8F8F | pdb_00008f8f

The structure of Rv2173 from M. tuberculosis (APO form)

PDB DOI: https://doi.org/10.2210/pdb8F8F/pdb

Classification: TRANSFERASE
Organism(s): Mycobacterium tuberculosis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-11-22 Released: 2023-11-29
Deposition Author(s): Johnston, J.M., Allison, T.M., Titterington, J.
Funding Organization(s): Ministry of Business, Innovation and Employment (New Zealand)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.238 (Depositor), 0.239 (DCC)
R-Value Work:
0.212 (Depositor), 0.213 (DCC)
R-Value Observed:
0.213 (Depositor)

Starting Model: other
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wwPDB Validation 3D Report Full Report

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

Literature

Structures of Mycobacterium tuberculosis isoprenyl diphosphate synthase Rv2173 in substrate-bound forms.

Titterington, J.A., Ho, N.A.T., Beasley, C.P.H., Mann, F., Baker, E.N., Allison, T.M., Johnston, J.M.

(2025) Acta Crystallogr F Struct Biol Commun 81: 193-200

PubMed: 40166974 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S2053230X25002298
Primary Citation Related Structures:
8F8F, 8F8K, 8F8L

PubMed Abstract:
We report structures of the Mycobacterium tuberculosis isoprenyl diphosphate synthase Rv2173 in three forms: apo and two substrate-bound forms [isoprenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP)]. The protein possesses a canonical all-α-helical trans-isoprenyl diphosphate synthase fold that is dimeric in each form. There are some differences between the structures: the IPP-bound form shows IPP bound in the DMAPP/allylic substrate-binding site with three divalent metal ions bound around the IPP and the complete C-terminus closing around the active site, while the apo and DMAPP-bound forms are more open, with some of the C-terminal region disordered, supporting suggestions that the C-terminus is important in substrate entry/product exit. In the DMAPP form DMAPP occupies the expected allylic substrate site, but only two metal ions are associated with the binding, with the DMAPP diphosphates adopting a slightly different binding pose compared with IPP in the same site, and the third metal-binding site is unoccupied. In no case is the IPP binding site occupied by IPP. There has been some uncertainty regarding product length for Rv2173, with variable lengths being reported. In the structures reported here, the `capping' residue at the bottom of the binding cavity is tryptophan and comparison with other IPP synthases suggests that the structure of Rv2173 is most consistent with a C ₁₀-C ₁₅ final product size.

Organizational Affiliation

Biomolecular Interaction Centre and School of Physical and Chemical Sciences, University of Canterbury. Christchurch, New Zealand.

Macromolecule Content

Total Structure Weight: 84.97 kDa
Atom Count: 5,642
Modeled Residue Count: 698
Deposited Residue Count: 774
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
(2E,6E)-farnesyl diphosphate synthase	A, B	387	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: idsA2, Rv2173 EC: 2.5.1.10 (PDB Primary Data), 2.5.1.1 (PDB Primary Data)
UniProt
Find proteins for O53507 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore O53507 Go to UniProtKB: O53507
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O53507
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL 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 F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] H [auth B] C [auth A], D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]