Summary: Terpene synthase family, metal binding domain
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This is the Wikipedia entry entitled "Terpene synthase C terminal domain". More...
Terpene synthase C terminal domain Edit Wikipedia article
| Terpene_synth_C | |||||||||
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5-epi-aristolochene synthase from nicotiana tabacum
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| Identifiers | |||||||||
| Symbol | Terpene_synth_C | ||||||||
| Pfam | PF03936 | ||||||||
| InterPro | IPR005630 | ||||||||
| SCOP | 5eau | ||||||||
| SUPERFAMILY | 5eau | ||||||||
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In molecular biology, this protein domain belongs to the terpene synthase family (TPS). Its role is to synthesize terpenes which are part of primary metabolism, such as sterols and carotene and also part of the secondary metabolism. This entry will focus on the C terminal domain of the TPS protein.
Function
Terpenes synthases have a role in producing important molecules in metabolism, these molecules are part of a large group called terpenoids . In particular, the C terminal domain catalyzes the cyclization of geranyl diphosphate, orienting and stabilizing multiple reactive carbocation intermediates. Or in simpler terms, the C terminal aids the synthesis of new molecules.
Structure
It is thought to have at least two alpha helices.[1]
Conservation
Sequences containing this protein domain belong to the terpene synthase family. It has been suggested that this gene family be designated tps (for terpene synthase). Sequence comparisons reveal similarities between the monoterpene (C10) synthases, sesquiterpene (C15) synthases and the diterpene (C20) synthases. It has been split into six subgroups on the basis of phylogeny, called Tpsa-Tpsf .[2]
- Tpsa includes vetispiridiene synthase.[3]
- Tpsb includes (-)-limonene synthase.[4]
- Tpsc includes copalyl diphosphate synthase (kaurene synthase A).[5]
- Tpsd includes taxadiene synthase,[6] pinene synthase,[7] and myrcene synthase.[8]
- Tpse includes ent-kaurene synthase B.[9]
- Tpsf includes linalool synthase.[10] In the fungus Phaeosphaeria sp. (strain L487) the synthesis of ent-kaurene from geranylgeranyl dophosphate is promoted by a single bifunctional protein.[11]
See also
Terpene synthase N terminal domain
References
- ^ Starks CM, Back K, Chappell J, Noel JP (1997). "Structural basis for cyclic terpene biosynthesis by tobacco 5-epi-aristolochene synthase". Science. 277 (5333): 1815–20. doi:10.1126/science.277.5333.1815. PMID 9295271.
- ^ Bohlmann J, Steele CL, Croteau R (August 1997). "Monoterpene synthases from grand fir (Abies grandis). cDNA isolation, characterization, and functional expression of myrcene synthase, (-)-(4S)-limonene synthase, and (-)-(1S,5S)-pinene synthase". J. Biol. Chem. 272 (35): 21784–92. doi:10.1074/jbc.272.35.21784. PMID 9268308.
- ^ [1], 5-epi- aristolochene synthase, [2] and (+)-delta-cadinene synthase SWISSPROT
- ^ "4S-limonene synthase precursor - Mentha spicata (Spearmint)". Uniprot.org. doi:10.1073/pnas.0700915104. Retrieved 2012-08-02.
- ^ "Ent-copalyl diphosphate synthase, chloroplastic precursor - Pisum sativum (Garden pea)". Uniprot.org. doi:10.1046/j.1365-313X.1997.11030443.x. Retrieved 2012-08-02.
- ^ "Taxadiene synthase - Taxus brevifolia (Pacific yew)". Uniprot.org. doi:10.1074/jbc.271.16.9201. Retrieved 2012-08-02.
- ^ "Pinene synthase, chloroplastic precursor - Abies grandis (Grand fir)". Uniprot.org. Retrieved 2012-08-02.
- ^ "Myrcene synthase, chloroplastic precursor - Abies grandis (Grand fir)". Uniprot.org. Retrieved 2012-08-02.
- ^ "Ent-kaur-16-ene synthase, chloroplastic precursor - Cucurbita maxima (Pumpkin)". Uniprot.org. doi:10.1046/j.1365-313X.1996.10020203.x. Retrieved 2012-08-02.
- ^ "Linalool synthase - Clarkia concinna (Red ribbons)". Uniprot.org. Retrieved 2012-08-02.
- ^ Kawaide H, Imai R, Sassa T, Kamiya Y (August 1997). "Ent-kaurene synthase from the fungus Phaeosphaeria sp. L487. cDNA isolation, characterization, and bacterial expression of a bifunctional diterpene cyclase in fungal gibberellin biosynthesis". J. Biol. Chem. 272 (35): 21706–12. doi:10.1074/jbc.272.35.21706. PMID 9268298.
This article incorporates text from the public domain Pfam and InterPro IPR005630
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Terpene synthase family, metal binding domain Provide feedback
It has been suggested that this gene family be designated tps (for terpene synthase) [1]. It has been split into six subgroups on the basis of phylogeny, called tpsa-tpsf. tpsa includes vetispiridiene synthase Q39979 5-epi- aristolochene synthase, Q40577 and (+)-delta-cadinene synthase P93665. tpsb includes (-)-limonene synthase, Q40322. tpsc includes kaurene synthase A, O04408. tpsd includes taxadiene synthase, Q41594 pinene synthase, O24475 and myrcene synthase, O24474. tpse includes kaurene synthase B. tpsf includes linalool synthase.
Literature references
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Bohlmann J, Steele CL, Croteau R; , J Biol Chem 1997;272:21784-21792.: Monoterpene synthases from grand fir (Abies grandis). cDNA isolation, characterization, and functional expression of myrcene synthase, (-)-(4S)-limonene synthase, and (-)-(1S,5S)-pinene synthase. PUBMED:9268308 EPMC:9268308
Internal database links
| SCOOP: | Terpene_syn_C_2 Terpene_synth TRI5 |
| Similarity to PfamA using HHSearch: | Terpene_syn_C_2 |
External database links
| SCOP: | 5eau |
This tab holds annotation information from the InterPro database.
InterPro entry IPR005630
Sequences containing this domain belong to the terpene synthase family. It has been suggested that this gene family be designated tps (for terpene synthase). Sequence comparisons reveal similarities between the monoterpene (C10) synthases, sesquiterpene (C15) synthases and the diterpene (C20) synthases. It has been split into six subgroups on the basis of phylogeny, called Tpsa-Tpsf [PUBMED:9268308].
- Tpsa includes vetispiradiene synthase SWISSPROT, 5-epi- aristolochene synthase, SWISSPROT and (+)-delta-cadinene synthase SWISSPROT.
- Tpsb includes (-)-limonene synthase, SWISSPROT.
- Tpsc includes copalyl diphosphate synthase (kaurene synthase A), SWISSPROT.
- Tpsd includes taxadiene synthase, SWISSPROT, pinene synthase, SWISSPROT and myrcene synthase, SWISSPROT.
- Tpse includes ent-kaurene synthase B SWISSPROT.
- Tpsf includes linalool synthase SWISSPROT.
In the fungus Phaeosphaeria sp. (strain L487) the synthesis of ent-kaurene from geranylgeranyl dophosphate is promoted by a single bifunctional protein [PUBMED:9268298].
This domain is involved in the cyclization of linear terpenes [PUBMED:9295272, PUBMED:12432096, PUBMED:17261032, PUBMED:20131801, PUBMED:20624401].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
| Molecular function | magnesium ion binding (GO:0000287) |
| lyase activity (GO:0016829) | |
| terpene synthase activity (GO:0010333) |
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
This family is a member of clan Terp_synthase (CL0613), which has the following description:
This superfamily includes a diverse range of terpene synthase enzymes which share an alpha helical core.
The clan contains the following 7 members:
HEPPP_synt_1 polyprenyl_synt SQS_PSY Terpene_syn_C_2 Terpene_synth_C TRI5 UbiAAlignments
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
| Seed (213) |
Full (4859) |
Representative proteomes | UniProt (8265) |
NCBI (14404) |
Meta (2) |
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| RP15 (139) |
RP35 (2237) |
RP55 (3676) |
RP75 (4758) |
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| PP/heatmap | 1 | ||||||||
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.
| Seed (213) |
Full (4859) |
Representative proteomes | UniProt (8265) |
NCBI (14404) |
Meta (2) |
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|---|---|---|---|---|---|---|---|---|---|
| RP15 (139) |
RP35 (2237) |
RP55 (3676) |
RP75 (4758) |
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| Raw Stockholm | |||||||||
| Gzipped | |||||||||
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
Trees
This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
Curation
| Seed source: | Pfam-B_728 (release 3.0) |
| Previous IDs: | none |
| Type: | Domain |
| Sequence Ontology: | SO:0000417 |
| Author: |
Finn RD  , Bateman A , Griffiths-Jones SR
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| Number in seed: | 213 |
| Number in full: | 4859 |
| Average length of the domain: | 196.90 aa |
| Average identity of full alignment: | 26 % |
| Average coverage of the sequence by the domain: | 43.21 % |
HMM information
| HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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| Model details: |
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| Model length: | 267 | ||||||||||||
| Family (HMM) version: | 17 | ||||||||||||
| Download: | download the raw HMM for this family |
Species distribution
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Colour assignments
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Interactions
Structures
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Terpene_synth_C domain has been found. There are 104 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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