Crystal Structure of a Conserved CBS Domain Protein TA0289 of Unknown Function from Thermoplasma acidophilum

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 

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Biochemical and structural characterization of a novel family of cystathionine beta-synthase domain proteins fused to a Zn ribbon-like domain

Proudfoot, M.Sanders, S.A.Singer, A.Zhang, R.Brown, G.Binkowski, A.Xu, L.Lukin, J.A.Murzin, A.G.Joachimiak, A.Arrowsmith, C.H.Edwards, A.M.Savchenko, A.V.Yakunin, A.F.

(2008) J Mol Biol 375: 301-315

  • DOI: https://doi.org/10.1016/j.jmb.2007.10.060
  • Primary Citation of Related Structures:  
    1PVM, 2QH1

  • PubMed Abstract: 

    We have identified a novel family of proteins, in which the N-terminal cystathionine beta-synthase (CBS) domain is fused to the C-terminal Zn ribbon domain. Four proteins were overexpressed in Escherichia coli and purified: TA0289 from Thermoplasma acidophilum, TV1335 from Thermoplasma volcanium, PF1953 from Pyrococcus furiosus, and PH0267 from Pyrococcus horikoshii. The purified proteins had a red/purple color in solution and an absorption spectrum typical of rubredoxins (Rds). Metal analysis of purified proteins revealed the presence of several metals, with iron and zinc being the most abundant metals (2-67% of iron and 12-74% of zinc). Crystal structures of both mercury- and iron-bound TA0289 (1.5-2.0 A resolution) revealed a dimeric protein whose intersubunit contacts are formed exclusively by the alpha-helices of two cystathionine beta-synthase subdomains, whereas the C-terminal domain has a classical Zn ribbon planar architecture. All proteins were reversibly reduced by chemical reductants (ascorbate or dithionite) or by the general Rd reductase NorW from E. coli in the presence of NADH. Reduced TA0289 was found to be capable of transferring electrons to cytochrome C from horse heart. Likewise, the purified Zn ribbon protein KTI11 from Saccharomyces cerevisiae had a purple color in solution and an Rd-like absorption spectrum, contained both iron and zinc, and was reduced by the Rd reductase NorW from E. coli. Thus, recombinant Zn ribbon domains from archaea and yeast demonstrate an Rd-like electron carrier activity in vitro. We suggest that, in vivo, some Zn ribbon domains might also bind iron and therefore possess an electron carrier activity, adding another physiological role to this large family of important proteins.

  • Organizational Affiliation

    Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Room 72, Toronto, ON, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
conserved hypothetical protein Ta0289
A, B
184Thermoplasma acidophilum DSM 1728Mutation(s): 0 
Gene Names: Ta0289
Find proteins for Q9HLD9 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165))
Explore Q9HLD9 
Go to UniProtKB:  Q9HLD9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HLD9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.735α = 90
b = 62.838β = 90
c = 97.278γ = 90
Software Package:
Software NamePurpose
d*TREKdata reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-01-20
    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: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Derived calculations