6KD7

Crystal structure of geranylgeranyl pyrophosphate synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of geranylgeranyl pyrophosphate synthase (crtE) from Nonlabens dokdonensis DSW-6.

Kim, S.Kim, E.J.Park, J.B.Kim, S.W.Kim, K.J.

(2019) Biochem.Biophys.Res.Commun. --: --

  • DOI: 10.1016/j.bbrc.2019.08.071

  • PubMed Abstract: 
  • Isoprenoids comprise a diverse group of natural products with a broad range of metabolic functions. Isoprenoids are synthesized from prenyl pyrophosphates by prenyltransferases that catalyze the isoprenoid chain-elongation process to different chain ...

    Isoprenoids comprise a diverse group of natural products with a broad range of metabolic functions. Isoprenoids are synthesized from prenyl pyrophosphates by prenyltransferases that catalyze the isoprenoid chain-elongation process to different chain lengths. We hereby present the crystal structure of geranylgeranyl pyrophosphate synthase from the marine flavobacterium Nonlabens dokdonensis DSW-6 (NdGGPPS). NdGGPPS forms a hexamer composed of homodimeric trimer, and the monomeric structure is composed of 15 α-helices (α1-α15). In this structure, we observed the binding of one pyrophosphate molecule and two glycerol molecules that mimicked substrate binding to the enzyme. The substrate binding site of NdGGPPS contains large hydrophobic residues such as Phe, His and Tyr, and structural and amino acids sequence analyses thereof suggest that the protein belongs to the short-chain prenyltransferase family.


    Organizational Affiliation

    Division of Applied Life Science (BK21 Plus), PMBBRC, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea. Electronic address: swkim@gnu.ac.kr.,School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu, 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 41566, Republic of Korea.,School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu, 41566, Republic of Korea.,School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu, 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 41566, Republic of Korea. Electronic address: kkim@knu.ac.kr.,Division of Applied Life Science (BK21 Plus), PMBBRC, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polyprenyl synthetase
A
335Nonlabens dokdonensis (strain DSM 17205 / KCTC 12402 / DSW-6)Mutation(s): 0 
Find proteins for L7W5I6 (Nonlabens dokdonensis (strain DSM 17205 / KCTC 12402 / DSW-6))
Go to UniProtKB:  L7W5I6
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PPV
Query on PPV

Download SDF File 
Download CCD File 
A
PYROPHOSPHATE
H4 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.222 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 194.718α = 90.00
b = 194.718β = 90.00
c = 107.544γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2019-07-01 
  • Released Date: 2019-09-11 
  • Deposition Author(s): Kim, S., Kim, K.-J.

Revision History 

  • Version 1.0: 2019-09-11
    Type: Initial release