7MY6 | pdb_00007my6

Se-CrtE C-term His-tag with IPP added


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 
    0.209 (Depositor) 
  • R-Value Work: 
    0.180 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7MY6

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Molecular characterization of cyanobacterial short-chain prenyltransferases and discovery of a novel GGPP phosphatase.

Satta, A.Esquirol, L.Ebert, B.E.Newman, J.Peat, T.S.Plan, M.Schenk, G.Vickers, C.E.

(2022) FEBS J 289: 6672-6693

  • DOI: https://doi.org/10.1111/febs.16556
  • Primary Citation Related Structures: 
    7MXZ, 7MY0, 7MY1, 7MY6, 7MY7

  • PubMed Abstract: 

    Cyanobacteria are photosynthetic prokaryotes with strong potential to be used for industrial terpenoid production. However, the key enzymes forming the principal terpenoid building blocks, called short-chain prenyltransferases (SPTs), are insufficiently characterized. Here, we examined SPTs in the model cyanobacteria Synechococcus elongatus sp. PCC 7942 and Synechocystis sp. PCC 6803. Each species has a single putative SPT (SeCrtE and SyCrtE, respectively). Sequence analysis identified these as type-II geranylgeranyl pyrophosphate synthases (GGPPSs) with high homology to GGPPSs found in the plastids of green plants and other photosynthetic organisms. In vitro analysis demonstrated that SyCrtE is multifunctional, producing geranylgeranyl pyrophosphate (GGPP; C 20 ) primarily but also significant amounts of farnesyl pyrophosphate (FPP, C 15 ) and geranyl pyrophosphate (GPP, C 10 ); whereas SeCrtE appears to produce only GGPP. The crystal structures were solved to 2.02 and 1.37 Å, respectively, and the superposition of the structures against the GGPPS of Synechococcus elongatus sp. PCC 7002 yield a root mean square deviation of 0.8 Å (SeCrtE) and 1.1 Å (SyCrtE). We also discovered that SeCrtE is co-encoded in an operon with a functional GGPP phosphatase, suggesting metabolic pairing of these two activities and a putative function in tocopherol biosynthesis. This work sheds light on the activity of SPTs and terpenoid synthesis in cyanobacteria. Understanding native prenyl phosphate metabolism is an important step in developing approaches to engineering the production of different chain-length terpenoids in cyanobacteria.


  • Organizational Affiliation
    • Australian Institute for Bioengineering and Biotechnology, The University of Queensland, St. Lucia, Australia.

Macromolecule Content 

  • Total Structure Weight: 68.33 kDa 
  • Atom Count: 4,695 
  • Modeled Residue Count: 573 
  • Deposited Residue Count: 620 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Farnesyl-diphosphate synthase
A, B
310Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
Gene Names: Synpcc7942_0776
EC: 2.5.1.10 (PDB Primary Data), 2.5.1.1 (UniProt)
UniProt
Find proteins for Q31Q61 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
Explore Q31Q61 
Go to UniProtKB:  Q31Q61
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ31Q61
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IPE
(Subject of Investigation/LOI)

Query on IPE



Download:Ideal Coordinates CCD File
C [auth A]3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
C5 H12 O7 P2
NUHSROFQTUXZQQ-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
E [auth A],
K [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
F [auth A],
M [auth B],
N [auth B],
O [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
D [auth A],
L [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
J [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth A]
P [auth B]
Q [auth B]
G [auth A],
H [auth A],
I [auth A],
P [auth B],
Q [auth B],
R [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free:  0.209 (Depositor) 
  • R-Value Work:  0.180 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.423α = 90
b = 144.627β = 95.249
c = 48.066γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-24
    Type: Initial release
  • Version 1.1: 2022-11-16
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description