BRENDA - Enzyme Database

Structure of ADP-aluminium fluoride-stabilized protochlorophyllide oxidoreductase complex

Moser, J.; Lange, C.; Krausze, J.; Rebelein, J.; Schubert, W.D.; Ribbe, M.W.; Heinz, D.W.; Jahn, D.; Proc. Natl. Acad. Sci. USA 110, 2094-2098 (2013)

Data extracted from this reference:

Crystallization (Commentary)
EC Number
Crystallization
Organism
1.3.1.33
the X-ray crystallographic structure of the substrate-bound, ADP-aluminium fluoride-stabilized (ADP-AlF3-stabilized) transition state complex between the DPOR components L2 and (NB)2 from the marine cyanobacterium Prochlorococcus marinus is reported
Prochlorococcus marinus
1.3.7.7
substrate-bound, ADP-aluminium fluoride-stabilized transition state complex between the DPOR components L2 and (NB)2, sitting drops by vapor diffusion, mixing of 0.001 ml of protein solution containing 7.5 mg/ml protein in 100 mM HEPES/NaOH, pH 7.5, 150 mM NaCl, 10 mM MgCl2, 50 mM NaF, and 2 mM AlCl3,with 0.001 ml of reservoir solution containing 0.1 M KCl, 0.1 M Tris, pH 8.5, and 3% wt/v PEG 6000, 17°C, X-ray diffraction structure determination and analysis at 2.1 A resolution
Prochlorococcus marinus
Engineering
EC Number
Amino acid exchange
Commentary
Organism
1.3.1.33
H394A
mutant retains only a moderate activity which points to a critical role of this residue in the specific protonation at C-18, probably by positioning a water molecule at a distance of 3.2 A from C-18 above the ring
Prochlorococcus marinus
Metals/Ions
EC Number
Metals/Ions
Commentary
Organism
Structure
1.3.7.7
Fe2+
two redox-active [4Fe-4S] clusters, both [4Fe-4S] clusters are centered around the extended axis: the L2 cluster is symmetrically ligated by four cysteinyl ligands between the two subunits, whereas the NB cluster is asymmetrically ligated by three cysteine residues from subunit N and one aspartate residue from subunit B
Prochlorococcus marinus
1.3.7.7
Mg2+
required
Prochlorococcus marinus
Molecular Weight [Da]
EC Number
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
1.3.1.33
360000
-
-
Prochlorococcus marinus
Natural Substrates/ Products (Substrates)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
1.3.7.7
protochlorophyllide a + reduced ferredoxin + 2 ATP + 2 H2O
Prochlorococcus marinus
-
chlorophyllide a + oxidized ferredoxin + 2 ADP + 2 phosphate
-
-
?
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
1.3.1.33
Prochlorococcus marinus
Q7VD39
-
-
1.3.7.7
Prochlorococcus marinus
Q7VD39
-
-
Purification (Commentary)
EC Number
Commentary
Organism
1.3.7.7
purification by immobilization of GST-tagged subunit L2 on glutathione resin, complex formation with purified subunits NB, and proteolytical cleavage
Prochlorococcus marinus
Reaction
EC Number
Reaction
Commentary
Organism
1.3.7.7
chlorophyllide a + oxidized ferredoxin + 2 ADP + 2 phosphate = protochlorophyllide a + reduced ferredoxin + 2 ATP + 2 H2O
dynamic switch mechanism of DPOR, catalytic mechanism and structure-function analysis, detailed overview
Prochlorococcus marinus
Substrates and Products (Substrate)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
1.3.7.7
protochlorophyllide a + reduced ferredoxin + 2 ATP + 2 H2O
-
726394
Prochlorococcus marinus
chlorophyllide a + oxidized ferredoxin + 2 ADP + 2 phosphate
-
-
-
?
1.3.7.7
protochlorophyllide a + reduced ferredoxin + 2 ATP + 2 H2O
DPOR catalyzes the formation of chlorophyllide a through ATP-dependent, stereospecific reduction of the C-17=C-18 double bond of Pchlide ring D
726394
Prochlorococcus marinus
chlorophyllide a + oxidized ferredoxin + 2 ADP + 2 phosphate
-
-
-
?
Subunits
EC Number
Subunits
Commentary
Organism
1.3.1.33
octamer
heterooctameric complex: subunits N and B are structurally homologous, generating a pseudo-2fold symmetry axis that is colinear with the molecular twofold axis of L2. Both [4Fe-4S] clusters are centered around this extended axis: the L2 cluster is symmetrically ligated by four cysteinyl ligands between the two subunits, whereas the NB cluster is asymmetrically ligated by three cysteine residues from N and one aspartate residue from B
Prochlorococcus marinus
1.3.7.7
octamer
(L2)2(NB)2 enzyme complex with perfect symmetry. Subunits L2 and NifH2 both contain a subunit-bridging [4Fe-4S] cluster, whereas the [4Fe-4S] cluster at the N/B subunit interface of (NB)2 is located in an analogous position as the [8Fe-7S] P-cluster at the NifD/NifK subunit interface of (NifDK)2
Prochlorococcus marinus
Cofactor
EC Number
Cofactor
Commentary
Organism
Structure
1.3.7.7
ATP
-
Prochlorococcus marinus
1.3.7.7
Ferredoxin
-
Prochlorococcus marinus
Cofactor (protein specific)
EC Number
Cofactor
Commentary
Organism
Structure
1.3.7.7
ATP
-
Prochlorococcus marinus
1.3.7.7
Ferredoxin
-
Prochlorococcus marinus
Crystallization (Commentary) (protein specific)
EC Number
Crystallization
Organism
1.3.1.33
the X-ray crystallographic structure of the substrate-bound, ADP-aluminium fluoride-stabilized (ADP-AlF3-stabilized) transition state complex between the DPOR components L2 and (NB)2 from the marine cyanobacterium Prochlorococcus marinus is reported
Prochlorococcus marinus
1.3.7.7
substrate-bound, ADP-aluminium fluoride-stabilized transition state complex between the DPOR components L2 and (NB)2, sitting drops by vapor diffusion, mixing of 0.001 ml of protein solution containing 7.5 mg/ml protein in 100 mM HEPES/NaOH, pH 7.5, 150 mM NaCl, 10 mM MgCl2, 50 mM NaF, and 2 mM AlCl3,with 0.001 ml of reservoir solution containing 0.1 M KCl, 0.1 M Tris, pH 8.5, and 3% wt/v PEG 6000, 17°C, X-ray diffraction structure determination and analysis at 2.1 A resolution
Prochlorococcus marinus
Engineering (protein specific)
EC Number
Amino acid exchange
Commentary
Organism
1.3.1.33
H394A
mutant retains only a moderate activity which points to a critical role of this residue in the specific protonation at C-18, probably by positioning a water molecule at a distance of 3.2 A from C-18 above the ring
Prochlorococcus marinus
Metals/Ions (protein specific)
EC Number
Metals/Ions
Commentary
Organism
Structure
1.3.7.7
Fe2+
two redox-active [4Fe-4S] clusters, both [4Fe-4S] clusters are centered around the extended axis: the L2 cluster is symmetrically ligated by four cysteinyl ligands between the two subunits, whereas the NB cluster is asymmetrically ligated by three cysteine residues from subunit N and one aspartate residue from subunit B
Prochlorococcus marinus
1.3.7.7
Mg2+
required
Prochlorococcus marinus
Molecular Weight [Da] (protein specific)
EC Number
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
1.3.1.33
360000
-
-
Prochlorococcus marinus
Natural Substrates/ Products (Substrates) (protein specific)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
1.3.7.7
protochlorophyllide a + reduced ferredoxin + 2 ATP + 2 H2O
Prochlorococcus marinus
-
chlorophyllide a + oxidized ferredoxin + 2 ADP + 2 phosphate
-
-
?
Purification (Commentary) (protein specific)
EC Number
Commentary
Organism
1.3.7.7
purification by immobilization of GST-tagged subunit L2 on glutathione resin, complex formation with purified subunits NB, and proteolytical cleavage
Prochlorococcus marinus
Substrates and Products (Substrate) (protein specific)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
1.3.7.7
protochlorophyllide a + reduced ferredoxin + 2 ATP + 2 H2O
-
726394
Prochlorococcus marinus
chlorophyllide a + oxidized ferredoxin + 2 ADP + 2 phosphate
-
-
-
?
1.3.7.7
protochlorophyllide a + reduced ferredoxin + 2 ATP + 2 H2O
DPOR catalyzes the formation of chlorophyllide a through ATP-dependent, stereospecific reduction of the C-17=C-18 double bond of Pchlide ring D
726394
Prochlorococcus marinus
chlorophyllide a + oxidized ferredoxin + 2 ADP + 2 phosphate
-
-
-
?
Subunits (protein specific)
EC Number
Subunits
Commentary
Organism
1.3.1.33
octamer
heterooctameric complex: subunits N and B are structurally homologous, generating a pseudo-2fold symmetry axis that is colinear with the molecular twofold axis of L2. Both [4Fe-4S] clusters are centered around this extended axis: the L2 cluster is symmetrically ligated by four cysteinyl ligands between the two subunits, whereas the NB cluster is asymmetrically ligated by three cysteine residues from N and one aspartate residue from B
Prochlorococcus marinus
1.3.7.7
octamer
(L2)2(NB)2 enzyme complex with perfect symmetry. Subunits L2 and NifH2 both contain a subunit-bridging [4Fe-4S] cluster, whereas the [4Fe-4S] cluster at the N/B subunit interface of (NB)2 is located in an analogous position as the [8Fe-7S] P-cluster at the NifD/NifK subunit interface of (NifDK)2
Prochlorococcus marinus
General Information
EC Number
General Information
Commentary
Organism
1.3.7.7
evolution
protein-protein interaction surfaces for transition state complexes of DPOR and nitrogenase, using PDB ID code 1M34, analysis of catalytic differences and similarities between DPOR and nitrogenase, overview
Prochlorococcus marinus
1.3.7.7
additional information
upon complex formation, substantial ATP-dependent conformational rearrangements of L2 trigger the protein-protein interactions with (NB)2 as well as the electron transduction via redox-active [4Fe-4S] clusters, dynamic interplay between L2 and (NB)2. Asp155 is responsible for positioning and/or activating a specific water molecule for the subsequent ATP hydrolysis, whereas Lys37 of the P-loop possibly assists the release of gamma-phosphate upon ATP hydrolysis
Prochlorococcus marinus
1.3.7.7
physiological function
during chlorophyll biosynthesis in photosynthetic bacteria, cyanobacteria, green algae and gymnosperms, dark-operative protochlorophyllide oxidoreductase, 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 energytransduction processes of photosynthesis
Prochlorococcus marinus
General Information (protein specific)
EC Number
General Information
Commentary
Organism
1.3.7.7
evolution
protein-protein interaction surfaces for transition state complexes of DPOR and nitrogenase, using PDB ID code 1M34, analysis of catalytic differences and similarities between DPOR and nitrogenase, overview
Prochlorococcus marinus
1.3.7.7
additional information
upon complex formation, substantial ATP-dependent conformational rearrangements of L2 trigger the protein-protein interactions with (NB)2 as well as the electron transduction via redox-active [4Fe-4S] clusters, dynamic interplay between L2 and (NB)2. Asp155 is responsible for positioning and/or activating a specific water molecule for the subsequent ATP hydrolysis, whereas Lys37 of the P-loop possibly assists the release of gamma-phosphate upon ATP hydrolysis
Prochlorococcus marinus
1.3.7.7
physiological function
during chlorophyll biosynthesis in photosynthetic bacteria, cyanobacteria, green algae and gymnosperms, dark-operative protochlorophyllide oxidoreductase, 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 energytransduction processes of photosynthesis
Prochlorococcus marinus