3WJN | pdb_00003wjn

Crystal structure of Octaprenyl Pyrophosphate synthase from Escherichia coli with farnesyl S-thiol-pyrophosphate (FSPP)

• PDB DOI: https://doi.org/10.2210/pdb3WJN/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli O104:H4 str. 2009EL-2071
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-10-12 Released: 2014-06-18 
• Deposition Author(s): Han, X., Chen, C.C., Kuo, C.J., Huang, C.H., Zheng, Y., Ko, T.P., Zhu, Z., Feng, X., Oldfield, E., Liang, P.H., Guo, R.T., Ma, Y.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.269 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.216 (DCC) 

Starting Model: experimental

Literature

Crystal structures of ligand-bound octaprenyl pyrophosphate synthase from Escherichia coli reveal the catalytic and chain-length determining mechanisms.

Han, X., Chen, C.C., Kuo, C.J., Huang, C.H., Zheng, Y., Ko, T.P., Zhu, Z., Feng, X., Wang, K., Oldfield, E., Wang, A.H., Liang, P.H., Guo, R.T., Ma, Y.

(2015) Proteins 83: 37-45

• PubMed: 24895191 
• DOI: https://doi.org/10.1002/prot.24618
• Primary Citation Related Structures: 
  3WJK, 3WJN, 3WJO


• PubMed Abstract: 
  

  Octaprenyl pyrophosphate synthase (OPPs) catalyzes consecutive condensation reactions of one allylic substrate farnesyl pyrophosphate (FPP) and five homoallylic substrate isopentenyl pyrophosphate (IPP) molecules to form a C40 long-chain product OPP, which serves as a side chain of ubiquinone and menaquinone. OPPs belongs to the trans-prenyltransferase class of proteins. The structures of OPPs from Escherichia coli were solved in the apo-form as well as in complexes with IPP and a FPP thio-analog, FsPP, at resolutions of 2.2-2.6 Å, and revealed the detailed interactions between the ligands and enzyme. At the bottom of the active-site tunnel, M123 and M135 act in concert to form a wall which determines the final chain length. These results represent the first ligand-bound crystal structures of a long-chain trans-prenyltransferase and provide new information on the mechanisms of catalysis and product chain elongation.

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Organizational Affiliation: 
• Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 74.34 kDa 
• Atom Count: 4,823 
• Modeled Residue Count: 608 
• Deposited Residue Count: 674 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Octaprenyl diphosphate synthase	A, B	337	Escherichia coli O104:H4 str. 2009EL-2071	Mutation(s): 0  Gene Names: O3O_22640 EC: 2.5.1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FPS	C [auth A]	S-[(2E,6E)-3,7,11-TRIMETHYLDODECA-2,6,10-TRIENYL] TRIHYDROGEN THIODIPHOSPHATE C15 H28 O6 P2 S MYMLCRQRXFRQGP-YFVJMOTDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.269 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.216 (DCC) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.742	α = 90
b = 128.239	β = 90
c = 46.54	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-06-18 
Deposition Author(s): Han, X., Chen, C.C., Kuo, C.J., Huang, C.H., Zheng, Y., Ko, T.P., Zhu, Z., Feng, X., Oldfield, E., Liang, P.H., Guo, R.T., Ma, Y.H.

Revision History  

• Version 1.0: 2014-06-18
  Type: Initial release
  
• Version 1.1: 2022-08-24
  Changes: Database references, Derived calculations
• Version 1.2: 2023-11-08
  Changes: Data collection, Refinement description