1RQI | pdb_00001rqi

Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate

PDB DOI: https://doi.org/10.2210/pdb1RQI/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2003-12-05 Released: 2004-03-02
Deposition Author(s): Hosfield, D.J., Zhang, Y., Dougan, D.R., Brooun, A., Tari, L.W., Swanson, R.V., Finn, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free:
0.259 (Depositor)
R-Value Work:
0.203 (Depositor)
R-Value Observed:
0.206 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Structural basis for bisphosphonate-mediated inhibition of isoprenoid biosynthesis

Hosfield, D.J., Zhang, Y., Dougan, D.R., Brooun, A., Tari, L.W., Swanson, R.V., Finn, J.

(2004) J Biological Chem 279: 8526-8529

PubMed: 14672944 Search on PubMed
DOI: https://doi.org/10.1074/jbc.C300511200
Primary Citation Related Structures:
1RQI, 1RQJ, 1RTR

PubMed Abstract:
Farnesyl pyrophosphate synthetase (FPPS) synthesizes farnesyl pyrophosphate through successive condensations of isopentyl pyrophosphate with dimethylallyl pyrophosphate and geranyl pyrophosphate. Nitrogen-containing bisphosphonate drugs used to treat osteoclast-mediated bone resorption and tumor-induced hypercalcemia are potent inhibitors of the enzyme. Here we present crystal structures of substrate and bisphosphonate complexes of FPPS. The structures reveal how enzyme conformational changes organize conserved active site residues to exploit metal-induced ionization and substrate positioning for catalysis. The structures further demonstrate how nitrogen-containing bisphosphonates mimic a carbocation intermediate to inhibit the enzyme. Together, these FPPS complexes provide a structural template for the design of novel inhibitors that may prove useful for the treatment of osteoporosis and other clinical indications including cancer.

Organizational Affiliation

Syrrx Inc., San Diego, California 92121, USA.

Macromolecule Content

Total Structure Weight: 65.88 kDa
Atom Count: 4,852
Modeled Residue Count: 598
Deposited Residue Count: 600
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Geranyltranstransferase	A, B	300	Escherichia coli	Mutation(s): 0 Gene Names: ISPA, B0421 EC: 2.5.1.10
UniProt
Find proteins for P22939 (Escherichia coli (strain K12)) Explore P22939 Go to UniProtKB: P22939
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P22939
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DST Query on DST Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B]	F [auth A], L [auth B]	DIMETHYLALLYL S-THIOLODIPHOSPHATE C₅ H₁₂ O₆ P₂ S ZWFWSISPSBLNGO-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain L [auth B]
IPR Query on IPR Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] mmCIF format, chain G [auth A] mmCIF format, chain M [auth B]	G [auth A], M [auth B]	ISOPENTYL PYROPHOSPHATE C₅ H₁₄ O₇ P₂ IPFXNYPSBSIFOB-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain M [auth B]
DPO Query on DPO Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	DIPHOSPHATE O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-J		Interactions Focus chain H [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	C [auth A] D [auth A] E [auth A] I [auth B] J [auth B] C [auth A], D [auth A], E [auth A], I [auth B], J [auth B], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free: 0.259 (Depositor)
R-Value Work: 0.203 (Depositor)
R-Value Observed: 0.206 (Depositor)

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.839	α = 90
b = 88.839	β = 90
c = 174.769	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2004-03-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-03-02
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 2.0: 2019-10-02
Changes: Data collection, Non-polymer description, Structure summary
Version 2.1: 2024-02-14
Changes: Data collection, Database references, Derived calculations, Structure summary