Crystal structure of Thermus thermophilus HB8 H-protein of the glycine cleavage system

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.186 

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Structure of Thermus thermophilus HB8 H-protein of the glycine-cleavage system, resolved by a six-dimensional molecular-replacement method.

Nakai, T.Ishijima, J.Masui, R.Kuramitsu, S.Kamiya, N.

(2003) Acta Crystallogr D Biol Crystallogr 59: 1610-1618

  • DOI: https://doi.org/10.1107/s0907444903014975
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The glycine-cleavage system is a multi-enzyme complex consisting of four different components (the P-, H-, T- and L-proteins). Recombinant H-protein corresponding to that from Thermus thermophilus HB8 has been overexpressed, purified and crystallized. Synchrotron radiation from BL44B2 at SPring-8 was used to collect a native data set to 2.5 A resolution. The crystals belonged to the hexagonal space group P6(5) and contained three molecules per asymmetric unit, with a solvent content of 39%. Because of the large number of molecules within a closely packed unit cell, this structure was solved by six-dimensional molecular replacement with the program EPMR using the pea H-protein structure as a search model and was refined to an R factor of 0.189 and a free R factor of 0.256. Comparison with the pea H-protein reveals two highly conserved regions surrounding the lipoyl-lysine arm. Both of these regions are negatively charged and each has additional properties that are conserved in H-proteins from many species, suggesting that these regions are involved in intermolecular interactions. One region has previously been proposed to constitute an interaction surface with T-protein, while the other may be involved in an interaction with P-protein. Meanwhile, the lipoyl-lysine arm of the T. thermophilus H-protein was found to be more flexible than that of the pea H-protein, supporting the hypothesis that H-protein does not form a stable complex with L-protein during the reaction.

  • Organizational Affiliation

    RIKEN Harima Institute/SPring-8, 1-1-1 Kouto, Mikazuki, Sayo-gun, Hyogo 679-5148, Japan. nakaix@spring8.or.jp

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
glycine cleavage system H protein
A, B, C
128Thermus thermophilusMutation(s): 0 
Gene Names: GcvH
Find proteins for Q5SKW9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SKW9 
Go to UniProtKB:  Q5SKW9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SKW9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.186 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.775α = 90
b = 55.775β = 90
c = 191.19γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-08-26
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Refinement description