4G9I

Crystal structure of T.kodakarensis HypF

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.50 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.279 
  • R-Value Observed: 0.279 

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Literature

Structure of the [NiFe]-hydrogenase maturation protein HypF from Thermococcus kodakarensis KOD1.

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

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 1153-1157

  • DOI: 10.1107/S1744309112036421
  • Primary Citation of Related Structures:  
    4G9I

  • PubMed Abstract: 

    • HypF is involved in the biosynthesis of the CN ligand of the NiFe(CN)(2)CO centre of [NiFe]-hydrogenases. Here, the full-length structure of HypF from Thermococcus kodakarenesis is reported at 4.5 Å resolution. The N-terminal acylphosphatase-like (ACP) domain interacts with the zinc-finger domain with some flexibility in its relative position ...

    HypF is involved in the biosynthesis of the CN ligand of the NiFe(CN)(2)CO centre of [NiFe]-hydrogenases. Here, the full-length structure of HypF from Thermococcus kodakarenesis is reported at 4.5 Å resolution. The N-terminal acylphosphatase-like (ACP) domain interacts with the zinc-finger domain with some flexibility in its relative position. Molecular-surface analysis shows that a deep pocket formed between the ACP and zinc-finger domains is highly conserved and has positive potential. These results suggest that the positively charged pocket identified is involved in the hydrolysis of carbamoyl phosphate and the formation of a carbamoyl intermediate.

    Organizational Affiliation: 

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



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hydrogenase maturation protein HypF
A, B, C, D, E, F
A, B, C, D, E, F
772Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: hypF, TK1997
EC: 6.2
UniProt
Find proteins for Q5JII4 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore Q5JII4 
Go to UniProtKB:  Q5JII4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5JII4
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.50 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.279 
  • R-Value Observed: 0.279 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 265.81α = 90
b = 265.81β = 90
c = 693.712γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
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: 2012-10-24
    Type: Initial release