Crystal structure of MqnD (TTHA1568), a menaquinone biosynthetic enzyme from Thermus thermophilus HB8 (Cys11 modified with beta-mercaptoethanol)

Experimental Data Snapshot

  • Resolution: 1.55 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.182 

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Crystal structure of MqnD (TTHA1568), a menaquinone biosynthetic enzyme from Thermus thermophilus HB8.

Arai, R.Murayama, K.Uchikubo-Kamo, T.Nishimoto, M.Toyama, M.Kuramitsu, S.Terada, T.Shirouzu, M.Yokoyama, S.

(2009) J Struct Biol 168: 575-581

  • DOI: https://doi.org/10.1016/j.jsb.2009.07.007
  • Primary Citation of Related Structures:  
    2CZL, 3A3U

  • PubMed Abstract: 

    In many microorganisms, menaquinone is an essential lipid-soluble electron carrier. Recently, an alternative menaquinone biosynthetic pathway was found in some microorganisms [Hiratsuka, T., Furihata, K., Ishikawa, J., Yamashita, H., Itoh, N., Seto, H., Dairi, T., 2008. An alternative menaquinone biosynthetic pathway operating in microorganisms. Science 321, 1670-1673]. Here, we report the 1.55 A crystal structure of MqnD (TTHA1568) from Thermus thermophilus HB8, an enzyme within the alternative menaquinone biosynthetic pathway. The structure comprises two domains with alpha/beta structures, a large domain and a small domain. L(+)-Tartaric acid was bound to the pocket between the two domains, suggesting that this pocket is a putative active site. The conserved glycine residues at positions 78, 80 and 82 seem to act as hinges, allowing the substrate to access the pocket. Highly conserved residues, such as Asp14, Asp38, Asn43, Ser57, Thr107, Ile144, His145, Glu146, Leu176 and Tyr234, are located at this pocket, suggesting that these residues are involved in substrate binding and/or catalysis, and especially, His145 could function as a catalytic base. Since humans and their commensal intestinal bacteria, including lactobacilli, lack the alternative menaquinone biosynthetic pathway, this enzyme in pathogenic species, such as Helicobacter pylori and Campylobacter jejuni, is an attractive target for the development of chemotherapeutics. This high-resolution structure may contribute toward the development of its inhibitors.

  • Organizational Affiliation

    International Young Researchers Empowerment Center, Shinshu University, Ueda, Nagano, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
hypothetical protein TTHA1568272Thermus thermophilus HB8Mutation(s): 0 
Gene Names: TTHA1568
Find proteins for Q5SI12 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SI12 
Go to UniProtKB:  Q5SI12
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SI12
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on CME
Experimental Data & Validation

Experimental Data

  • Resolution: 1.55 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.182 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.236α = 90
b = 60.236β = 90
c = 171.276γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-13
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance