3WQL | pdb_00003wql

Crystal structure of Rv3378c with Mg2+ and PPi

PDB DOI: https://doi.org/10.2210/pdb3WQL/pdb

Classification: HYDROLASE
Organism(s): Mycobacterium tuberculosis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-01-28 Released: 2014-02-19
Deposition Author(s): Chan, H.C., Feng, X., Ko, T.P., Huang, C.H., Hu, Y., Zheng, Y., Bogue, S., Nakano, C., Hoshino, T., Zhang, L., Lv, P., Liu, W., Crick, D.C., Liang, P.H., Wang, A.H., Oldfield, E., Guo, R.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.239 (Depositor), 0.239 (DCC)
R-Value Work:
0.198 (Depositor), 0.198 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Structure and inhibition of tuberculosinol synthase and decaprenyl diphosphate synthase from Mycobacterium tuberculosis.

Chan, H.C., Feng, X., Ko, T.P., Huang, C.H., Hu, Y., Zheng, Y., Bogue, S., Nakano, C., Hoshino, T., Zhang, L., Lv, P., Liu, W., Crick, D.C., Liang, P.H., Wang, A.H., Oldfield, E., Guo, R.T.

(2014) J Am Chem Soc 136: 2892-2896

PubMed: 24475925 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/ja413127v
Primary Citation Related Structures:
3WQK, 3WQL, 3WQM, 3WQN, 4KT8, 4ONC

PubMed Abstract:
We have obtained the structure of the bacterial diterpene synthase, tuberculosinol/iso-tuberculosinol synthase (Rv3378c) from Mycobacterium tuberculosis , a target for anti-infective therapies that block virulence factor formation. This phosphatase adopts the same fold as found in the Z- or cis-prenyltransferases. We also obtained structures containing the tuberculosinyl diphosphate substrate together with one bisphosphonate inhibitor-bound structure. These structures together with the results of site-directed mutagenesis suggest an unusual mechanism of action involving two Tyr residues. Given the similarity in local and global structure between Rv3378c and the M. tuberculosis cis-decaprenyl diphosphate synthase (DPPS; Rv2361c), the possibility exists for the development of inhibitors that target not only virulence but also cell wall biosynthesis, based in part on the structures reported here.

Organizational Affiliation

Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology , Tianjin 300308, China.

Macromolecule Content

Total Structure Weight: 136.48 kDa
Atom Count: 10,271
Modeled Residue Count: 1,139
Deposited Residue Count: 1,184
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diterpene synthase	A, B, C, D	296	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: Rv3378c, MT3488 EC: 3.1.7.9 (PDB Primary Data), 3.1.7.8 (PDB Primary Data), 2.5.1.153 (UniProt)
UniProt
Find proteins for P9WJ61 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WJ61 Go to UniProtKB: P9WJ61
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WJ61
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain K [auth D] SDF format, chain J [auth C] SDF format, chain I [auth C] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain L [auth D] MOL2 format, chain K [auth D] MOL2 format, chain J [auth C] MOL2 format, chain I [auth C] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain L [auth D] mmCIF format, chain K [auth D] mmCIF format, chain J [auth C] mmCIF format, chain I [auth C] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth B] H [auth B] I [auth C] E [auth A], F [auth A], G [auth B], H [auth B], I [auth C], J [auth C], K [auth D], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.239 (Depositor), 0.239 (DCC)
R-Value Work: 0.198 (Depositor), 0.198 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 208.42	α = 90
b = 56.525	β = 90.28
c = 114.435	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-02-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-02-19
Type: Initial release
Version 1.1: 2014-10-01
Changes: Database references
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description