7MXZ | pdb_00007mxz

Sy-CrtE apo structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 
    0.185 (Depositor), 0.186 (DCC) 
  • R-Value Work: 
    0.160 (Depositor), 0.163 (DCC) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7MXZ

This is version 1.3 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: 67.1 kDa 
  • Atom Count: 5,096 
  • 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
Geranylgeranyl pyrophosphate synthaseA [auth AAA],
B [auth BBB]
310Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Gene Names: crtE
EC: 2.5.1.1
UniProt
Find proteins for P72683 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore P72683 
Go to UniProtKB:  P72683
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP72683
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free:  0.185 (Depositor), 0.186 (DCC) 
  • R-Value Work:  0.160 (Depositor), 0.163 (DCC) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.497α = 90
b = 73.65β = 95.675
c = 132.172γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MoRDaphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-01
    Type: Initial release
  • Version 1.1: 2022-08-24
    Changes: Database references
  • Version 1.2: 2022-11-16
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description