Summary: DAHP synthetase I family

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Wikipedia: DAHP synthase
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DAHP synthase Edit Wikipedia article

3-deoxy-7-phosphoheptulonate synthase

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PDB structures

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NCBI	proteins

DAHP synthetase I domain

Structure of Aquifex aeolicus kdo8ps in complex with z-methyl-pep 2-dehydro-3-deoxyphosphooctonate aldolase.^[1]

Identifiers

Symbol

DAHP_synth_1

Pfam clan

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

3-Deoxy-D-arabinoheptulosonate 7-phosphate (DAHP) synthase (EC 2.5.1.54) is the first enzyme in a series of metabolic reactions known as the shikimate pathway, which is responsible for the biosynthesis of the amino acids phenylalanine, tyrosine, and tryptophan. Since it is the first enzyme in the shikimate pathway, it controls the amount of carbon entering the pathway. Enzyme inhibition is the primary method of regulating the amount of carbon entering the pathway.^[2] Forms of this enzyme differ between organisms, but can be considered DAHP synthase based upon the reaction that is catalyzed by this enzyme.

In enzymology, a DAHP synthase (EC 2.5.1.54) is an enzyme that catalyzes the chemical reaction

phosphoenolpyruvate + D-erythrose 4-phosphate + H₂O

\rightleftharpoons

3-deoxy-D-arabino-hept-2-ulosonate 7-phosphate + phosphate

The three substrates of this enzyme are phosphoenolpyruvate, D-erythrose 4-phosphate, and H₂O, whereas its two products are 3-deoxy-D-arabino-hept-2-ulosonate 7-phosphate and phosphate.

Nomenclature

This 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:D-erythrose-4-phosphate C-(1-carboxyvinyl)transferase (phosphate-hydrolysing, 2-carboxy-2-oxoethyl-forming). Other names in common use include 2-dehydro-3-deoxy-phosphoheptonate aldolase, 2-keto-3-deoxy-D-arabino-heptonic acid 7-phosphate synthetase, 3-deoxy-D-arabino-2-heptulosonic acid 7-phosphate synthetase, 3-deoxy-D-arabino-heptolosonate-7-phosphate synthetase, 3-deoxy-D-arabino-heptulosonate 7-phosphate synthetase, 7-phospho-2-keto-3-deoxy-D-arabino-heptonate D-erythrose-4-phosphate, lyase (pyruvate-phosphorylating), 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate, D-erythrose-4-phosphate lyase (pyruvate-phosphorylating), D-erythrose-4-phosphate-lyase, D-erythrose-4-phosphate-lyase (pyruvate-phosphorylating), DAH7-P synthase, DAHP synthase, DS-Co, DS-Mn, KDPH synthase, KDPH synthetase, deoxy-D-arabino-heptulosonate-7-phosphate synthetase, phospho-2-dehydro-3-deoxyheptonate aldolase, phospho-2-keto-3-deoxyheptanoate aldolase, phospho-2-keto-3-deoxyheptonate aldolase, phospho-2-keto-3-deoxyheptonic aldolase, and phospho-2-oxo-3-deoxyheptonate aldolase.

Biological function

The primary function of DAHP synthase is to catalyze the reaction of phosphoenolpyruvate and D-erythrose 4-phosphate to DAHP and phosphate. However, another biological function of the enzyme is to regulate the amount of carbon that enters the shikimate pathway. This is accomplished primarily through two different methods, feedback inhibition and transcriptional control.^[2] Feedback inhibition and transcriptional control are both mechanisms of regulating carbon in bacteria, but the only mechanism of regulation found in DAHP synthase found in plants is transcriptional control.^[2]

In Escherichia coli, a species of bacteria, DAHP synthase is found as three isoenzymes, each of which sensitive to one of the amino acids produced in the shikimate pathway.^[3] In a study of DAHP synthase sensitive to tyrosine in E. coli, it was determined that the enzyme is inhibited by tyrosine through noncompetitive inhibition with respect to phosphoenolpyruvate, the first substrate of the reaction catalyzed by DAHP synthase, while the enzyme is inhibited by tyrosine through competitive inhibition with respect to D-erythrose 4-phosphate, the second substrate of the reaction catalyzed by DAHP synthase when the concentration of tyrosine is above 10 μM.^[3] It was also determined that the enzyme is inhibited by inorganic phosphate through noncompetitive inhibition with respect to both substrates and inhibited by DAHP through competitive inhibition with respect to phosphoenolpyruvate and noncompetitive inhibition with respect to D-erythrose 4-phosphate.^[3] Studies of product inhibition have shown that phosphoenolpyruvate is the first substrate to bind to the enzyme complex, inorganic phosphate is the first product to dissociate from the enzyme complex.^[3] Thus the amount of carbon entering the shikimate pathway can be controlled by inhibiting DAHP synthase from catalyzing the reaction that forms DAHP.

Carbon flow into the shikimate pathway in plants is regulated by transcriptional control.^[3] This method is also found in bacteria, but feedback inhibition is more prevalent.^[2] In plants, as the plants progressed through the growth cycle, the activity of DAHP synthase changed.^[2]

Catalytic activity

Metal ions are required in order for DAHP synthase to catalyze reactions.^[2] In DAHP synthase, it has been shown that binding site contains patterns of cysteine and histidine residues bound to metal ions in a Cys-X-X-His fashion.^[2]

It has been shown that, in general, DAHP synthases require a bivalent metal ion cofactor in order for the enzyme to function properly.^[4] Metal ions that can function as cofactors include Mn²⁺, Fe²⁺, Co²⁺, Zn²⁺, Cu²⁺, and Ca²⁺.^[4] Studies have suggested that one metal ion bonds to each monomer of DAHP synthase.^[4]

The reaction catalyzed by DAHP synthase is shown below.

This is the reaction catalyzed by DAHP synthase.

Structure

This image shows the quaternary structure of DAHP synthase.

This image shows the quaternary structure of DAHP synthase, with the secondary and tertiary structures illustrated in cartoon form.

The quaternary structure of DAHP synthase consists of two tightly bound dimers, which means that DAHP synthase is a tetramer.^[5]

To the right is an image of DAHP synthase that shows the quaternary structure of DAHP synthase. This image shows that DAHP synthase consists of two tightly bound dimers. Each of the monomer chains is colored differently.

Below the first image to the right is an image of DAHP synthase that also shows quaternary structure, however this image is in a cartoon view. This view also shows each of the four monomers colored differently. In addition, this view can also be used to show secondary and tertiary structures. As shown, two of the monomers have beta sheets that interact on one side of the enzyme, while the other two monomers have beta sheets that interact on the opposite side.

Structural studies

As of late 2007, four structures have been solved for this class of enzymes, with PDB accession codes 1RZM, 1VR6, 1VS1, and 2B7O.

Class-II DAHP synthetase family

Identifiers

Symbol

DAHP_synth_2

Pfam clan

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

References

^ Xu X, Wang J, Grison C, Petek S, Coutrot P, Birck MR et al. (2003). "Structure-based design of novel inhibitors of 3-deoxy-D-manno-octulosonate 8-phosphate synthase.". Drug Des Discov 18 (2-3): 91–9. doi:10.3109/10559610290271787. PMID 14675946.
^ ^a ^b ^c ^d ^e ^f ^g Herrmann, K.; Entus, R. (2001). "Shikimate Pathway: Aromatic Amino Acids and Beyond". Encyclopedia of Life Sciences. doi:10.1038/npg.els.0001315. ISBN 0470016175. edit
^ ^a ^b ^c ^d ^e Schoner, R.; Herrmann, K. M. (1976). "3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase. Purification, properties, and kinetics of the tyrosine-sensitive isoenzyme from Escherichia coli". The Journal of Biological Chemistry 251 (18): 5440–5447. PMID 9387. edit
^ ^a ^b ^c Stephens, C. M.; Bauerle, R. (1991). "Analysis of the metal requirement of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from Escherichia coli". The Journal of Biological Chemistry 266 (31): 20810–20817. PMID 1682314. edit
^ Shumilin, I. A.; Kretsinger, R. H.; Bauerle, R. H. (1999). "Crystal structure of phenylalanine-regulated 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from Escherichia coli". Structure 7 (7): 865–875. doi:10.1016/S0969-2126(99)80109-9. PMID 10425687. edit

DAHP synthetase I family Provide feedback

Members of this family catalyse the first step in aromatic amino acid biosynthesis from chorismate. E-coli has three related synthetases, which are inhibited by different aromatic amino acids. This family also includes KDSA which has very similar catalytic activity but is involved in the first step of liposaccharide biosynthesis. The enzyme is also part of the shikimate pathway, EC:2.5.1.54.

Literature references

Shumilin IA, Kretsinger RH, Bauerle RH; , Structure Fold Des 1999;7:865-875.: Crystal structure of phenylalanine-regulated 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from Escherichia coli. PUBMED:10425687 EPMC:10425687

Internal database links

Similarity to PfamA using HHSearch:

NeuB

External database links

HOMSTRAD:	DAHP_synth_1
PANDIT:	PF00793
Pseudofam:	PF00793
SCOP:	1qr7
SYSTERS:	DAHP_synth_1

This tab holds annotation information from the InterPro database.

InterPro entry IPR006218

Members of the 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthetase family catalyse the first step in aromatic amino acid biosynthesis from chorismate. Class I includes bacterial and yeast enzymes; class II includes higher plants and various microorganisms (see INTERPRO) [PUBMED:8760910].

The first step in the common pathway leading to the biosynthesis of aromatic compounds is the stereospecific condensation of phosphoenolpyruvate (PEP) and D-erythrose-4-phosphate (E4P) giving rise to 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP). This reaction is catalyzed by DAHP synthase, a metal-activated enzyme, which in microorganisms is the target for negative-feedback regulation by pathway intermediates or by end products. In Escherichia coli there are three DAHP synthetase isoforms, each specifically inhibited by one of the three aromatic amino acids. The crystal structure of the phenylalanine-regulated form of DAHP synthetase shows the fold as is a (beta/alpha)8 barrel with several additional beta strands and alpha helices [PUBMED:10425687].

Gene Ontology

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

Biological process

biosynthetic process (GO:0009058)

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 TIM_barrel (CL0036), which has the following description:

This large superfamily of TIM barrel enzymes all contain a common phosphate binding site. The phosphate is found in a variety of cofactors and ligands such as FMN [1,2].

The clan contains the following 57 members:

Ala_racemase_N ALAD Aldolase AP_endonuc_2 BtpA CdhD CutC DAHP_synth_1 DAHP_synth_2 DeoC DHDPS DHO_dh DHquinase_I DUF1341 DUF2090 DUF556 DUF561 DUF692 DUF993 Dus F_bP_aldolase FMN_dh G3P_antiterm Glu_syn_central Glu_synthase His_biosynth HMGL-like IGPS IMPDH iPGM_N MtrH NanE NAPRTase NeuB NMO OMPdecase Orn_Arg_deC_N Oxidored_FMN PcrB PdxJ PhosphMutase PRAI Pterin_bind QRPTase_C Racemase_4 RhaA Ribul_P_3_epim SOR_SNZ Tagatose_6_P_K ThiG TIM TIM-br_sig_trns TMP-TENI Transaldolase Trp_syntA UvdE UxuA

Alignments

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RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
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	Seed (28)	Full (8958)	Representative proteomes				NCBI (5818)	Meta (4302)
	Seed (28)	Full (8958)	RP15 (632)	RP35 (1204)	RP55 (1652)	RP75 (1994)	NCBI (5818)	Meta (4302)
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¹Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: available, not generated, — not available.

Format an alignment

	Seed (28)	Full (8958)	Representative proteomes				NCBI (5818)	Meta (4302)
	Seed (28)	Full (8958)	RP15 (632)	RP35 (1204)	RP55 (1652)	RP75 (1994)	NCBI (5818)	Meta (4302)
Alignment:
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	Seed (28)	Full (8958)	Representative proteomes				NCBI (5818)	Meta (4302)
	Seed (28)	Full (8958)	RP15 (632)	RP35 (1204)	RP55 (1652)	RP75 (1994)	NCBI (5818)	Meta (4302)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download	Download
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

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Curation and family details

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Curation

Seed source:

Pfam-B_1032 (release 2.1)

Previous IDs:

DAHP_synthetase;

Type:

Domain

Author:

Bateman A, Griffiths-Jones SR

Number in seed:

28

Number in full:

8958

Average length of the domain:

285.30 aa

Average identity of full alignment:

28 %

Average coverage of the sequence by the domain:

87.41 %

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	19.8	19.8
Trusted cut-off	20.5	20.1
Noise cut-off	19.3	19.6

Model length:

272

Family (HMM) version:

15

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Species distribution

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Interactive tree

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Interactions

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

DAHP_synth_1

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 DAHP_synth_1 domain has been found. There are 276 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: DAHP_synth_1 (PF00793)

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Summary: DAHP synthetase I family

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DAHP synthase Edit Wikipedia article

Contents

Nomenclature

Biological function

Catalytic activity

Structure

Structural studies

References

Further reading

DAHP synthetase I family Provide feedback

Literature references

Internal database links

External database links

InterPro entry IPR006218

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