2YNM

Structure of the ADPxAlF3-Stabilized Transition State of the Nitrogenase-like Dark-Operative Protochlorophyllide Oxidoreductase Complex from Prochlorococcus marinus with Its Substrate Protochlorophyllide a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of Adp-Aluminium Fluoride-Stabilized Protochlorophyllide Oxidoreductase Complex.

Moser, J.Lange, C.Krausze, J.Rebelein, J.Schubert, W.Ribbe, M.W.Heinz, D.W.Jahn, D.

(2013) Proc Natl Acad Sci U S A 110: 2094

  • DOI: 10.1073/pnas.1218303110
  • Primary Citation of Related Structures:  
    2YNM

  • PubMed Abstract: 
  • Photosynthesis uses chlorophylls for the conversion of light into chemical energy, the driving force of life on Earth. During chlorophyll biosynthesis in photosynthetic bacteria, cyanobacteria, green algae and gymnosperms, dark-operative protochlorophyllide oxidoreductase (DPOR), a nitrogenase-like metalloenzyme, catalyzes the chemically challenging two-electron reduction of the fully conjugated ring system of protochlorophyllide a ...

    Photosynthesis uses chlorophylls for the conversion of light into chemical energy, the driving force of life on Earth. During chlorophyll biosynthesis in photosynthetic bacteria, cyanobacteria, green algae and gymnosperms, dark-operative protochlorophyllide oxidoreductase (DPOR), a nitrogenase-like metalloenzyme, catalyzes the chemically challenging two-electron reduction of the fully conjugated ring system of protochlorophyllide a. The reduction of the C-17=C-18 double bond results in the characteristic ring architecture of all chlorophylls, thereby altering the absorption properties of the molecule and providing the basis for light-capturing and energy-transduction processes of photosynthesis. We report the X-ray crystallographic structure of the substrate-bound, ADP-aluminium fluoride-stabilized (ADP·AlF(3)-stabilized) transition state complex between the DPOR components L(2) and (NB)(2) from the marine cyanobacterium Prochlorococcus marinus. Our analysis permits a thorough investigation of the dynamic interplay between L(2) and (NB)(2). Upon complex formation, substantial ATP-dependent conformational rearrangements of L(2) trigger the protein-protein interactions with (NB)(2) as well as the electron transduction via redox-active [4Fe-4S] clusters. We also present the identification of artificial "small-molecule substrates" of DPOR in correlation with those of nitrogenase. The catalytic differences and similarities between DPOR and nitrogenase have broad implications for the energy transduction mechanism of related multiprotein complexes that are involved in the reduction of chemically stable double and/or triple bonds.


    Organizational Affiliation

    Institut für Mikrobiologie, Technische Universität Braunschweig, D-38106 Braunschweig, Germany. j.moser@tu-bs.de



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE IRON-SULFUR ATP-BINDING PROTEINA, B301Prochlorococcus marinusMutation(s): 0 
EC: 1.3.7.7 (PDB Primary Data), 1.18 (PDB Primary Data)
Find proteins for Q7VD39 (Prochlorococcus marinus (strain SARG / CCMP1375 / SS120))
Explore Q7VD39 
Go to UniProtKB:  Q7VD39
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE SUBUNIT NC426Prochlorococcus marinusMutation(s): 0 
EC: 1.3.7.7 (PDB Primary Data), 1.18 (PDB Primary Data)
Find proteins for Q7VD37 (Prochlorococcus marinus (strain SARG / CCMP1375 / SS120))
Explore Q7VD37 
Go to UniProtKB:  Q7VD37
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE SUBUNIT BD530Prochlorococcus marinusMutation(s): 0 
EC: 1.3.7.7 (PDB Primary Data), 1.18 (PDB Primary Data)
Find proteins for Q7VD38 (Prochlorococcus marinus (strain SARG / CCMP1375 / SS120))
Explore Q7VD38 
Go to UniProtKB:  Q7VD38
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PMR
Query on PMR

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S [auth C]Protochlorophyllide
C35 H32 Mg N4 O5
ZHFORNQMLKGQNN-DEOLMCFKDB
 Ligand Interaction
ADP
Query on ADP

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I [auth A], P [auth B]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
SF4
Query on SF4

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K [auth A], R [auth C]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
EPE
Query on EPE

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F [auth A], G [auth A], M [auth B], T [auth D]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
1PE
Query on 1PE

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E [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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L [auth A], Q [auth C], U [auth D], W [auth D]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
AF3
Query on AF3

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H [auth A], O [auth B]ALUMINUM FLUORIDE
Al F3
KLZUFWVZNOTSEM-UHFFFAOYSA-K
 Ligand Interaction
K
Query on K

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V [auth D]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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J [auth A], N [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 308.4α = 90
b = 74.11β = 91.24
c = 74.23γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-30
    Type: Initial release
  • Version 1.1: 2013-03-06
    Changes: Database references