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Overview for MACiE Entry M0089

Version history

General Information

EC Number: 4.2.3.7 (A member of the Lyases, Carbon-oxygen lyases, Acting on phosphates)

Enzyme Name: pentalenene synthase

Biological Species: Streptomyces sp. (Bacteria)

Catalytic Chain UniprotKB Accession Codes:

Representative PDB Code: 1ps1 - PENTALENENE SYNTHASE (Resolution = 2.60 Å).

Catalytic CATH Codes:

Display structure information

Overall Reaction:

Image of 2-trans,6-trans-farnesyl diphosphate

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Image of proton

Image of pentalenene

Image of diphosphate

2-trans,6-trans-farnesyl diphosphate
C00448
CHEBI:175763
proton
C00080
CHEBI:24636
pentalenene
C01841
CHEBI:17251
diphosphate
C00013
CHEBI:18361

Overall Comment: Identity of the Mg ion in the reaction is arbitrarily assigned due to lack of metal ions in the crystal structure.


View similar reactions


Stepwise Description of the Reaction

Step 1The substrate undergoes heterolysis. The diphosphate product remains associated with the active site, and the cabocation is delocalised over the three terminal carbon atoms of the intermediate.
Step 2The terminal double bond adds to the terminal carbocation in an intramolecular electrophilic addition resulting in a cyclic intermediate.
Step 3His309 deprotonates the carbon adjacent to the newly formed carbocation, forming a new double bond in the humulene intermediate.
Step 4In a second intramolecular electrophilic addition, a double bond adds across the cycle forming a five membered ring and a new carbocation.
Step 5In a third intramolecular electrophilic addition, the remaining double bond adds across the cycle to form the three five membered ring motif of pentalenene, this also causes a [1,2]-hydride shift and the carbocation shifting to a different carbon atom
Step 6His309 deprotonates the carbon adjacent to the new carbocation, forming the final double bond of pentalenene.
Step 7Water deprotonates His309 in an inferred step to regenerate the enzyme active site.

View similar reactions (composite manual annotation)


Catalytic Residues Involved

Type Number Chain Location of Function
Phe 76 A Side Chain
Phe 77 A Side Chain
Asn 219 A Side Chain
Trp 308 A Side Chain
His 309 A Side Chain

Metal Cofactors for M0089

Type Het group Number Chain
magnesium MG(not in PDB) 1 x Overview

References

  1. C. A. Lesburg et al. (1997), Science, 277, 1820-1824. Crystal structure of pentalenene synthase: mechanistic insights on terpenoid cyclization reactions in biology.
    Medline: 9295272
  2. M. Seemann et al. (1999), J. Am. Chem. Soc., 121, 591-592. Pentalenene synthase. Histidine-309 is not required for catalytic activity.

Homologue information for M0089 (1ps1)

CSA Homologues

MACiE Homologues (within the PDB)

MACiE Homologues (within UniprotKB/SwissProt)



Entries with at least one Catalytic CATH code in common (different mechanisms):

MACiE Entry Enzyme Name
EC Number
PDB code CATH code Composite
Reaction Similarity
Catalytic Machinery
Similarity
M0253 geranyltranstransferase
2.5.1.10
1uby 1.10.600.10
0.31810.2719Compare
M0264 squalene synthase
2.5.1.21
1ezf 1.10.600.10
0.58820.1636Compare
M0262 trichodiene synthase
4.2.3.6
1jfg 1.10.600.10
0.65510.0097Compare
M0261 aristolochene synthase
4.2.3.9
1di1 1.10.600.10
0.83670.5204Compare
M0265 aristolochene synthase
4.2.3.9
5eat 1.10.600.10
0.50.0408Compare
M0259 bornyl diphosphate synthase
5.5.1.8
1n20 1.10.600.10
0.49090.3375Compare

View a comparison of the other reactions in MACiE with the CATH domain 1.10.600.10


Links to this entry in other databases

Link to EC-PDB-SUM Link to PDB-SUM Link to RCSB PDB Link to PDBe Link to CSA
Link to MetaCyc Link to KEGG Link to BRENDA Link to ExplorENZ
Link to EzCatDB Link to SFLD

GOA logo
magnesium ion binding (molecular function)
lyase activity (molecular function)
antibiotic biosynthetic process (biological process)
metal ion binding (molecular function)
pentalenene synthase activity (molecular function)
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