1TKU | pdb_00001tku

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

• PDB DOI: https://doi.org/10.2210/pdb1TKU/pdb

• Classification: ISOMERASE
• Organism(s): Candida albicans SC5314
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-06-09 Released: 2004-09-07 
• Deposition Author(s): Echt, S., Bauer, S., Steinbacher, S., Huber, R., Bacher, A., Fischer, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 
  0.218 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.185 (DCC) 

Starting Model: experimental

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

• PubMed: 15328619 
• DOI: https://doi.org/10.1016/j.jmb.2004.06.053
• Primary Citation 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.

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Organizational Affiliation: 
• Lehrstuhl für Organische Chemie und Biochemie, Technische Universität München, Garching, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 45.83 kDa 
• Atom Count: 3,734 
• Modeled Residue Count: 392 
• Deposited Residue Count: 408 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3,4-Dihydroxy-2-butanone 4-phosphate Synthase	A, B	204	Candida albicans SC5314	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5RP	C [auth A], D [auth B]	RIBULOSE-5-PHOSPHATE C5 H11 O8 P FNZLKVNUWIIPSJ-UHNVWZDZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free:  0.218 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.185 (DCC) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.2	α = 66.4
b = 47.9	β = 72.3
c = 59.8	γ = 89.9

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-09-07 
Deposition Author(s): Echt, S., Bauer, S., Steinbacher, S., Huber, R., Bacher, A., Fischer, M.

Revision History  

• 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