3Q7F | pdb_00003q7f

Cryptococcus neoformans protein farnesyltransferase in complex with FPP and ethylenediamine inhibitor 1

PDB DOI: https://doi.org/10.2210/pdb3Q7F/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Cryptococcus neoformans H99
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-01-04 Released: 2011-08-03
Deposition Author(s): Hast, M.A., Beese, L.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.213 (Depositor), 0.215 (DCC)
R-Value Work:
0.191 (Depositor), 0.194 (DCC)
R-Value Observed:
0.192 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Structures of Cryptococcus neoformans Protein Farnesyltransferase Reveal Strategies for Developing Inhibitors That Target Fungal Pathogens.

Hast, M.A., Nichols, C.B., Armstrong, S.M., Kelly, S.M., Hellinga, H.W., Alspaugh, J.A., Beese, L.S.

(2011) J Biological Chem 286: 35149-35162

PubMed: 21816822 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1074/jbc.M111.250506
Primary Citation Related Structures:
3Q73, 3Q75, 3Q78, 3Q79, 3Q7A, 3Q7F, 3SFX, 3SFY

PubMed Abstract:
Cryptococcus neoformans is a fungal pathogen that causes life-threatening infections in immunocompromised individuals, including AIDS patients and transplant recipients. Few antifungals can treat C. neoformans infections, and drug resistance is increasing. Protein farnesyltransferase (FTase) catalyzes post-translational lipidation of key signal transduction proteins and is essential in C. neoformans. We present a multidisciplinary study validating C. neoformans FTase (CnFTase) as a drug target, showing that several anticancer FTase inhibitors with disparate scaffolds can inhibit C. neoformans and suggesting structure-based strategies for further optimization of these leads. Structural studies are an essential element for species-specific inhibitor development strategies by revealing similarities and differences between pathogen and host orthologs that can be exploited. We, therefore, present eight crystal structures of CnFTase that define the enzymatic reaction cycle, basis of ligand selection, and structurally divergent regions of the active site. Crystal structures of clinically important anticancer FTase inhibitors in complex with CnFTase reveal opportunities for optimization of selectivity for the fungal enzyme by modifying functional groups that interact with structurally diverse regions. A substrate-induced conformational change in CnFTase is observed as part of the reaction cycle, a feature that is mechanistically distinct from human FTase. Our combined structural and functional studies provide a framework for developing FTase inhibitors to treat invasive fungal infections.

Organizational Affiliation

Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA.

Macromolecule Content

Total Structure Weight: 100.49 kDa
Atom Count: 7,003
Modeled Residue Count: 798
Deposited Residue Count: 869
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Farnesyltransferase alpha subunit	A	349	Cryptococcus neoformans H99	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Farnesyltransferase beta subunit	B	520	Cryptococcus neoformans H99	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	C, D, E	2		N/A	Interactions Focus chain C Focus chain D Focus chain E Interactions & Density Focus chain C Focus chain D Focus chain E
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ED2 Query on ED2 Download:Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	N-benzyl-N-(2-{(4-cyanophenyl)[(1-methyl-1H-imidazol-5-yl)methyl]amino}ethyl)-1-methyl-1H-imidazole-4-sulfonamide C₂₅ H₂₇ N₇ O₂ S IDHGAQOVWWBGFK-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
FPP Query on FPP Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	FARNESYL DIPHOSPHATE C₁₅ H₂₈ O₇ P₂ VWFJDQUYCIWHTN-YFVJMOTDSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
3CX Query on 3CX Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	G [auth B], H [auth B], I [auth B]	(2S)-3-(cyclohexylamino)-2-hydroxypropane-1-sulfonic acid C₉ H₁₉ N O₄ S INEWUCPYEUEQTN-VIFPVBQESA-N		Interactions Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003 Query on PRD_900003	C, D, E	sucrose	Oligosaccharide / Nutrient		Interactions Focus chain C Focus chain D Focus chain E Interactions & Density Focus chain C Focus chain D Focus chain E

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.213 (Depositor), 0.215 (DCC)
R-Value Work: 0.191 (Depositor), 0.194 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.58	α = 90
b = 143.58	β = 90
c = 130.723	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-08-03

Deposition Author(s):

Hast, M.A.

Beese, L.S.

Revision History (Full details and data files)

Version 1.0: 2011-08-03
Type: Initial release
Version 1.1: 2011-10-19
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2024-02-21
Changes: Data collection, Database references, Structure summary