3VYS

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1016/j.str.2012.09.018
  • Primary Citation of Related Structures:  

  • 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 H ...

    [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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hydrogenase expression/formation protein HypC
A
74Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)Mutation(s): 0 
Gene Names: Tk-hypC
Find proteins for Q5JII0 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Go to UniProtKB:  Q5JII0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hydrogenase expression/formation protein HypD
B
372Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)Mutation(s): 0 
Gene Names: Tk-hypD
Find proteins for Q5JII1 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Go to UniProtKB:  Q5JII1
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Hydrogenase expression/formation protein HypE
C
338Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)Mutation(s): 0 
Find proteins for Q5JII7 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Go to UniProtKB:  Q5JII7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4
Download SDF File 
Download CCD File 
B
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
MG
Query on MG
Download SDF File 
Download CCD File 
C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.218 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 78.567α = 90.00
b = 99.201β = 97.69
c = 104.025γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction
CNSrefinement

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2012-10-02 
  • Released Date: 2012-11-28 
  • Deposition Author(s): Watanabe, S., Miki, K.

Revision History 

  • Version 1.0: 2012-11-28
    Type: Initial release
  • Version 1.1: 2013-07-31
    Type: Database references