Q55012 (PENA_STREX) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Pentalenene synthase
Short name=PS
EC=4.2.3.7

Alternative name(s):
Pentalenolactone biosynthesis protein A
Sesquiterpene cyclase
Sesquiterpene synthase

Gene names

Name:

penA

Organism

Streptomyces exfoliatus (Streptomyces hydrogenans)

Taxonomic identifier

1905 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Actinobacteria › Actinobacteria › Actinobacteridae › Actinomycetales › Streptomycineae › Streptomycetaceae › Streptomyces

Protein attributes

Sequence length	337 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the cyclization of farnesyl diphosphate (FPP) to the tricyclic sesquiterpene pentalenene, which is the hydrocarbon precursor of the pentalenolactone family of antibiotics produced by a variety of Streptomyces species. Ref.1
Catalytic activity	(2E,6E)-farnesyl diphosphate = pentalenene + diphosphate. Ref.5
Cofactor	Binds 3 magnesium ions per subunit By similarity. Ref.1
Pathway	Sesquiterpene biosynthesis; pentalenene biosynthesis; pentalenene from farnesyl diphosphate: step 1/1. Antibiotic biosynthesis; pentalenolactone biosynthesis.
Subunit structure	Monomer. Ref.1
Domain	The Asp-Asp-Xaa-Xaa-Asp/Glu (DDXXD/E) motif is important for the catalytic activity, presumably through binding to Mg2+.
Miscellaneous	All the mutants (Ref.3 and Ref.5) retained substantial pentalenene synthase activity accompanied by production of varying proportions of abortive cyclization products such as germacrene A, protoilludene and beta-caryophyllene. This is a true derailment or diversion of the normal cyclization reaction, and not simply the consequence of trapping of a normally cryptic, cationic intermediate.
Sequence similarities	Belongs to the terpene synthase family.
Biophysicochemical properties	Kinetic parameters: KM=310 nM for FPP Ref.1 pH dependence: Optimum pH is 8.2-8.4.

Ontologies

Keywords
Biological process	Antibiotic biosynthesis
Ligand	Magnesium Metal-binding
Molecular function	Lyase
PTM	Disulfide bond
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological_process	antibiotic biosynthetic process Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	magnesium ion binding Inferred from electronic annotation. Source: InterPro pentalenene synthase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.1

Chain

2 – 337

336

Pentalenene synthase

PRO_0000097092

Regions

Motif

80 – 84

5

DDXXD motif

Sites

Metal binding

80

1

Magnesium 1

Metal binding

80

1

Magnesium 2

Metal binding

84

1

Magnesium 1

Metal binding

84

1

Magnesium 2

Metal binding

219

1

Magnesium 3

Metal binding

223

1

Magnesium 3 By similarity

Metal binding

227

1

Magnesium 3 By similarity

Amino acid modifications

Disulfide bond

128 ↔ 136

Experimental info

Mutagenesis

76

1

F → A: Loss of activity. Ref.5

Mutagenesis

77

1

F → A: Loss of activity. Ref.5

Mutagenesis

77

1

F → Y: 20-fold decrease in activity and catalytic efficiency. Ref.5

Mutagenesis

80

1

D → E: 150-fold decrease in activity. 20-fold increase in Km for FPP. Ref.5

Mutagenesis

81

1

D → E: 50-fold decrease in activity. 9-fold increase in Km for FPP. Ref.5

Mutagenesis

84

1

D → E: 2.5-fold increase in activity. 7-fold increase in Km for FPP. Ref.5

Mutagenesis

219

1

N → A: Loss of activity. Ref.5

Mutagenesis

219

1

N → D: 60-fold decrease in activity. 55-fold increase in Km for FPP. Ref.5

Mutagenesis

219

1

N → L: Loss of activity. Ref.5

Mutagenesis

308 – 309

2

WH → FF: 12-fold decrease in activity. 25-fold decrease in catalytic efficiency. Ref.3 Ref.5

Mutagenesis

308

1

W → F: 4-fold decrease in activity. 2-fold decrease in catalytic efficiency. Ref.5

Mutagenesis

309

1

H → A: 3-fold decrease in activity. Ref.3 Ref.5

Mutagenesis

309

1

H → C: 4-fold decrease in activity. Ref.3 Ref.5

Mutagenesis

309

1

H → F: 17-fold decrease in activity. 5-fold increase in Km for FPP. Ref.3 Ref.5

Mutagenesis

309

1

H → S: 3-fold decrease in activity. Ref.3 Ref.5

Sequence conflict

118

1

H → W AA sequence Ref.1

Secondary structure

1

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337

Helix Strand Turn

Details...

Helix

19 – 24

6

Helix

28 – 32

5

Helix

39 – 46

8

Helix

50 – 57

8

Helix

64 – 81

18

Helix

86 – 89

4

Helix

91 – 102

12

Helix

103 – 105

3

Helix

115 – 128

14

Helix

133 – 154

22

Helix

166 – 176

11

Helix

179 – 190

12

Helix

196 – 199

4

Helix

202 – 222

21

Helix

224 – 229

6

Helix

236 – 244

9

Helix

248 – 279

32

Helix

284 – 296

13

Helix

298 – 308

11

Turn

309 – 311

3

Sequences

	Sequence		Length	Mass (Da)
	Q55012 [UniParc]. Last modified January 23, 2007. Version 4. Checksum: 417FCE6D8C4BB18C	FASTA	337	38,002
	10 20 30 40 50 60 MPQDVDFHIP LPGRQSPDHA RAEAEQLAWP RSLGLIRSDA AAERHLRGGY ADLASRFYPH 70 80 90 100 110 120 ATGADLDLGV DLMSWFFLFD DLFDGPRGEN PEDTKQLTDQ VAAALDGPLP DTAPPIAHGF 130 140 150 160 170 180 ADIWRRTCEG MTPAWCARSA RHWRNYFDGY VDEAESRFWN APCDSAAQYL AMRRHTIGVQ 190 200 210 220 230 240 PTVDLAERAG RFEVPHRVFD SAVMSAMLQI AVDVNLLLND IASLEKEEAR GEQNNMVMIL 250 260 270 280 290 300 RREHGWSKSR SVSHMQNEVR ARLEQYLLLE SCLPKVGEIY QLDTAEREAL ERYRTDAVRT 310 320 330 VIRGSYDWHR SSGRYDAEFA LAAGAQGYLE ELGSSAH

References

[1]	"Pentalenene synthase. Purification, molecular cloning, sequencing, and high-level expression in Escherichia coli of a terpenoid cyclase from Streptomyces UC5319." Cane D.E., Sohng J.-K., Lamberson C.R., Rudnicki S.M., Wu Z., Lloyd M.D., Oliver J.S., Hubbard B.R. Biochemistry 33:5846-5857(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-28; 57-73; 96-120 AND 145-157, FUNCTION, SUBUNIT, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES. Strain: UC5319.
[2]	"Genome mining in streptomyces. Discovery of an unprecedented P450-catalyzed oxidative rearrangement that is the final step in the biosynthesis of pentalenolactone." Zhu D., Seo M.J., Ikeda H., Cane D.E. J. Am. Chem. Soc. 133:2128-2131(2011) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: UC5319.
[3]	"Pentalenene synthase. Histidine-309 is not required for catalytic activity." Seemann M., Zhai G., Umezawa K., Cane D.E. J. Am. Chem. Soc. 121:591-592(1999) Cited for: MUTAGENESIS OF HIS-309.
[4]	"Crystal structure of pentalenene synthase: mechanistic insights on terpenoid cyclization reactions in biology." Lesburg C.A., Zhai G., Cane D.E., Christianson D.W. Science 277:1820-1824(1997) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS).
[5]	"Pentalenene synthase. Analysis of active site residues by site-directed mutagenesis." Seemann M., Zhai G., de Kraker J.-W., Paschall C.M., Christianson D.W., Cane D.E. J. Am. Chem. Soc. 124:7681-7689(2002) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) OF MUTANT LEU-219, CATALYTIC ACTIVITY, MUTAGENESIS OF PHE-76; PHE-77; ASP-80; ASP-81; ASP-84; ASN-219; 308-TRP-HIS-309; TRP-308 AND HIS-309.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U05213 Unassigned DNA. Translation: AAA19131.1.
HQ292066 Genomic DNA. Translation: ADO85594.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1HM4	X-ray	3.47	A/B	2-337	[»]
1HM7	X-ray	2.90	A/B	2-337	[»]
1PS1	X-ray	2.60	A/B	1-337	[»]

ProteinModelPortal

Q55012.

SMR

Q55012. Positions 7-311.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Enzyme and pathway databases

BioCyc

MetaCyc:MONOMER-16834.

BRENDA

4.2.3.7. 6094.

UniPathway

UPA00171; UER00581.
UPA00974.

Family and domain databases

Gene3D

1.10.600.10. 1 hit.

InterPro

IPR005630. Terpene_synthase_metal-bd.
IPR008949. Terpenoid_synth.
[Graphical view]

Pfam

PF03936. Terpene_synth_C. 1 hit.
[Graphical view]

SUPFAM

SSF48576. Terpenoid_synth. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

Q55012.

Entry information

Entry name

PENA_STREX

Accession

Primary (citable) accession number: Q55012
Secondary accession number(s): E3VWK6

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	January 23, 2007
Last modified:	April 3, 2013
This is version 78 of the entry and version 4 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program