9IMR | pdb_00009imr

Crystal structure of geranylgeranyl pyrophosphate synthase Rv0562 from Mycobacterium tuberculosis in complex with IPP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 
    0.193 (Depositor), 0.204 (DCC) 
  • R-Value Work: 
    0.142 (Depositor), 0.155 (DCC) 
  • R-Value Observed: 
    0.144 (Depositor) 

Starting Model: experimental
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Literature

Structural insight of a bi-functional isoprenyl diphosphate synthase Rv0562 from Mycobacterium tuberculosis.

Wang, Q.Yang, Y.He, B.Huang, J.W.Kuo, C.J.Chen, C.C.Guo, R.T.

(2025) Int J Biol Macromol : 145171-145171

  • DOI: https://doi.org/10.1016/j.ijbiomac.2025.145171
  • Primary Citation of Related Structures:  
    9IMQ, 9IMR, 9IMS, 9KUQ

  • PubMed Abstract: 

    Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis. Mtb uses MK-9(II-H 2 ), which consists of an isoprenyl side chain containing nine isoprene units, with one being hydrogenated in the β-position, as an essential element in the electron transport system. Rv0562 that can operate geranylgeranyl diphosphate synthase (GGPPs) activity catalyzes the synthesis of MK-9(II-H 2 ) by condensing one molecule of DMAPP with eight molecules of isopentenyl diphosphate (IPP) to form a C 45 long-chain isoprenoid product. In this study, the structures of Rv0562 were determined in the apo-form at a resolution of 2.54 Å and in complex with IPP and Mg 2+ at a resolution of 1.89 Å, revealing detailed interactions between the enzyme and substrates. Moreover, the crystal structure of the Rv0562-DM variant was determined at 2.27 Å resolution in complex with polyethylene glycol (PEG), which occupies the substrate binding tunnel, mimicking the long-chain product. The chain length determination mechanism of Rv0562 is also probed through mutagenesis experiments. The obtained structures help us understand how Rv0562 catalyzes isoprenyl chain elongation, showing implications in developing new anti-Mtb treatments.


  • Organizational Affiliation

    State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life Sciences, Hubei University, Wuhan 430062, PR China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nonaprenyl diphosphate synthase
A, B
335Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: grcC1Rv0562
EC: 2.5.1.85 (PDB Primary Data), 2.5.1.10 (PDB Primary Data), 2.5.1.29 (PDB Primary Data)
UniProt
Find proteins for O06428 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore O06428 
Go to UniProtKB:  O06428
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO06428
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IPE (Subject of Investigation/LOI)
Query on IPE

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
K [auth B],
L [auth B]
3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
C5 H12 O7 P2
NUHSROFQTUXZQQ-UHFFFAOYSA-N
BCN
Query on BCN

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
P [auth B],
Q [auth B]
BICINE
C6 H13 N O4
FSVCELGFZIQNCK-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
J [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
M [auth B]
N [auth B]
E [auth A],
F [auth A],
G [auth A],
M [auth B],
N [auth B],
O [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free:  0.193 (Depositor), 0.204 (DCC) 
  • R-Value Work:  0.142 (Depositor), 0.155 (DCC) 
  • R-Value Observed: 0.144 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.796α = 90
b = 115.643β = 90
c = 119.27γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SAINTdata scaling
SAINTdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-09
    Type: Initial release