of the transient interactions that take place during the maturation process. HypC binds to the conserved region of HypD through extensive hydrophobic interactions. The ternary complex formation between HypE and the HypCD complex involves both HypC and HypD, rendering the HypE conformation favorable for cyanide transfer. In the complex, the conserved cysteines of HypC and HypD form an Fe binding site. The conserved C-terminal cysteine of HypE can access the thiol redox cascade of HypD. These results provide structural insights into the Fe atom cyanation in the HypCDE complex.


  • Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hydrogenase expression/formation protein HypC74Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: Tk-hypC
UniProt
Find proteins for Q5JII0 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore Q5JII0 
Go to UniProtKB:  Q5JII0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5JII0
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hydrogenase expression/formation protein HypD372Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: Tk-hypD
UniProt
Find proteins for Q5JII1 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore Q5JII1 
Go to UniProtKB:  Q5JII1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5JII1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Hydrogenase expression/formation protein HypE338Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: TK1993
UniProt
Find proteins for Q5JII7 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore Q5JII7 
Go to UniProtKB:  Q5JII7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5JII7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.333α = 90
b = 99.412β = 97.79
c = 103.923γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-28
    Type: Initial release
  • Version 1.1: 2013-07-31
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description