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106  structures 137  species 0  interactions 6531  sequences 115  architectures

Family: Terpene_synth_C (PF03936)

Summary: Terpene synthase family, metal binding domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Terpene synthase C terminal domain". More...

Terpene synthase C terminal domain Edit Wikipedia article

Terpene_synth_C
PDB 5eau EBI.jpg
5-epi-aristolochene synthase from nicotiana tabacum
Identifiers
Symbol Terpene_synth_C
Pfam PF03936
InterPro IPR005630
SCOP 5eau
SUPERFAMILY 5eau

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]

See also

Terpene synthase N terminal domain

References

  1. ^ 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. 
  2. ^ 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. 
  3. ^ [1], 5-epi- aristolochene synthase, [2] and (+)-delta-cadinene synthase SWISSPROT
  4. ^ "4S-limonene synthase precursor - Mentha spicata (Spearmint)". Uniprot.org. doi:10.1073/pnas.0700915104. Retrieved 2012-08-02. 
  5. ^ "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. 
  6. ^ "Taxadiene synthase - Taxus brevifolia (Pacific yew)". Uniprot.org. doi:10.1074/jbc.271.16.9201. Retrieved 2012-08-02. 
  7. ^ "Pinene synthase, chloroplastic precursor - Abies grandis (Grand fir)". Uniprot.org. Retrieved 2012-08-02. 
  8. ^ "Myrcene synthase, chloroplastic precursor - Abies grandis (Grand fir)". Uniprot.org. Retrieved 2012-08-02. 
  9. ^ "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. 
  10. ^ "Linalool synthase - Clarkia concinna (Red ribbons)". Uniprot.org. Retrieved 2012-08-02. 
  11. ^ 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

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

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

  1. 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

External database links

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 (C 10 ) synthases, sesquiterpene (C 15 ) synthases and the diterpene (C 20 ) 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 diphosphate 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.

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 UbiA

Alignments

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 and the UniProtKB sequence database. More...

View options

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
(203)
Full
(6531)
Representative proteomes UniProt
(11527)
RP15
(402)
RP35
(3330)
RP55
(5280)
RP75
(7134)
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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(203)
Full
(6531)
Representative proteomes UniProt
(11527)
RP15
(402)
RP35
(3330)
RP55
(5280)
RP75
(7134)
Alignment:
Format:
Order:
Sequence:
Gaps:
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Download options

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
(203)
Full
(6531)
Representative proteomes UniProt
(11527)
RP15
(402)
RP35
(3330)
RP55
(5280)
RP75
(7134)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

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 View help on the curation process

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
Number in seed: 203
Number in full: 6531
Average length of the domain: 200.00 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 43.13 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.3 26.3
Trusted cut-off 26.3 26.3
Noise cut-off 26.2 26.2
Model length: 267
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

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Selections

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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 106 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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0N7KFI7 View 3D Structure Click here
A0A0N7KHA7 View 3D Structure Click here
A0A0N7KIV4 View 3D Structure Click here
A0A0P0V2G2 View 3D Structure Click here
A0A0P0VIP3 View 3D Structure Click here
A0A0P0VXM7 View 3D Structure Click here
A0A0P0VXR2 View 3D Structure Click here
A0A0P0VY91 View 3D Structure Click here
A0A0P0VYI4 View 3D Structure Click here
A0A0P0W8S0 View 3D Structure Click here
A0A0P0W8Y6 View 3D Structure Click here
A0A0P0W8Y6 View 3D Structure Click here
A0A0P0W942 View 3D Structure Click here
A0A0P0W963 View 3D Structure Click here
A0A0P0W9A3 View 3D Structure Click here
A0A0P0XC15 View 3D Structure Click here
A0A0P0XCB8 View 3D Structure Click here
A0A0P0XCC9 View 3D Structure Click here
A0A0P0XWI8 View 3D Structure Click here
A0A0P0Y268 View 3D Structure Click here
A0A0R0EGA8 View 3D Structure Click here
A0A0R0EWB7 View 3D Structure Click here
A0A0R0G697 View 3D Structure Click here
A0A0R0GVB3 View 3D Structure Click here
A0A0R0H3H1 View 3D Structure Click here
A0A0R0H610 View 3D Structure Click here
A0A0R0H721 View 3D Structure Click here
A0A0R0H721 View 3D Structure Click here
A0A0R0HF70 View 3D Structure Click here
A0A0R0I8P4 View 3D Structure Click here
A0A0R0IHS3 View 3D Structure Click here
A0A0R0JUM5 View 3D Structure Click here
A0A0R0JUM5 View 3D Structure Click here
A0A0R0KJG5 View 3D Structure Click here
A0A1D6DZU6 View 3D Structure Click here
A0A1D6EEQ1 View 3D Structure Click here
A0A1D6EEQ1 View 3D Structure Click here
A0A1D6EFQ5 View 3D Structure Click here
A0A1D6EFT8 View 3D Structure Click here
A0A1D6HQM5 View 3D Structure Click here
A0A1D6HQM5 View 3D Structure Click here
A0A1D6IY12 View 3D Structure Click here
A0A1D6IY12 View 3D Structure Click here
A0A1D6IZJ0 View 3D Structure Click here
A0A1D6IZJ1 View 3D Structure Click here
A0A1D6IZJ6 View 3D Structure Click here
A0A1D6IZJ6 View 3D Structure Click here
A0A1D6IZQ3 View 3D Structure Click here
A0A1D6J0W6 View 3D Structure Click here
A0A1D6J0W8 View 3D Structure Click here
A0A1D6K2Z5 View 3D Structure Click here
A0A1D6K5Q3 View 3D Structure Click here
A0A1D6K6U5 View 3D Structure Click here
A0A1D6LHV7 View 3D Structure Click here
A0A1D6LTV0 View 3D Structure Click here
A0A1D6NT87 View 3D Structure Click here
A0A1D6NT87 View 3D Structure Click here
A0A1D6PQN8 View 3D Structure Click here
A0A1D6PZ01 View 3D Structure Click here
A0A368UGG7 View 3D Structure Click here
A0A368UHB0 View 3D Structure Click here
A0A368UHD4 View 3D Structure Click here
A0A3L6G2C1 View 3D Structure Click here
A0A3L6G998 View 3D Structure Click here
A0A581LX25 View 3D Structure Click here
A0A581NG33 View 3D Structure Click here
A0A5H1ZRW3 View 3D Structure Click here
A3ASK1 View 3D Structure Click here
A4FVP2 View 3D Structure Click here
A4KAG8 View 3D Structure Click here
B2C4D0 View 3D Structure Click here
C7IZP5 View 3D Structure Click here
I1LRT2 View 3D Structure Click here
I1LUT1 View 3D Structure Click here
I1M2G5 View 3D Structure Click here
I1MS82 View 3D Structure Click here
K7KF95 View 3D Structure Click here
K7KY89 View 3D Structure Click here
K7L2K6 View 3D Structure Click here
K7L2K8 View 3D Structure Click here
K7L2N5 View 3D Structure Click here
K7L745 View 3D Structure Click here
K7LUR1 View 3D Structure Click here
K7LVZ0 View 3D Structure Click here
K7LVZ2 View 3D Structure Click here
K7M2G2 View 3D Structure Click here
K7M2U1 View 3D Structure Click here
K7M2U3 View 3D Structure Click here
K7N247 View 3D Structure Click here
K7TKS3 View 3D Structure Click here
K7TR87 View 3D Structure Click here
O22184 View 3D Structure Click here
O23651 View 3D Structure Click here
O65434 View 3D Structure Click here
O65435 View 3D Structure Click here
P0DI76 View 3D Structure Click here
P0DI77 View 3D Structure Click here
Q0E088 View 3D Structure Click here
Q0JA81 View 3D Structure Click here
Q0JA82 View 3D Structure Click here
Q0JA83 View 3D Structure Click here
Q0JE23 View 3D Structure Click here
Q0JEZ8 View 3D Structure Click here
Q1EG72 View 3D Structure Click here
Q29VN1 View 3D Structure Click here
Q29VN2 View 3D Structure Click here
Q29VN3 View 3D Structure Click here
Q2NM15 View 3D Structure Click here
Q2QQJ5 View 3D Structure Click here
Q38802 View 3D Structure Click here
Q41771 View 3D Structure Click here
Q4KSH9 View 3D Structure Click here
Q5GJ60 View 3D Structure Click here
Q6BDZ9 View 3D Structure Click here
Q6ET36 View 3D Structure Click here
Q6JD69 View 3D Structure Click here
Q6JD70 View 3D Structure Click here
Q6JD71 View 3D Structure Click here
Q6JD73 View 3D Structure Click here
Q6Z5I0 View 3D Structure Click here
Q6Z5J6 View 3D Structure Click here
Q6ZH94 View 3D Structure Click here
Q84UU4 View 3D Structure Click here
Q84UU9 View 3D Structure Click here
Q84UV0 View 3D Structure Click here
Q84ZW8 View 3D Structure Click here
Q8L7G4 View 3D Structure Click here
Q93YV0 View 3D Structure Click here
Q9C6W6 View 3D Structure Click here
Q9C748 View 3D Structure Click here
Q9C749 View 3D Structure Click here
Q9C8E3 View 3D Structure Click here
Q9FI27 View 3D Structure Click here
Q9LH31 View 3D Structure Click here
Q9LIA1 View 3D Structure Click here
Q9LQ27 View 3D Structure Click here
Q9LRR2 View 3D Structure Click here
Q9LRZ6 View 3D Structure Click here
Q9LS76 View 3D Structure Click here
Q9LUE0 View 3D Structure Click here
Q9LUE2 View 3D Structure Click here
Q9LVP7 View 3D Structure Click here
Q9SAK2 View 3D Structure Click here
Q9T0J9 View 3D Structure Click here
Q9T0K1 View 3D Structure Click here
Q9ZQD0 View 3D Structure Click here
Q9ZUH4 View 3D Structure Click here