7TUX

Crystal Structure of Plasmodium falciparum Hypoxanthine-Guanine-Xanthine Phosphoribosyltransferase in complex with [(3S)-4-Hydroxy-3-[({2-amino-4-hydroxy-5H-pyrrolo[3,2-d]pyrimidin-7-yl}methyl)amino]butyl]phosphonic acid

PDB DOI: https://doi.org/10.2210/pdb7TUX/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Plasmodium falciparum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-02-03 Released: 2022-12-07
Deposition Author(s): Harijan, R.K., Minnow, Y.V.T., Bonanno, J.B., Almo, S.C., Schramm, V.L.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free: 0.195
R-Value Work: 0.170
R-Value Observed: 0.171

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Inhibition and Mechanism of Plasmodium falciparum Hypoxanthine-Guanine-Xanthine Phosphoribosyltransferase.

V T Minnow, Y., Suthagar, K., Clinch, K., Ducati, R.G., Ghosh, A., Buckler, J.N., Harijan, R.K., Cahill, S.M., Tyler, P.C., Schramm, V.L.

(2022) ACS Chem Biol 17: 3407-3419

PubMed: 36413975 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/acschembio.2c00546
Primary Citation of Related Structures:
7TUX

PubMed Abstract:
Plasmodium falciparum hypoxanthine-guanine-xanthine phosphoribosyltransferase ( Pf HGXPRT) is essential for purine salvage of hypoxanthine into parasite purine nucleotides. Transition state analogue inhibitors of Pf HGXPRT are characterized by kinetic analysis, thermodynamic parameters, and X-ray crystal structures. Compound 1 , 9-deazaguanine linked to an acyclic ribocation phosphonate mimic, shows a kinetic K _i of 0.5 nM. Isothermal titration calorimetry (ITC) experiments of 1 binding to Pf HGXPRT reveal enthalpically driven binding with negative cooperativity for the binding of two inhibitor molecules in the tetrameric enzyme. Crystal structures of 1 bound to Pf HGXPRT define the hydrogen bond and ionic contacts to complement binding thermodynamics. Dynamics of ribosyl transfer from 5-phospho-α-d-ribosyl 1-pyrophosphate (PRPP) to hypoxanthine were examined by ¹⁸O isotope exchange at the bridging phosphoryl oxygen of PRPP pyrophosphate. Rotational constraints or short transition state lifetimes prevent torsional rotation and positional isotope exchange of bridging to nonbridging oxygen in the α-pyrophosphoryl group. Thermodynamic analysis of the transition state analogue and magnesium pyrophosphate binding reveal random and cooperative binding to Pf HGXPRT, unlike the obligatory ordered reaction kinetics reported earlier for substrate kinetics.

Organizational Affiliation

Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States.

Macromolecule Content

Total Structure Weight: 118.36 kDa
Atom Count: 8,671
Modelled Residue Count: 922
Deposited Residue Count: 1,000
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypoxanthine-guanine-xanthine phosphoribosyltransferase	A, B, C, D	250	Plasmodium falciparum	Mutation(s): 0 Gene Names: LACZ EC: 2.4.2.22 (PDB Primary Data), 2.4.2.8 (PDB Primary Data)
UniProt
Find proteins for P20035 (Plasmodium falciparum (isolate FCR-3 / Gambia)) Explore P20035 Go to UniProtKB: P20035
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P20035
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YBM (Subject of Investigation/LOI) Query on YBM Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain HA [auth C] SDF format, chain R [auth B] SDF format, chain WA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain R [auth B] MOL2 format, chain WA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain R [auth B] mmCIF format, chain WA [auth D]	E [auth A], HA [auth C], R [auth B], WA [auth D]	[(3S)-3-{[(2-amino-4-hydroxy-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]amino}-4-hydroxybutyl]phosphonic acid C₁₁ H₁₈ N₅ O₅ P WDBHHLGLZFXXDD-ZETCQYMHSA-N		Interactions Focus chain E [auth A] Focus chain HA [auth C] Focus chain R [auth B] Focus chain WA [auth D] Interactions & Density Focus chain E [auth A] Focus chain HA [auth C] Focus chain R [auth B] Focus chain WA [auth D]
POP Query on POP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain IA [auth C] SDF format, chain S [auth B] SDF format, chain XA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain S [auth B] MOL2 format, chain XA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain S [auth B] mmCIF format, chain XA [auth D]	F [auth A], IA [auth C], S [auth B], XA [auth D]	PYROPHOSPHATE 2- H₂ O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain IA [auth C] Focus chain S [auth B] Focus chain XA [auth D] Interactions & Density Focus chain F [auth A] Focus chain IA [auth C] Focus chain S [auth B] Focus chain XA [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth D] SDF format, chain BA [auth B] SDF format, chain BB [auth D] SDF format, chain CA [auth B] SDF format, chain CB [auth D] SDF format, chain DA [auth B] SDF format, chain DB [auth D] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain M [auth A] SDF format, chain MA [auth C] SDF format, chain N [auth A] SDF format, chain NA [auth C] SDF format, chain O [auth A] SDF format, chain OA [auth C] SDF format, chain P [auth A] SDF format, chain PA [auth C] SDF format, chain QA [auth C] SDF format, chain RA [auth C] SDF format, chain SA [auth C] SDF format, chain TA [auth C] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain ZA [auth D] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth D] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain CB [auth D] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth D] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain SA [auth C] MOL2 format, chain TA [auth C] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth D] mmCIF format, chain AA [auth B] mmCIF format, chain AB [auth D] mmCIF format, chain BA [auth B] mmCIF format, chain BB [auth D] mmCIF format, chain CA [auth B] mmCIF format, chain CB [auth D] mmCIF format, chain DA [auth B] mmCIF format, chain DB [auth D] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth C] mmCIF format, chain QA [auth C] mmCIF format, chain RA [auth C] mmCIF format, chain SA [auth C] mmCIF format, chain TA [auth C] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth D]	AA [auth B] AB [auth D] BA [auth B] BB [auth D] CA [auth B] AA [auth B], AB [auth D], BA [auth B], BB [auth D], CA [auth B], CB [auth D], DA [auth B], DB [auth D], EA [auth B], FA [auth B], H [auth A], I [auth A], J [auth A], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], MA [auth C], N [auth A], NA [auth C], O [auth A], OA [auth C], P [auth A], PA [auth C], QA [auth C], RA [auth C], SA [auth C], TA [auth C], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B], ZA [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth D] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Focus chain ZA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth D] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Focus chain ZA [auth D]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain EB [auth D] SDF format, chain FB [auth D] SDF format, chain GA [auth B] SDF format, chain Q [auth A] SDF format, chain UA [auth C] SDF format, chain VA [auth C] MOL2 format, chain EB [auth D] MOL2 format, chain FB [auth D] MOL2 format, chain GA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain UA [auth C] MOL2 format, chain VA [auth C] mmCIF format, chain EB [auth D] mmCIF format, chain FB [auth D] mmCIF format, chain GA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain UA [auth C] mmCIF format, chain VA [auth C]	EB [auth D] FB [auth D] GA [auth B] Q [auth A] UA [auth C] EB [auth D], FB [auth D], GA [auth B], Q [auth A], UA [auth C], VA [auth C]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain EB [auth D] Focus chain FB [auth D] Focus chain GA [auth B] Focus chain Q [auth A] Focus chain UA [auth C] Focus chain VA [auth C] Interactions & Density Focus chain EB [auth D] Focus chain FB [auth D] Focus chain GA [auth B] Focus chain Q [auth A] Focus chain UA [auth C] Focus chain VA [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain JA [auth C] SDF format, chain T [auth B] SDF format, chain YA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain T [auth B] MOL2 format, chain YA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain T [auth B] mmCIF format, chain YA [auth D]	G [auth A], JA [auth C], T [auth B], YA [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain JA [auth C] Focus chain T [auth B] Focus chain YA [auth D] Interactions & Density Focus chain G [auth A] Focus chain JA [auth C] Focus chain T [auth B] Focus chain YA [auth D]