Aquifex aeolicus KDO8P synthase H185G mutant in complex with PEP and Cadmium

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.207 

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Function of His185 in Aquifex aeolicus 3-Deoxy-D-manno-octulosonate 8-Phosphate Synthase

Wang, J.Duewel, H.S.Stuckey, J.A.Woodard, R.W.Gatti, D.L.

(2002) J Mol Biol 324: 205-214

  • DOI: https://doi.org/10.1016/s0022-2836(02)01096-3
  • Primary Citation of Related Structures:  
    1LRN, 1LRO, 1LRQ

  • PubMed Abstract: 

    Aquifex aeolicus 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8PS) catalyzes the condensation of arabinose 5-phosphate (A5P) and phosphoenolpyruvate (PEP) by favoring the activation of a water molecule coordinated to the active-site metal ion. Cys11, His185, Glu222 and Asp233 are the other metal ligands. Wild-type KDO8PS is purified with Zn(2+) or Fe(2+) in the active site, but maximal activity in vitro is achieved when the endogenous metal is replaced with Cd(2+). The H185G enzyme retains 8% of the wild-type activity. ICP mass spectrometry analysis indicates that loss of His185 decreases the enzyme affinity for Fe(2+), but not for Zn(2+). However, maximal activity is again achieved by substitution of the endogenous metal with Cd(2+). We have determined the X-ray structures of the Cd(2+) H185G enzyme in its substrate-free form, and in complex with PEP, and PEP plus A5P. These structures show a normal amount of Cd(2+) bound, suggesting that coordination by His185 is not essential to retain Cd(2+) in the active site. Nonetheless, there are significant changes in the coordination sphere of Cd(2+) with respect to the wild-type enzyme, as the carboxylate moiety of PEP binds directly to the metal ion and replaces water and His185 as ligands. These observations indicate that the primary function of His185 in A.aeolicus KDO8PS is to orient PEP in the active site of the enzyme in such a way that a water molecule on the sinister (si) side of PEP can be activated by direct coordination to the metal ion.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI 48201, USA.

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
KDO-8-phosphate synthetase
A, B
267Aquifex aeolicusMutation(s): 1 
Find proteins for O66496 (Aquifex aeolicus (strain VF5))
Explore O66496 
Go to UniProtKB:  O66496
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO66496
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.207 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.45α = 90
b = 84.45β = 90
c = 160.581γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-11-27
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.5: 2024-02-14
    Changes: Data collection