Summary: EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase)

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EPSP synthase Edit Wikipedia article

EPSP Synthase (3-phosphoshikimate 1-carboxyvinyltransferase)

EPSP synthase liganded with shikimate.^[1]

Identifiers

Databases

PDB structures

AmiGO / EGO

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PMC	articles
PubMed	articles
NCBI	proteins

EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase)

Ribbon diagram of EPSP synthase

Identifiers

Symbol

EPSP_synthase

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

5-enolpyruvylshikimate-3-phosphate (EPSP) synthase is an enzyme that catalyzes the chemical reaction:

phosphoenolpyruvate + 3-phosphoshikimate $\rightleftharpoons$ phosphate + 5-enolpyruvylshikimate-3-phosphate (EPSP)

Thus, the two substrates of this enzyme are phosphoenolpyruvate and 3-phospho-shikimate, whereas its two products are phosphate and 5-enolpyruvylshikimate-3-phosphate.

[edit] Nomenclature

The enzyme belongs to the family of transferases, to be specific those transferring aryl or alkyl groups other than methyl groups. The systematic name of this enzyme class is phosphoenolpyruvate:3-phosphoshikimate 5-O-(1-carboxyvinyl)-transferase. Other names in common use include:

5-enolpyruvylshikimate-3-phosphate synthase,
3-enolpyruvylshikimate 5-phosphate synthase,
3-enolpyruvylshikimic acid-5-phosphate synthetase,
5'-enolpyruvylshikimate-3-phosphate synthase,
5-enolpyruvyl-3-phosphoshikimate synthase,
5-enolpyruvylshikimate-3-phosphate synthetase,
5-enolpyruvylshikimate-3-phosphoric acid synthase,
enolpyruvylshikimate phosphate synthase, and
3-phosphoshikimate 1-carboxyvinyl transferase.

[edit] Function

The enzyme participates in biosynthesis of the aromatic amino acids phenylalanine, tyrosine and tryptophan. The enzyme is a target for herbicides as these amino acids are only synthesized in plants and microorganisms. Glyphosate acts as a competitive inhibitor for phosphoenolpyruvate and is used as a broad-spectrum systemic herbicide.^[2]^[3]

[edit] Shikimate pathway

The shikimate pathway is a seven step metabolic route used by bacteria, fungi, and plants for the biosythesis of aromatic amino acids (phenylalanine, tyrosine, and tryptophan). The fourth aromatic amino acid tyrosine can be synthesized from phenylalanine. This pathway is not found in animals and in humans, hence the products of this pathway represent essential amino acids that must be obtained from the animal's diet.

[edit] Structure

EPSP synthase is a monomeric enzyme. It is composed of two domains, which are joined by protein strands. This strand acts as a hinge, and can bring the two protein domains closer together. When a substrate binds to the enzyme, ligand bonding causes the two parts of the enzyme to clamp down around the substrate in the active site.

[edit] Reaction

EPSP synthase catalyzes the reaction which converts shikimate-3-phosphate plus phosphoenolpyruvate to 5-enolpyruvylshikimate-3-phosphate (EPSP).

[edit] Applications

[edit] Herbicides

Roundup is a chemical herbicide which kills plants by inhbiting the shikimate pathway. It targets EPSP synthase, the enzyme that catalyzes the conversion of shikimate-3-phosphate and phosphoenolpyruvate into EPSP. The active ingredient in roundup, glyphosate, is a competitive inhibitor of the enzyme. Glyphosate resembles the transition state that transforms the reactants into products in the reaction that is catalyzed by EPSP synthase. Hence glyphosate (as a transition state analog) binds more tightly to EPSP synthase than its natural substrate and thereby prevents binding of substrate to the enzyme.^[2]

This binding leads to the inhibition of the enzyme, and consequently shuts down the entire pathway. Since plants require the shikimate pathway to produce aromatic amino acids, this kills the plant. This also means that Roundup is generally harmless to animals and humans, since they are not dependent on the shikimate pathway for the synthesis of Phe, Trp, and Tyr and instead obtain these amino acids from their diet.

[edit] References

^ Priestman MA, Healy ML, Funke T, Becker A, Schönbrunn E (October 2005). "Molecular basis for the glyphosate-insensitivity of the reaction of 5-enolpyruvylshikimate 3-phosphate synthase with shikimate". FEBS Lett. 579 (25): 5773–80. doi:10.1016/j.febslet.2005.09.066. PMID 16225867.
^ ^a ^b Schönbrunn E, Eschenburg S, Shuttleworth WA, Schloss JV, Amrhein N, Evans JN, Kabsch W (February 2001). "Interaction of the herbicide glyphosate with its target enzyme 5-enolpyruvylshikimate 3-phosphate synthase in atomic detail". Proc. Natl. Acad. Sci. U.S.A. 98 (4): 1376–80. doi:10.1073/pnas.98.4.1376. PMC 29264. PMID 11171958.
^ Pollegioni L, Schonbrunn E, Siehl D (August 2011). "Molecular basis of glyphosate resistance-different approaches through protein engineering". FEBS J. 278 (16): 2753–66. doi:10.1111/j.1742-4658.2011.08214.x. PMID 21668647.

[edit] Further reading

Morell H, Clark MJ, Knowles PF, Sprinson DB (1967). "The enzymic synthesis of chorismic and prephenic acids from 3-enolpyruvylshikimic acid 5-phosphate". J. Biol. Chem. 242 (1): 82–90. PMID 4289188.

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EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) Provide feedback

No Pfam abstract.

External database links

HOMSTRAD:	EPSP_syntase
PANDIT:	PF00275
PROSITE:	PDOC00097
Pseudofam:	PF00275
SCOP:	1eps
SYSTERS:	EPSP_synthase

This tab holds annotation information from the InterPro database.

InterPro entry IPR001986

This entry represents the core domain of 3-phosphoshikimate 1-carboxyvinyltransferase and UDP-N-acetylglucosamine 1-carboxyvinyltransferase. It transfers enolpryruvate from phosphoenolpyruvate to 3-phosphoshikimate and UDP-N-acetyl-alpha-D-glucosamine respectively.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Molecular function

transferase activity, transferring alkyl or aryl (other than methyl) groups (GO:0016765)

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 EPT_RTPC (CL0290), which contains the following 2 members:

EPSP_synthase RTC

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.

Alignment types

We make a range of alignments for each Pfam-A family:

seed: the curated alignment from which the HMM for the family is built
full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
NCBI: alignment generated by searching the NCBI sequence database using the family HMM
meta: alignment generated by searching the metagenomics sequence database using the family HMM

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Reformatting

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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 (23)	Full (10932)	Representative proteomes				NCBI (7857)	Meta (8210)
	Seed (23)	Full (10932)	RP15 (809)	RP35 (1563)	RP55 (2026)	RP75 (2360)	NCBI (7857)	Meta (8210)
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HTML	View		View	View	View	View
PP/heatmap	₁		View	View	View	View
Pfam viewer	View	View

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

Key: available, not generated, — not available.

Format an alignment

	Seed (23)	Full (10932)	Representative proteomes				NCBI (7857)	Meta (8210)
	Seed (23)	Full (10932)	RP15 (809)	RP35 (1563)	RP55 (2026)	RP75 (2360)	NCBI (7857)	Meta (8210)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

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 (23)	Full (10932)	Representative proteomes				NCBI (7857)	Meta (8210)
	Seed (23)	Full (10932)	RP15 (809)	RP35 (1563)	RP55 (2026)	RP75 (2360)	NCBI (7857)	Meta (8210)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download	Download
Gzipped	Download	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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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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.

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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:

Prosite

Previous IDs:

EPSP_syntase;

Type:

Family

Author:

Finn RD

Number in seed:

23

Number in full:

10932

Average length of the domain:

390.10 aa

Average identity of full alignment:

27 %

Average coverage of the sequence by the domain:

90.26 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	19.7	19.7
Trusted cut-off	19.7	19.7
Noise cut-off	19.6	19.6

Model length:

419

Family (HMM) version:

15

Download:

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Species distribution

Sunburst
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How the sunburst is generated

The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.

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As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.

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Unmapped species names

The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.

So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".

Sub-species

Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.

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For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.

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Species trees

We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.

Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.

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Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.

We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

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Interactions

There is 1 interaction for this family. More...

EPSP_synthase

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 EPSP_synthase domain has been found. There are 176 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 seqence.

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Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: EPSP_synthase (PF00275)

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Summary: EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase)

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EPSP synthase Edit Wikipedia article

Contents

[edit] Nomenclature

[edit] Function

[edit] Shikimate pathway

[edit] Structure

[edit] Reaction

[edit] Applications

[edit] Herbicides

[edit] References

[edit] Further reading

EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) Provide feedback

External database links

InterPro entry IPR001986

Gene Ontology

Domain organisation

Pfam Clan

Alignments

Alignment types

Viewing

Reformatting

Downloading

View options

Format an alignment

Download options

External links

HMM logo

Trees

Curation and family details

Curation

HMM information

Species distribution

Sunburst controls

Weight segments by...

Change the size of the sunburst

Colour assignments

Selections

Currently selected:

How the sunburst is generated

Colouring and labels

Anomalies in the taxonomy tree

Missing taxonomic levels

Unmapped species names

Sub-species

Too many species/sequences

Tree controls

Annotation

Download tree

Selected sequences

Species trees

Interactive tree

Interactions

Structures