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Information on EC 4.2.3.7 - pentalenene synthase and Organism(s) Streptomyces exfoliatus and UniProt Accession Q55012

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EC Tree
     4 Lyases
         4.2 Carbon-oxygen lyases
             4.2.3 Acting on phosphates
                4.2.3.7 pentalenene synthase
IUBMB Comments
Isolated from Streptomyces avermitilis. The enzyme is involved in the biosynthesis of pentalenolactone and related antibiotics. The 9si hydrogen of farnesyl diphosphate undergoes a 1,2-hydride shift where it becomes the 1alpha hydrogen of pentalenene.
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Streptomyces exfoliatus
UNIPROT: Q55012
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Word Map
The taxonomic range for the selected organisms is: Streptomyces exfoliatus
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
Synonyms
pentalenene synthase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pentalenene synthase
-
pentalenene synthetase
-
-
-
-
synthetase, pentalenene
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
P-O bond cleavage
-
-
-
-
SYSTEMATIC NAME
IUBMB Comments
(2E,6E)-farnesyl diphosphate diphosphate-lyase (cyclizing, pentalenene-forming)
Isolated from Streptomyces avermitilis. The enzyme is involved in the biosynthesis of pentalenolactone and related antibiotics. The 9si hydrogen of farnesyl diphosphate undergoes a 1,2-hydride shift where it becomes the 1alpha hydrogen of pentalenene.
CAS REGISTRY NUMBER
COMMENTARY hide
90597-46-9
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(2E,6E)-farnesyl diphosphate
pentalenene + diphosphate
show the reaction diagram
2-trans,6-trans-farnesyl diphosphate
pentalenene + diphosphate
show the reaction diagram
the study describes theoretical studies on the cyclization reaction
-
-
?
farnesyl diphosphate
pentalenene + diphosphate
show the reaction diagram
additional information
?
-
isotopically sensitive branching experiments support a mechanism for pentalenene formation involving a 7-protoilludyl cation intermediate
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-
?
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
(2E,6E)-farnesyl diphosphate
pentalenene + diphosphate
show the reaction diagram
2-trans,6-trans-farnesyl diphosphate
pentalenene + diphosphate
show the reaction diagram
the study describes theoretical studies on the cyclization reaction
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00016 - 0.0166
(2E,6E)-farnesyl diphosphate
0.0003 - 0.00031
farnesyl diphosphate
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0032
diphosphate
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.324
30°C, pH 8.2
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
expression in Xanthophyllomyces dendrorhous with concurrent knock out of the native crtE or crtYB genes. The transformations result in white colonies, showing a complete shutdown of the carotenoid production. All the mutant strains produce the sesquiterpene pentalenene and show no difference in growth when compared to the wild-type strain
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
PENA_STREX
337
0
38002
Swiss-Prot
-
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
41000
x * 41000, SDS-PAGE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
x * 41000, SDS-PAGE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
hanging drop vapor diffusion method, using 1-1.4 M sodium citrate or 1.4-1.8 M ammonium sulfate as precipitant
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D80E
the mutation influences binding of the required divalent Mg2+ cofactor
D81E
the mutation influences binding of the required divalent Mg2+ cofactor
D84E
the mutation influences binding of the required divalent Mg2+ cofactor
H309A
H309C
H309F
H309S
N219A
catalytically inactive
N219D
N219L
W308F
W308F/H309F
reaction products are pentalene plus varying proportions of (+)-germacrene A
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
hydroxyapatite column chromatography and Sephadex 200 gel filtration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli
expression in Xanthophyllomyces dendrorhous
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
synthesis
production of pentalenene by expression of pentalenene synthase gene in Xanthophyllomyces dendrorhous with concurrent knock out of the native crtE or crtYB genes. Culturing the yeast in presence of dodecane traps the volatile compounds produced, and no other terpenoids are found as by products
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Cane, D.E.; Sohng, J.K.; Lamberson, C.R.; Rudnicki, S.M.; Wu, Z.; Lloyd, M.D.; Oliver, J.S.; Hubbard, B.R.
Pentalenene synthase. Purification, molecular cloning, sequencing, and high-level expression in Escherichia coli of a terpenoid cyclase from Streptomyces UC5319
Biochemistry
33
5846-5857
1994
Streptomyces exfoliatus (Q55012), Streptomyces exfoliatus UC5319 (Q55012)
Manually annotated by BRENDA team
Lesburg, C.A.; Zhai, G.; Cane, D.E.; Christianson, D.W.
Crystal structure of pentalenene synthase: mechanistic insights on terpenoid cyclization reactions in biology
Science
277
1820-1824
1997
Streptomyces exfoliatus (Q55012), Streptomyces exfoliatus UC5319 (Q55012)
Manually annotated by BRENDA team
Seemann, M.; Zhai, G.; Umezawa, K.; Cane, D.
Pentalenene synthase. Histidine-309 is not required for catalytic activity
J. Am. Chem. Soc.
121
591-592
1999
Streptomyces exfoliatus (Q55012)
-
Manually annotated by BRENDA team
Seemann, M.; Zhai, G.; de Kraker, J.W.; Paschall, C.M.; Christianson, D.W.; Cane, D.E.
Pentalenene synthase. Analysis of active site residues by site-directed mutagenesis
J. Am. Chem. Soc.
124
7681-7689
2002
Streptomyces exfoliatus (Q55012)
Manually annotated by BRENDA team
Gutta, P.; Tantillo, D.J.
Theoretical studies on farnesyl cation cyclization: pathways to pentalenene
J. Am. Chem. Soc.
128
6172-6179
2006
Streptomyces exfoliatus (Q55012)
Manually annotated by BRENDA team
Lesburg, C.A.; Lloyd, M.D.; Cane, D.E.; Christianson, D.W.
Crystallization and preliminary X-ray diffraction analysis of recombinant pentalenene synthase
Protein Sci.
4
2436-2438
1995
Streptomyces exfoliatus (Q55012)
Manually annotated by BRENDA team
Zu, L.; Xu, M.; Lodewyk, M.W.; Cane, D.E.; Peters, R.J.; Tantillo, D.J.
Effect of isotopically sensitive branching on product distribution for pentalenene synthase: support for a mechanism predicted by quantum chemistry
J. Am. Chem. Soc.
134
11369-11371
2012
Streptomyces exfoliatus (Q55012)
Manually annotated by BRENDA team
Melillo, E.; Muntendam, R.; Quax, W.J.; Kayser, O.
Heterologous expression of pentalenene synthase (PSS) from Streptomyces UC5319 in Xanthophyllomyces dendrorhous
J. Biotechnol.
161
302-307
2012
Streptomyces exfoliatus (Q55012)
Manually annotated by BRENDA team
Pemberton, T.A.; Christianson, D.W.
General base-general acid catalysis by terpenoid cyclases
J. Antibiot.
69
486-493
2016
Streptomyces exfoliatus, Streptomyces exfoliatus UC5319
Manually annotated by BRENDA team
Rosso, C.; Ermondi, G.; Caron, G.
GRID/BIOCUBE4mf to rank the influence of mutations on biological processes to design ad hoc mutants
Med. Chem. Res.
24
2612-2620
2015
Streptomyces exfoliatus (Q55012), Streptomyces exfoliatus UC5319 (Q55012)
-
Manually annotated by BRENDA team