Crystal structure of formyltetrahydrofolate deformylase from Thermus thermophilus HB8

Experimental Data Snapshot

  • Resolution: 2.71 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 

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Structures and reaction mechanisms of the two related enzymes, PurN and PurU

Sampei, G.Kanagawa, M.Baba, S.Shimasaki, T.Taka, H.Mitsui, S.Fujiwara, S.Yanagida, Y.Kusano, M.Suzuki, S.Terao, K.Kawai, H.Fukai, Y.Nakagawa, N.Ebihara, A.Kuramitsu, S.Yokoyama, S.Kawai, G.

(2013) J Biochem 154: 569-579

  • DOI: https://doi.org/10.1093/jb/mvt090
  • Primary Citation of Related Structures:  
    2YWR, 3AUF, 3AV3, 3W7B

  • PubMed Abstract: 

    The crystal structures of glycinamide ribonucleotide transformylases (PurNs) from Aquifex aeolicus (Aa), Geobacillus kaustophilus (Gk) and Symbiobacterium toebii (St), and of formyltetrahydrofolate hydrolase (PurU) from Thermus thermophilus (Tt) were determined. The monomer structures of the determined PurN and PurU were very similar to the known structure of PurN, but oligomeric states were different; AaPurN and StPurN formed dimers, GkPurN formed monomer and PurU formed tetramer in the crystals. PurU had a regulatory ACT domain in its N-terminal side. So far several structures of PurUs have been determined, yet, the mechanisms of the catalysis and the regulation of PurU have not been elucidated. We, therefore, modelled ligand-bound structures of PurN and PurU, and performed molecular dynamics simulations to elucidate the reaction mechanisms. The evolutionary relationship of the two enzymes is discussed based on the comparisons of the structures and the catalytic mechanisms.

  • Organizational Affiliation

    Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan; RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Sayo, Hyogo 679-5148, Japan; Structural Biology Group, SPring-8/JASRI, 1-1-1 Kouto, Sayo, Sayo, Hyogo 679-5198, Japan; Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan; and Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Formyltetrahydrofolate deformylase
A, B
285Thermus thermophilus HB8Mutation(s): 0 
Gene Names: TTHA1321purU
Find proteins for Q5SIP8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SIP8 
Go to UniProtKB:  Q5SIP8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SIP8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.71 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.592α = 90
b = 90.726β = 90
c = 87.483γ = 90
Software Package:
Software NamePurpose
BSSdata collection
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: 2014-01-08
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Refinement description