4ESW

Crystal structure of C. albicans Thi5 H66G mutant

• PDB DOI: https://doi.org/10.2210/pdb4ESW/pdb

• Classification: TRANSFERASE
• Organism(s): Candida albicans WO-1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-04-23 Released: 2012-09-19 
• Deposition Author(s): Fenwick, M.K., Huang, S., Zhang, Y., Lai, R., Hazra, A., Rajashankar, K., Philmus, B., Kinsland, C., Sanders, J., Begley, T.P., Ealick, S.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.191 
• R-Value Work: 0.162 
• R-Value Observed: 0.164 

Literature

Thiamin pyrimidine biosynthesis in Candida albicans : a remarkable reaction between histidine and pyridoxal phosphate.

Lai, R.Y., Huang, S., Fenwick, M.K., Hazra, A., Zhang, Y., Rajashankar, K., Philmus, B., Kinsland, C., Sanders, J.M., Ealick, S.E., Begley, T.P.

(2012) J Am Chem Soc 134: 9157-9159

• PubMed: 22568620 
• DOI: https://doi.org/10.1021/ja302474a
• Primary Citation of Related Structures:  
  4ESW, 4ESX


• PubMed Abstract: 
  

  In Saccharomyces cerevisiae , thiamin pyrimidine is formed from histidine and pyridoxal phosphate (PLP). The origin of all of the pyrimidine atoms has been previously determined using labeling studies and suggests that the pyrimidine is formed using remarkable chemistry that is without chemical or biochemical precedent. Here we report the overexpression of the closely related Candida albicans pyrimidine synthase (THI5p) and the reconstitution and preliminary characterization of the enzymatic activity. A structure of the C. albicans THI5p shows PLP bound at the active site via an imine with Lys62 and His66 in close proximity to the PLP. Our data suggest that His66 of the THI5 protein is the histidine source for pyrimidine formation and that the pyrimidine synthase is a single-turnover enzyme.

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Organizational Affiliation: 

Department of Chemistry, Texas A&M University, College Station, 77843, United States.

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: 77.63 kDa 
• Atom Count: 6,506 
• Modelled Residue Count: 684 
• Deposited Residue Count: 684 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyrimidine biosynthesis enzyme THI13	A, B	342	Candida albicans WO-1	Mutation(s): 1  Gene Names: CAWG_02199
UniProt
Find proteins for C4YMW2 (Candida albicans (strain WO-1)) Explore C4YMW2  Go to UniProtKB:  C4YMW2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	C [auth A], D [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.191 
• R-Value Work: 0.162 
• R-Value Observed: 0.164 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.386	α = 90
b = 99.474	β = 90
c = 126.389	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MLPHARE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-19 
Deposition Author(s): Fenwick, M.K., Huang, S., Zhang, Y., Lai, R., Hazra, A., Rajashankar, K., Philmus, B., Kinsland, C., Sanders, J., Begley, T.P., Ealick, S.E.

Revision History  

• Version 1.0: 2012-09-19
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Structure summary
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations