1TKU

Crystal Structure of 3,4-Dihydroxy-2-butanone 4-phosphate Synthase of Candida albicans in complex with Ribulose-5-phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 
    0.218 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.170 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.3 of the entry. See complete history


Literature

Potential anti-infective targets in pathogenic yeasts: structure and properties of 3,4-dihydroxy-2-butanone 4-phosphate synthase of Candida albicans.

Echt, S.Bauer, S.Steinbacher, S.Huber, R.Bacher, A.Fischer, M.

(2004) J Mol Biology 341: 1085-1096

  • DOI: https://doi.org/10.1016/j.jmb.2004.06.053
  • Primary Citation of Related Structures:  
    1TKS, 1TKU

  • PubMed Abstract: 

    A synthetic gene specifying a putative 3,4-dihydroxy-2-butanone 4-phosphate synthase of Candida albicans directed the synthesis of a 22.5 kDa peptide in a recombinant Escherichia coli strain. The recombinant protein was purified to apparent homogeneity by two chromatographic steps and was shown to catalyze the formation of L-3,4-dihydroxy-2-butanone 4-phosphate from ribulose 5-phosphate at a rate of 332 nmol mg(-1) min(-1). Hydrodynamic studies indicated a native molecular mass of 41 kDa in line with a homodimer structure. The protein was crystallized in its apoform. Soaking yielded crystals in complex with the substrate ribulose 5-phosphate. The structures were solved at resolutions of 1.6 and 1.7 angstroms, respectively, using 3,4-dihydroxy-2-butanone 4-phosphate synthase of E. coli for molecular replacement. Structural comparison with the orthologs of Magnaporthe grisea and Methanococcus jannaschii revealed a hitherto unknown conformation of the essential acidic active-site loop.


  • Organizational Affiliation

    Lehrstuhl für Organische Chemie und Biochemie, Technische Universität München, Garching, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3,4-Dihydroxy-2-butanone 4-phosphate Synthase
A, B
204Candida albicans SC5314Mutation(s): 0 
Gene Names: CARib3
EC: 5.4.99 (PDB Primary Data), 4.1.99.12 (UniProt)
UniProt
Find proteins for Q5A3V6 (Candida albicans (strain SC5314 / ATCC MYA-2876))
Explore Q5A3V6 
Go to UniProtKB:  Q5A3V6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5A3V6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free:  0.218 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.170 (DCC) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.2α = 66.4
b = 47.9β = 72.3
c = 59.8γ = 89.9
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 5RPClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-09-07
    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
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description