1QZF | pdb_00001qzf

Crystal structure of DHFR-TS from Cryptosporidium hominis

• PDB DOI: https://doi.org/10.2210/pdb1QZF/pdb

• Classification: OXIDOREDUCTASE, TRANSFERASE
• Organism(s): Cryptosporidium hominis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-09-16 Released: 2003-11-11 
• Deposition Author(s): O'Neil, R.H., Lilien, R.H., Donald, B.R., Stroud, R.M., Anderson, A.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.245 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Models: experimental

Literature

Phylogenetic classification of protozoa based on the structure of the linker domain in the bifunctional enzyme, dihydrofolate reductase-thymidylate synthase

O'Neil, R.H., Lilien, R.H., Donald, B.R., Stroud, R.M., Anderson, A.C.

(2003) J Biological Chem 278: 52980-52987

• PubMed: 14555647 
• DOI: https://doi.org/10.1074/jbc.M310328200
• Primary Citation Related Structures: 
  1QZF


• PubMed Abstract: 
  

  We have determined the crystal structure of dihydrofolate reductase-thymidylate synthase (DHFR-TS) from Cryptosporidium hominis, revealing a unique linker domain containing an 11-residue alpha-helix that has extensive interactions with the opposite DHFR-TS monomer of the homodimeric enzyme. Analysis of the structure of DHFR-TS from C. hominis and of previously solved structures of DHFR-TS from Plasmodium falciparum and Leishmania major reveals that the linker domain primarily controls the relative orientation of the DHFR and TS domains. Using the tertiary structure of the linker domains, we have been able to place a number of protozoa in two distinct and dissimilar structural families corresponding to two evolutionary families and provide the first structural evidence validating the use of DHFR-TS as a tool of phylogenetic classification. Furthermore, the structure of C. hominis DHFR-TS calls into question surface electrostatic channeling as the universal means of dihydrofolate transport between TS and DHFR in the bifunctional enzyme.

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Organizational Affiliation: 
• Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, USA.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 311.17 kDa 
• Atom Count: 22,196 
• Modeled Residue Count: 2,595 
• Deposited Residue Count: 2,605 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
bifunctional dihydrofolate reductase-thymidylate synthase	A, B, C, D, E	521	Cryptosporidium hominis	Mutation(s): 0  EC: 1.5.1.3 (PDB Primary Data), 2.1.1.45 (PDB Primary Data)
UniProt
Find proteins for Q27552 (Cryptosporidium parvum) Explore Q27552  Go to UniProtKB:  Q27552

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	I [auth A], M [auth B], Q [auth C], U [auth D], Y [auth E]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
CB3	G [auth A], K [auth B], O [auth C], S [auth D], W [auth E]	10-PROPARGYL-5,8-DIDEAZAFOLIC ACID C24 H23 N5 O6 LTKHPMDRMUCUEB-IBGZPJMESA-N
FOL	H [auth A], L [auth B], P [auth C], T [auth D], X [auth E]	FOLIC ACID C19 H19 N7 O6 OVBPIULPVIDEAO-LBPRGKRZSA-N
UMP	F [auth A], J [auth B], N [auth C], R [auth D], V [auth E]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C9 H13 N2 O8 P JSRLJPSBLDHEIO-SHYZEUOFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.245 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 214.9	α = 90
b = 116.3	β = 95.23
c = 219.7	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-11-11 
Deposition Author(s): O'Neil, R.H., Lilien, R.H., Donald, B.R., Stroud, R.M., Anderson, A.C.

Revision History  

• Version 1.0: 2003-11-11
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description