Top Level Name

  ⌊ Superfamily (core) Isoprenoid Synthase Type I

    ⌊ Subgroup Terpene Cyclase Like 2

     ⌊ Family   private

  ⌊ FunctionalDomain pentalenene synthase (ID 3642)

Superfamily Assignment Evidence Code(s) FSM PubMed:9295272 PubMed:12083921 PubMed:8180213
Family Assignment Evidence Code CFM PubMed:9295272 PubMed:12083921 PubMed:8180213
This entry was last updated onJune 10, 2017

References to Other Databases

Genbank

SpeciesGIAccessionProteome
Streptomyces exfoliatus Taxon ID: 1905 309753138 ADO85594.1 (Genbank)
Streptomyces sp. Taxon ID: 1931 451846 AAA19131.1 (Genbank)
Streptomyces exfoliatus Taxon ID: 1905 3114507
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Uniprot

Protein NameAccessionEC Number Identifier
Pentalenene synthase Q55012 4.2.3.7 PENA_STREX (Swiss-Prot)

Sequence

Length of Enzyme (full-length): 337 | Length of Functional Domain: 337

1       10        20        30        40        50        60

MPQDVDFHIPLPGRQSPDHARAEAEQLAWPRSLGLIRSDAAAERHLRGGYADLASRFYPH
ATGADLDLGVDLMSWFFLFDDLFDGPRGENPEDTKQLTDQVAAALDGPLPDTAPPIAHGF
ADIWRRTCEGMTPAWCARSARHWRNYFDGYVDEAESRFWNAPCDSAAQYLAMRRHTIGVQ
PTVDLAERAGRFEVPHRVFDSAVMSAMLQIAVDVNLLLNDIASLEKEEARGEQNNMVMIL
RREHGWSKSRSVSHMQNEVRARLEQYLLLESCLPKVGEIYQLDTAEREALERYRTDAVRT
VIRGSYDWHRSSGRYDAEFALAAGAQGYLEELGSSAH
This shows the full-length sequence of the enzyme. The region of the functional domain is highlighted in black letters, while the residual residues are shown in grey. The Superfamily domain, when present, is shown using underlining. In many cases the functional domain is the full-length sequence.
Conserved catalytic residues (as determined by automated alignment to family, subgroup, or superfamily HMMs) are shown with teal highlighting . Conserved catalytic residues which do not matched the Conserved Alignment Residue are shown with maroon highlighting . Information regarding their function can be found in the Conserved Residues section below.
FASTA formatted full-length sequence.
BLAST this sequence against SFLD.
Scan SFLD-HMMs with this sequence.

Conserved Residues
Superfamily CAR This EFD conserves 3/3 Superfamily-specific Conserved Alignment Residues.
Position Amino Acid Location Function Role Evidence Code Reference
80 Asp (D) side chain None --
84 Asp (D) side chain None --
219 Asn (N) side chain None --
Subgroup CAR This EFD conserves 8/8 Subgroup-specific Conserved Alignment Residues.
Position Amino Acid Location Function Role Evidence Code Reference
80 Asp (D) side chain Metal ligand metal ligand -- binding ICS PubMed:20131801
81 Asp (D) side chain Forms hydrogen bond with R767 that facilitates active site closure activation -- spectator ICS PubMed:21562622
173 Arg (R) side chain Hydrogen bonds to PPi anion electrostatic stabiliser -- spectator ICS PubMed:20131801
219 Asn (N) side chain Metal ligand metal ligand -- binding ICS PubMed:20131801
220 Asp (D) side chain None -- ISS
223 Ser (S) side chain Metal ligand metal ligand -- binding ICS PubMed:20131801
227 Glu (E) side chain Metal ligand metal ligand -- binding ICS PubMed:20131801
314 Arg (R) side chain Forms hydrogen bond with D219 that facilitates active site closure; Hydrogen bonds to PPi anion activation -- spectator ICS PubMed:21562622
Family CAR This EFD conserves 10/10 Family-specific Conserved Alignment Residues.
Position Amino Acid Location Function Role Evidence Code Reference
76 Phe (F) side chain Stabilizes carbocation intermediates through quadrupole-charge interactions electrostatic stabiliser -- spectator ICS PubMed:9295272
77 Phe (F) side chain Stabilizes carbocation intermediates through quadrupole-charge interactions electrostatic stabiliser -- spectator ICS PubMed:9295272
80 Asp (D) side chain Coordinates required divalent metal metal ligand -- binding ICS PubMed:9295272
84 Asp (D) side chain Coordinates required divalent metal metal ligand -- binding ICS PubMed:9295272
157 Arg (R) side chain Stabilizes pyrophosphate leaving group electrostatic stabiliser -- spectator ICS PubMed:9295272
173 Arg (R) side chain Stabilizes pyrophosphate leaving group electrostatic stabiliser -- spectator ICS PubMed:9295272
219 Asn (N) main chain carbonyl group Backbone carbonyl stabilizes carbocation intermediate through dipole-charge interaction electrostatic stabiliser -- spectator ICS PubMed:9295272
226 Lys (K) side chain Stabilizes pyrophosphate leaving group electrostatic stabiliser -- spectator ICS PubMed:9295272
230 Arg (R) side chain Stabilizes pyrophosphate leaving group electrostatic stabiliser -- spectator ICS PubMed:9295272
308 Trp (W) side chain Stabilizes carbocation intermediates through quadrupole-charge interactions electrostatic stabiliser -- spectator ICS PubMed:9295272

Structures

PDB ID Title Molecule Name Number of
EFDs		 Resolution (Å) Mutant? Het group Links
1PS1 Pentalenene Synthase Pentalenene Synthase 2 2.6 Trimethyl Lead Ion CSA • PDB • PDBSum
1HM4 N219L Pentalenene Synthase Pentalenene Synthase 2 3.47 Yes CSA • PDB • PDBSum
1HM7 N219L Pentalenene Synthase Pentalenene Synthase 2 2.9 Yes CSA • PDB • PDBSum
Percent identity and alignment length from the BLAST match of the Functional Domain sequence to the PDB sequence.
"Yes" indicates that a GI associated with this Functional Domain was mapped to the PDB ID via UniProtKB.

Curation History
Time Change Annotation Old Value New Value
April 30, 2014, 11:58 a.m. update curation agent holliday setDomainBoundaries.py
update domain end position 328 337
EC number assigned by UniProtKB accession ID.