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243  structures 8249  species 0  interactions 20550  sequences 111  architectures

Family: EPSP_synthase (PF00275)

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

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EPSP synthase Edit Wikipedia article

EPSP Synthase (3-phosphoshikimate 1-carboxyvinyltransferase)
EPSP synthase.PNG
EPSP synthase liganded with shikimate.[1]
Identifiers
EC no.2.5.1.19
CAS no.9068-73-9
Databases
IntEnzIntEnz view
BRENDABRENDA entry
ExPASyNiceZyme view
KEGGKEGG entry
MetaCycmetabolic pathway
PRIAMprofile
PDB structuresRCSB PDB PDBe PDBsum
Gene OntologyAmiGO / QuickGO
EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase)
EPSP synthase cartoon.PNG
Ribbon diagram of EPSP synthase
Identifiers
SymbolEPSP_synthase
PfamPF00275
InterProIPR001986
PROSITEPDOC00097
SCOP21eps / SCOPe / SUPFAM

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

phosphoenolpyruvate + 3-phosphoshikimate 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.

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
  • EPSP synthase.

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]

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.

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.

Reaction

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

File:EPSPreactionII.tif EPSP, the product of the reaction

Applications

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.

References

  1. ^ Priestman MA, Healy ML, Funke T, Becker A, Schönbrunn E (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. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  2. ^ a b Schönbrunn E, Eschenburg S, Shuttleworth WA, Schloss JV, Amrhein N, Evans JN, Kabsch W (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. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  3. ^ Pollegioni L, Schonbrunn E, Siehl D (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. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)

Further reading

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

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Internal database links

External database links

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.

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 has the following description:

This superfamily includes Enolpyruvate transferase (EPT) and RNA 3'-terminal phosphate cyclase (RTPC).

The clan 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 (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
(19)
Full
(20550)
Representative proteomes UniProt
(102054)
RP15
(2882)
RP35
(10331)
RP55
(21156)
RP75
(35900)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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  Seed
(19)
Full
(20550)
Representative proteomes UniProt
(102054)
RP15
(2882)
RP35
(10331)
RP55
(21156)
RP75
(35900)
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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
(19)
Full
(20550)
Representative proteomes UniProt
(102054)
RP15
(2882)
RP35
(10331)
RP55
(21156)
RP75
(35900)
Raw Stockholm Download   Download   Download   Download   Download   Download    
Gzipped 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.

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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 View help on the curation process

Seed source: Prosite
Previous IDs: EPSP_syntase;
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD
Number in seed: 19
Number in full: 20550
Average length of the domain: 392.5 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 83.06 %

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 22.8 22.8
Trusted cut-off 23.0 22.9
Noise cut-off 22.7 22.7
Model length: 416
Family (HMM) version: 23
Download: download the raw HMM for this family

Species distribution

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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 EPSP_synthase domain has been found. There are 243 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
A0A077ZF85 View 3D Structure Click here
A0A077ZK46 View 3D Structure Click here
A0A0D2FBH4 View 3D Structure Click here
A0A0H3GV01 View 3D Structure Click here
A0A0H3GYZ6 View 3D Structure Click here
A0A0N7KLH2 View 3D Structure Click here
A0A175VQK6 View 3D Structure Click here
A0A1C1CEP6 View 3D Structure Click here
A0A1D6NVZ6 View 3D Structure Click here
A0B7Z0 View 3D Structure Click here
A0KQ23 View 3D Structure Click here
A0L408 View 3D Structure Click here
A0L6Y9 View 3D Structure Click here
A0LJ00 View 3D Structure Click here
A0LLU6 View 3D Structure Click here
A0LS98 View 3D Structure Click here
A0Q388 View 3D Structure Click here
A1ANP7 View 3D Structure Click here
A1AWP4 View 3D Structure Click here
A1AWR5 View 3D Structure Click here
A1B3F9 View 3D Structure Click here
A1B474 View 3D Structure Click here
A1BEN1 View 3D Structure Click here
A1BIP2 View 3D Structure Click here
A1CP85 View 3D Structure Click here
A1D244 View 3D Structure Click here
A1S6D3 View 3D Structure Click here
A1SA71 View 3D Structure Click here
A1STZ0 View 3D Structure Click here
A1SYM0 View 3D Structure Click here
A1T5Z3 View 3D Structure Click here
A1TKY2 View 3D Structure Click here
A1UCN4 View 3D Structure Click here
A1VK35 View 3D Structure Click here
A1WR98 View 3D Structure Click here
A1WUI9 View 3D Structure Click here
A1WYW6 View 3D Structure Click here
A2SU05 View 3D Structure Click here
A3CNV3 View 3D Structure Click here
A3DK03 View 3D Structure Click here