6OJS | pdb_00006ojs

Crystal structure of TS-DHFR from Cryptosporidium hominis in complex with NADPH, FdUMP, MTX and 2-amino-4-oxo-4,7-dihydro-pyrrolo[2,3-d]pyrimidine-methyl-phenyl-D-glutamic acid

PDB DOI: https://doi.org/10.2210/pdb6OJS/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Cryptosporidium hominis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-04-12 Released: 2019-06-19
Deposition Author(s): Czyzyk, D.J., Anderson, K.S., Jorgensen, W.L., Valhondo, M.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.21 Å
R-Value Free:
0.232 (Depositor), 0.232 (DCC)
R-Value Work:
0.218 (Depositor), 0.220 (DCC)
R-Value Observed:
0.219 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Understanding the structural basis of species selective, stereospecific inhibition for Cryptosporidium and human thymidylate synthase.

Czyzyk, D.J., Valhondo, M., Jorgensen, W.L., Anderson, K.S.

(2019) FEBS Lett 593: 2069-2078

PubMed: 31172516 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/1873-3468.13474
Primary Citation Related Structures:
6OJS, 6OJU, 6OJV

PubMed Abstract:
Thymidylate synthase (TS), found in all organisms, is an essential enzyme responsible for the de novo synthesis of deoxythymidine monophosphate. The TS active sites of the protozoal parasite Cryptosporidium hominis and human are relatively conserved. Evaluation of antifolate compound 1 and its R-enantiomer 2 against both enzymes reveals divergent inhibitor selectivity and enzyme stereospecificity. To establish how C. hominis and human TS (ChTS and hTS) selectively discriminate 1 and 2, respectively, we determined crystal structures of ChTS complexed with 2 and hTS complexed with 1 or 2. Coupled with the previously determined structure of ChTS complexed with 1, we discuss a possible mechanism for enzyme stereospecificity and inhibitor selectivity.

Organizational Affiliation

Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA.

Macromolecule Content

Total Structure Weight: 311.01 kDa
Atom Count: 20,926
Modeled Residue Count: 2,540
Deposited Residue Count: 2,605
Unique protein chains: 1

Macromolecules

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| 3D Structure

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 Gene Names: CHUDEA4_4460
UniProt
Find proteins for A0A0S4TER9 (Cryptosporidium hominis) Explore A0A0S4TER9 Go to UniProtKB: A0A0S4TER9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0S4TER9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP Query on NDP Download:Ideal Coordinates CCD File SDF format, chain V [auth E] SDF format, chain R [auth D] SDF format, chain N [auth C] SDF format, chain J [auth B] SDF format, chain F [auth A] MOL2 format, chain V [auth E] MOL2 format, chain R [auth D] MOL2 format, chain N [auth C] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] mmCIF format, chain V [auth E] mmCIF format, chain R [auth D] mmCIF format, chain N [auth C] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A]	F [auth A], J [auth B], N [auth C], R [auth D], V [auth E]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D] Focus chain V [auth E] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D] Focus chain V [auth E]
MTX Query on MTX Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain U [auth D] SDF format, chain Y [auth E] SDF format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth D] MOL2 format, chain Y [auth E] MOL2 format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain U [auth D] mmCIF format, chain Y [auth E] mmCIF format, chain I [auth A]	I [auth A], M [auth B], Q [auth C], U [auth D], Y [auth E]	METHOTREXATE C₂₀ H₂₂ N₈ O₅ FBOZXECLQNJBKD-ZDUSSCGKSA-N		Interactions Focus chain I [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain Y [auth E] Interactions & Density Focus chain I [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain Y [auth E]
D96 Query on D96 Download:Ideal Coordinates CCD File SDF format, chain X [auth E] SDF format, chain T [auth D] SDF format, chain P [auth C] SDF format, chain L [auth B] SDF format, chain H [auth A] MOL2 format, chain X [auth E] MOL2 format, chain T [auth D] MOL2 format, chain P [auth C] MOL2 format, chain L [auth B] MOL2 format, chain H [auth A] mmCIF format, chain X [auth E] mmCIF format, chain T [auth D] mmCIF format, chain P [auth C] mmCIF format, chain L [auth B] mmCIF format, chain H [auth A]	H [auth A], L [auth B], P [auth C], T [auth D], X [auth E]	N-{4-[(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzene-1-carbonyl}-D-glutamic acid C₁₉ H₁₉ N₅ O₆ VDHBMZRBPMTLGE-GFCCVEGCSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D] Focus chain X [auth E] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D] Focus chain X [auth E]
UFP Query on UFP Download:Ideal Coordinates CCD File SDF format, chain W [auth E] SDF format, chain S [auth D] SDF format, chain O [auth C] SDF format, chain K [auth B] SDF format, chain G [auth A] MOL2 format, chain W [auth E] MOL2 format, chain S [auth D] MOL2 format, chain O [auth C] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] mmCIF format, chain W [auth E] mmCIF format, chain S [auth D] mmCIF format, chain O [auth C] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A]	G [auth A], K [auth B], O [auth C], S [auth D], W [auth E]	5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE C₉ H₁₂ F N₂ O₈ P HFEKDTCAMMOLQP-RRKCRQDMSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth D] Focus chain W [auth E] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth D] Focus chain W [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.21 Å
R-Value Free: 0.232 (Depositor), 0.232 (DCC)
R-Value Work: 0.218 (Depositor), 0.220 (DCC)
R-Value Observed: 0.219 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 212.622	α = 90
b = 116.188	β = 95.48
c = 220.884	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-06-19

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI083146
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	5T32AI007404

Revision History (Full details and data files)

Version 1.0: 2019-06-19
Type: Initial release
Version 1.1: 2019-08-21
Changes: Data collection, Database references
Version 1.2: 2019-12-18
Changes: Author supporting evidence
Version 1.3: 2023-10-11
Changes: Data collection, Database references, Refinement description