2XDQ

Dark Operative Protochlorophyllide Oxidoreductase (ChlN-ChlB)2 Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of the Nitrogenase-Like Dark Operative Protochlorophyllide Oxidoreductase Catalytic Complex (Chln/Chlb)2.

Broecker, M.J.Schomburg, S.Heinz, D.W.Jahn, D.Schubert, W.-D.Moser, J.

(2010) J.Biol.Chem. 285: 27336

  • DOI: 10.1074/jbc.M110.126698

  • PubMed Abstract: 
  • During (bacterio)chlorophyll biosynthesis of many photosynthetically active organisms, dark operative protochlorophyllide oxidoreductase (DPOR) catalyzes the two-electron reduction of ring D of protochlorophyllide to form chlorophyllide. DPOR is comp ...

    During (bacterio)chlorophyll biosynthesis of many photosynthetically active organisms, dark operative protochlorophyllide oxidoreductase (DPOR) catalyzes the two-electron reduction of ring D of protochlorophyllide to form chlorophyllide. DPOR is composed of the subunits ChlL, ChlN, and ChlB. Homodimeric ChlL(2) bearing an intersubunit [4Fe-4S] cluster is an ATP-dependent reductase transferring single electrons to the heterotetrameric (ChlN/ChlB)(2) complex. The latter contains two intersubunit [4Fe-4S] clusters and two protochlorophyllide binding sites, respectively. Here we present the crystal structure of the catalytic (ChlN/ChlB)(2) complex of DPOR from the cyanobacterium Thermosynechococcus elongatus at a resolution of 2.4 A. Subunits ChlN and ChlB exhibit a related architecture of three subdomains each built around a central, parallel beta-sheet surrounded by alpha-helices. The (ChlN/ChlB)(2) crystal structure reveals a [4Fe-4S] cluster coordinated by an aspartate oxygen alongside three cysteine ligands. Two equivalent substrate binding sites enriched in aromatic residues for protochlorophyllide substrate binding are located at the interface of each ChlN/ChlB half-tetramer. The complete octameric (ChlN/ChlB)(2)(ChlL(2))(2) complex of DPOR was modeled based on the crystal structure and earlier functional studies. The electron transfer pathway via the various redox centers of DPOR to the substrate is proposed.


    Organizational Affiliation

    Institut für Mikrobiologie, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE SUBUNIT N
A
460Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: chlN
EC: 1.3.7.7
Find proteins for Q8DGH2 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DGH2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE SUBUNIT B
B
511Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: chlB
EC: 1.3.7.7
Find proteins for Q8DGC6 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DGC6
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MGX
Query on MGX

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Download CCD File 
A
1-METHYLGUANIDINE
C2 H7 N3
CHJJGSNFBQVOTG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.201 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 192.095α = 90.00
b = 192.095β = 90.00
c = 132.504γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SHELXphasing
HKL-2000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-06-16
    Type: Initial release
  • Version 1.1: 2015-04-29
    Type: Data collection, Version format compliance
  • Version 1.2: 2017-04-19
    Type: Data collection
  • Version 1.3: 2019-05-08
    Type: Data collection, Experimental preparation