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176  structures 4830  species 1  interaction 10932  sequences 37  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 number 2.5.1.19
CAS number 9068-73-9
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / EGO
EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase)
EPSP synthase cartoon.PNG
Ribbon diagram of EPSP synthase
Identifiers
Symbol EPSP_synthase
Pfam PF00275
InterPro IPR001986
PROSITE PDOC00097
SCOP 1eps
SUPERFAMILY 1eps

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.

Nomenclature[edit]

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.

Function[edit]

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[edit]

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, hence the products of this pathway represent essential amino acids that must be obtained from the animal's diet.

Structure[edit]

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[edit]

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

EPSPreactionII.tif

Applications[edit]

Herbicides[edit]

Glyphosate 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. 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 glyphosate 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[edit]

  1. ^ 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. 
  2. ^ 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. 
  3. ^ 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. 

Further reading[edit]

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.

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

No Pfam abstract.

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

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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)
RP15
(809)
RP35
(1563)
RP55
(2026)
RP75
(2360)
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  Seed
(23)
Full
(10932)
Representative proteomes NCBI
(7857)
Meta
(8210)
RP15
(809)
RP35
(1563)
RP55
(2026)
RP75
(2360)
Alignment:
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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
(23)
Full
(10932)
Representative proteomes NCBI
(7857)
Meta
(8210)
RP15
(809)
RP35
(1563)
RP55
(2026)
RP75
(2360)
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.

Pfam alignments:

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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

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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 View help on HMM parameters

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: download the raw HMM for this family

Species distribution

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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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