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Information on EC 4.2.3.18 - abieta-7,13-diene synthase and Organism(s) Abies grandis and UniProt Accession Q38710

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EC Tree
     4 Lyases
         4.2 Carbon-oxygen lyases
             4.2.3 Acting on phosphates
                4.2.3.18 abieta-7,13-diene synthase
IUBMB Comments
Part of a bifunctional enzyme involved in the biosynthesis of abietadiene. See also EC 5.5.1.12, copalyl diphosphate synthase. Requires Mg2+.
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This record set is specific for:
Abies grandis
UNIPROT: Q38710
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The taxonomic range for the selected organisms is: Abies grandis
The enzyme appears in selected viruses and cellular organisms
Synonyms
pdabs, pttps-las, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
abietadiene synthase
-
(-)-abietadiene synthase
-
-
-
-
abietadiene cyclase
-
-
-
-
abietadiene synthase
-
-
cyclase, abietadiene
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
(+)-copalyl diphosphate = abieta-7,13-diene + diphosphate
show the reaction diagram
reactions leading from intermediate abieta-8(14)-en-13-yl cation to product are driven by the electrostatic effect of the ionized diphopshate group
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
cyclization
elimination of diphosphate
-
-
-
-
SYSTEMATIC NAME
IUBMB Comments
(+)-copalyl-diphosphate diphosphate-lyase [cyclizing, abieta-7,13-diene-forming]
Part of a bifunctional enzyme involved in the biosynthesis of abietadiene. See also EC 5.5.1.12, copalyl diphosphate synthase. Requires Mg2+.
CAS REGISTRY NUMBER
COMMENTARY hide
157972-08-2
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(+)-copalyl diphosphate
abieta-7,13-diene + diphosphate
show the reaction diagram
-
-
-
?
(+)-copalyl-diphosphate
abieta-7,13-diene + abieta-8(14),13(15)-diene + abieta-8(14),12-diene + diphosphate
show the reaction diagram
reaction intermediate is abieta-8(14)-en-13-yl cation
-
-
?
geranylgeranyl diphosphate + diphosphate
(+)-copalyl diphosphate
show the reaction diagram
-
-
-
?
(+)-copalyl-diphosphate
(-)-abietadiene + diphosphate
show the reaction diagram
-
-
-
-
?
8alpha-hydroxy-17-nor copalyl diphosphate
17-normanoyl oxide + diphosphate
show the reaction diagram
-
-
-
-
?
copalyl diphosphate
abietadienes + diphosphate
show the reaction diagram
-
class I terpene synthase reaction
-
-
ir
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
(+)-copalyl diphosphate
abieta-7,13-diene + diphosphate
show the reaction diagram
-
-
-
?
(+)-copalyl-diphosphate
(-)-abietadiene + diphosphate
show the reaction diagram
-
-
-
-
?
copalyl diphosphate
abietadienes + diphosphate
show the reaction diagram
-
class I terpene synthase reaction
-
-
ir
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
K+
-
100 mM included in assay medium
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(13alpha)-N,13-dimethylpodocarp-8(14)-en-13-aminium chloride
-
-
14,15-dihydro-15-aza-geranylgeranyl diphosphate
-
-
14,15-dihydro-15-azageranylgeranyl diphosphate
-
-
geranylgeranyl diphosphate
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0002 - 138
copalyl diphosphate
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.05 - 2
copalyl diphosphate
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.2
-
assay at
8.7
-
with copalyl diphosphate as substrate
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30
-
assay at
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
SwissProt
Manually annotated by BRENDA team
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
TPSDV_ABIGR
868
0
99536
Swiss-Prot
Chloroplast (Reliability: 1)
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
80000
-
gel filtration
90000
-
gel filtration
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
monomer
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
hanging drop vapor diffusion method, using 24% (v/v) PEG 8000, 0.1 M sodium citrate, pH 5.1, 0.1 M dibasic ammonium phosphate
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
A723S
product is switched from abietadienes to 75% isopimara-7,15-diene + 21% sandaracopimaradiene
D621A
this substitution eliminates the subsequently acting class I activity
H348A/D621A
the mutant also produces 8alpha-hydroxy-copalyl diphosphate from geranylgeranyl diphosphate
N451A
this mutation reduces class II (protonation-initiated cyclization) activity about 100fold, with essentially no effect on class I (ionization-initiated cyclization) activity
D361A
-
lower turnover with geranylgeranyl diphosphate than wild-type
D402A
-
lower turnover with geranylgeranyl diphosphate than wild-type
D402E
-
lower turnover with geranylgeranyl diphosphate than wild-type
D402N
-
lower turnover with geranylgeranyl diphosphate than wild-type
D404A
D404E
-
lower turnover with geranylgeranyl diphosphate than wild-type
D404N
-
lower turnover with geranylgeranyl diphosphate than wild-type
D405A
-
lower turnover with geranylgeranyl diphosphate than wild-type
D405E
-
lower turnover with geranylgeranyl diphosphate than wild-type
D405N
-
lower turnover with geranylgeranyl diphosphate than wild-type
D621A
D625A
-
no effect on geranylgeranyl diphosphate reaction, but lower turnover with copalyl diphosphate than wild-type
D766A
-
no effect on geranylgeranyl diphosphate reaction, but lower turnover with copalyl diphosphate than wild-type
D845A
-
no effect on geranylgeranyl diphosphate reaction, but lower turnover with copalyl diphosphate than wild-type
DELTA:107-868
-
lower turnover with copalyl diphosphate than wild-type
DELTA:85-849
-
no turnover with copalyl diphosphate
E499A
-
lower turnover with geranylgeranyl diphosphate than wild-type
E589A
-
no effect on geranylgeranyl diphosphate reaction, but lower turnover with copalyl diphosphate than wild-type
E699A
-
no effect on geranylgeranyl diphosphate reaction, but lower turnover with copalyl diphosphate than wild-type
E773A
-
no effect on geranylgeranyl diphosphate reaction, but lower turnover with copalyl diphosphate than wild-type
E778A
-
no effect on geranylgeranyl diphosphate reaction, but lower turnover with copalyl diphosphate than wild-type
N765A
-
no effect on geranylgeranyl diphosphate reaction, but lower turnover with copalyl diphosphate than wild-type
R365A
-
lower turnover with geranylgeranyl diphosphate than wild-type
R411A
-
lower turnover with geranylgeranyl diphosphate than wild-type
R454A
-
lower turnover with geranylgeranyl diphosphate than wild-type
R584A
-
no effect on geranylgeranyl diphosphate reaction, but lower turnover with copalyl diphosphate than wild-type
R586A
-
no effect on geranylgeranyl diphosphate reaction, but lower turnover with copalyl diphosphate than wild-type
R762A
-
no effect on geranylgeranyl diphosphate reaction, but lower turnover with copalyl diphosphate than wild-type
rAS:D96A
-
nearly the same turnover with copalyl diphosphate like wild-type
rAS:K86A/R87A
-
lower turnover with copalyl diphosphate than wild-type
S721A
-
no effect on geranylgeranyl diphosphate reaction, but lower turnover with copalyl diphosphate than wild-type
T617A
-
no effect on geranylgeranyl diphosphate reaction, but lower turnover with copalyl diphosphate than wild-type
T769A
T769G
-
is active
T769S
-
is active
T848A
-
no effect on geranylgeranyl diphosphate reaction, but lower turnover with copalyl diphosphate than wild-type
W358A
-
lower turnover with geranylgeranyl diphosphate than wild-type
Y520A
-
lower turnover with geranylgeranyl diphosphate than wild-type
Y841F
-
no effect on geranylgeranyl diphosphate reaction, but lower turnover with copalyl diphosphate than wild-type
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-80°C, purified enzyme in 10 mM Bis-Tris, pH 6.8, 10% (v/v) glycerol,150 mM KCl, 10 mM MgCl2, and 5 mM dithiohtreitol, several months, without significant loss of activity
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
Mono Q column chromatography and type II ceramic hydroxyapatite column chromatography
purification using Ni-NTA His-bind resin in batch mode
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli C41 OverExpress and B834(DE3) cells
expression in Escherichia coli
-
Site-directed mutagenesis is carried out via PCR amplification with overlapping mutagenic primers, and the mutant genes verify by complete sequencing. The resulting wild type and mutant genes are then transferred via directional recombination to the T7-promoter and N-terminal 6his fusion expression vector pDEST17. Use of the pDEST17 vector results in a 25 amino acid residue linker between the 6 His-tag and the cloned protein.
-
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Ravn, M.M.; Coates, R.M.; Flory, J.E.; Peters, R.J.; Croteau, R.
Stereochemistry of the cyclization-rearrangement of (+)-copalyl diphosphate to (-)-abietadiene catalyzed by recombinant abietadiene synthase from Abies grandis
Org. Lett.
2
573-576
2000
Abies grandis
Manually annotated by BRENDA team
Peters, R.J.; Flory, J.E.; Jetter, R.; Ravn, M.M.; Lee, H.J.; Coates, R.M.; Croteau, R.B.
Abietadiene synthase from grand fir (Abies grandis): characterization and mechanism of action of the "pseudomature" recombinant enzyme
Biochemistry
39
15592-15602
2000
Abies grandis
Manually annotated by BRENDA team
Peters, R.J.; Ravn, M.M.; Coates, R.M.; Croteau, R.B.
Bifunctional abietadiene synthase: Free diffusive transfer of the (+)-copalyl diphosphate intermediate between two distinct active sites
J. Am. Chem. Soc.
123
8974-8978
2001
Abies grandis
Manually annotated by BRENDA team
Peters, R.J.; Croteau, R.B.
Abietadiene synthase catalysis: conserved residues involved in protonation-initiated cyclization of geranylgeranyl diphosphate to (+)-copalyl diphosphate
Biochemistry
41
1836-1842
2002
Abies grandis
Manually annotated by BRENDA team
Peters, R.J.; Croteau, R.B.
Abietadiene synthase catalysis: mutational analysis of a prenyl diphosphate ionization-initiated cyclization and rearrangement
Proc. Natl. Acad. Sci. USA
99
580-584
2002
Abies grandis
Manually annotated by BRENDA team
Ravn, M.M.; Peters, R.J.; Coates, R.M.; Croteau, R.
Mechanism of abietadiene synthase catalysis: stereochemistry and stabilization of the cryptic pimarenyl carbocation intermediates
J. Am. Chem. Soc.
124
6998-7006
2002
Abies grandis
Manually annotated by BRENDA team
Peters, R.J.; Carter, O.A.; Zhang, Y.; Matthews, B.W.; Croteau, R.B.
Bifunctional abietadiene synthase: mutual structural dependence of the active sites for protonation-initiated and ionization-initiated cyclizations
Biochemistry
42
2700-2707
2003
Abies grandis
Manually annotated by BRENDA team
Vogel, B.S.; Wildung, M.R.; Vogel, G.; Croteau, R.
Abietadiene synthase from grand fir (Abies grandis). cDNA isolation, characterization, and bacterial expression of a bifunctional diterpene cyclase involved in resin acid biosynthesis
J. Biol. Chem.
271
23262-23268
1996
Abies grandis
Manually annotated by BRENDA team
Wilderman, P.R.; Peters, R.J.
A single residue switch converts abietadiene synthase into a pimaradiene specific cyclase
J. Am. Chem. Soc.
129
15736-15737
2007
Abies grandis (Q38710)
Manually annotated by BRENDA team
Zhou, K.; Peters, R.J.
Investigating the conservation pattern of a putative second terpene synthase divalent metal binding motif in plants
Phytochemistry
70
366-369
2009
Abies grandis
Manually annotated by BRENDA team
Zhou, K.; Gao, Y.; Hoy, J.A.; Mann, F.M.; Honzatko, R.B.; Peters, R.J.
Insights into diterpene cyclization from structure of bifunctional abietadiene synthase from Abies grandis
J. Biol. Chem.
287
6840-6850
2012
Abies grandis (Q38710)
Manually annotated by BRENDA team
Criswell, J.; Potter, K.; Shephard, F.; Beale, M.H.; Peters, R.J.
A single residue change leads to a hydroxylated product from the class II diterpene cyclization catalyzed by abietadiene synthase
Org. Lett.
14
5828-5831
2012
Abies grandis (Q38710)
Manually annotated by BRENDA team