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108  structures 151  species 0  interactions 7034  sequences 111  architectures

Family: Terpene_synth (PF01397)

Summary: Terpene synthase, N-terminal domain

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

Terpene synthase N terminal domain Edit Wikipedia article

Terpene_synth
PDB 1n24 EBI.jpg
(+)-bornyl diphosphate synthase: complex with mg and product
Identifiers
Symbol Terpene_synth
Pfam PF01397
InterPro IPR001906
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 N 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 N terminal domain has feature of the copalyl diphosphate synthase (CPS) active site.[1]

Structure

The N-terminal domain forms an alpha-barrel similar to that of the sesquiterpene cyclase epiaristolochene synthase.[2]

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 .[3]

See also

Terpene synthase C terminal domain

References

  1. ^ Chen F, Tholl D, Bohlmann J, Pichersky E (2011). "The family of terpene synthases in plants: a mid-size family of genes for specialized metabolism that is highly diversified throughout the kingdom". Plant J. 66 (1): 212–29. doi:10.1111/j.1365-313X.2011.04520.x. PMID 21443633. 
  2. ^ Whittington DA, Wise ML, Urbansky M, Coates RM, Croteau RB, Christianson DW (2002). "Bornyl diphosphate synthase: structure and strategy for carbocation manipulation by a terpenoid cyclase". Proc Natl Acad Sci U S A. 99 (24): 15375–80. doi:10.1073/pnas.232591099. PMC 137724Freely accessible. PMID 12432096. 
  3. ^ 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. 
  4. ^ [1], 5-epi- aristolochene synthase, [2] and (+)-delta-cadinene synthase SWISSPROT
  5. ^ "4S-limonene synthase precursor - Mentha spicata (Spearmint)". Uniprot.org. doi:10.1073/pnas.0700915104. Retrieved 2012-08-02. 
  6. ^ "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. 
  7. ^ "Taxadiene synthase - Taxus brevifolia (Pacific yew)". Uniprot.org. doi:10.1074/jbc.271.16.9201. Retrieved 2012-08-02. 
  8. ^ "Pinene synthase, chloroplastic precursor - Abies grandis (Grand fir)". Uniprot.org. Retrieved 2012-08-02. 
  9. ^ "Myrcene synthase, chloroplastic precursor - Abies grandis (Grand fir)". Uniprot.org. Retrieved 2012-08-02. 
  10. ^ "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. 
  11. ^ "Linalool synthase - Clarkia concinna (Red ribbons)". Uniprot.org. Retrieved 2012-08-02. 
  12. ^ 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 IPR001906

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, N-terminal 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 IPR001906

Sequences containing this domain belong to the terpene synthase family [ PUBMED:28841019 ]. 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 vetispiridiene 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 ].

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 6_Hairpin (CL0059), which has the following description:

This Clan includes CAZy clans GH-L, GH-M and GH-G. The members of this clan share a common structure composed of 6 helical hairpins. Most members of this superfamily are glycosyl hydrolase enzymes.

The clan contains the following 30 members:

Bac_rhamnosid6H C5-epim_C Cobalamin_bind DUF608 GDE_C GlcNAc_2-epim Glyco_hydro81C Glyco_hydro_100 Glyco_hydro_125 Glyco_hydro_127 Glyco_hydro_15 Glyco_hydro_36 Glyco_hydro_47 Glyco_hydro_48 Glyco_hydro_63 Glyco_hydro_65m Glyco_hydro_76 Glyco_hydro_8 Glyco_hydro_88 Glyco_hydro_9 Glycoamylase LANC_like Ldi Pec_lyase Prenyltrans SQHop_cyclase_C SQHop_cyclase_N TED_complement Terpene_synth Trehalase

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...

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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
(167)
Full
(7034)
Representative proteomes UniProt
(12030)
RP15
(616)
RP35
(3699)
RP55
(6018)
RP75
(7806)
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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
(167)
Full
(7034)
Representative proteomes UniProt
(12030)
RP15
(616)
RP35
(3699)
RP55
(6018)
RP75
(7806)
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
(167)
Full
(7034)
Representative proteomes UniProt
(12030)
RP15
(616)
RP35
(3699)
RP55
(6018)
RP75
(7806)
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: Repeat
Sequence Ontology: SO:0001068
Author: Finn RD , Bateman A
Number in seed: 167
Number in full: 7034
Average length of the domain: 163.20 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 31.09 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 37.6 37.6
Trusted cut-off 37.6 37.6
Noise cut-off 37.5 37.5
Model length: 192
Family (HMM) version: 24
Download: download the raw HMM for this family

Species distribution

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Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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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 domain has been found. There are 108 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
A0A0N7KSX2 View 3D Structure Click here
A0A0P0V2G2 View 3D Structure Click here
A0A0P0VIP3 View 3D Structure Click here
A0A0P0VKW2 View 3D Structure Click here
A0A0P0VXM7 View 3D Structure Click here
A0A0P0VXR2 View 3D Structure Click here
A0A0P0VY91 View 3D Structure Click here
A0A0P0VYH6 View 3D Structure Click here
A0A0P0VYI4 View 3D Structure Click here
A0A0P0VYK6 View 3D Structure Click here
A0A0P0W6H1 View 3D Structure Click here
A0A0P0W8U0 View 3D Structure Click here
A0A0P0W8Y6 View 3D Structure Click here
A0A0P0W963 View 3D Structure Click here
A0A0P0W9A3 View 3D Structure Click here
A0A0P0W9G0 View 3D Structure Click here
A0A0P0XBL8 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
A0A0P0YAB9 View 3D Structure Click here
A0A0R0EGA8 View 3D Structure Click here
A0A0R0EWB7 View 3D Structure Click here
A0A0R0G697 View 3D Structure Click here
A0A0R0H3H1 View 3D Structure Click here
A0A0R0H610 View 3D Structure Click here
A0A0R0HF70 View 3D Structure Click here
A0A0R0HFK8 View 3D Structure Click here
A0A0R0I8P4 View 3D Structure Click here
A0A0R0IHS3 View 3D Structure Click here
A0A0R0KJG5 View 3D Structure Click here
A0A1D6DZU6 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
A0A1D6IY12 View 3D Structure Click here