Summary: 3-dehydroquinate synthase II

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Wikipedia: 3-dehydroquinate synthase II
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This is the Wikipedia entry entitled "3-dehydroquinate synthase II". More...

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3-dehydroquinate synthase II Edit Wikipedia article

3-dehydroquinate synthase II

Identifiers

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PDB structures

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NCBI	proteins

3-dehydroquinate synthase II (EC 1.4.1.24, DHQ synthase II, MJ1249 (gene), aroB' (gene)) is an enzyme with systematic name 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate:NAD⁺ oxidoreductase (deaminating).^[1] This enzyme catalyses the following chemical reaction

2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate + H₂O + NAD⁺

\rightleftharpoons

3-dehydroquinate + NH₃ + NADH + H⁺

The enzyme was isolated from the archaeon Methanocaldococcus jannaschii.

References

^ White RH (June 2004). "L-Aspartate semialdehyde and a 6-deoxy-5-ketohexose 1-phosphate are the precursors to the aromatic amino acids in Methanocaldococcus jannaschii". Biochemistry. 43 (23): 7618â€“27. doi:10.1021/bi0495127. PMID 15182204.

External links

3-dehydroquinate+synthase+II at the US National Library of Medicine Medical Subject Headings (MeSH)

v t e CH-NH₂ oxidoreductases (EC 1.4) - primarily amino acid oxidoreductases
1.4.1: NAD/NADP acceptor	Glutamate dehydrogenase GLUD1 GLUD2 Glutamate synthase (NADPH)
1.4.3: oxygen acceptor	D-amino acid oxidase Amine oxidase (Copper-containing (Lysyl Diamine Primary-amine)) (Flavin-containing (Monoamine)))
1.4.4: disulfide acceptor	Glycine cleavage system
1.4.99: other acceptors	D-amino acid dehydrogenase Amine dehydrogenase

v t e Enzymes
Activity	Active site Binding site Catalytic triad Oxyanion hole Enzyme promiscuity Catalytically perfect enzyme Coenzyme Cofactor Enzyme catalysis
Regulation	Allosteric regulation Cooperativity Enzyme inhibitor Enzyme activator
Classification	EC number Enzyme superfamily Enzyme family List of enzymes
Kinetics	Enzyme kinetics Eadieâ€“Hofstee diagram Hanesâ€“Woolf plot Lineweaverâ€“Burk plot Michaelisâ€“Menten kinetics
Types	EC1 Oxidoreductases (list) EC2 Transferases (list) EC3 Hydrolases (list) EC4 Lyases (list) EC5 Isomerases (list) EC6 Ligases (list) EC7 Translocases (list)

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.

3-dehydroquinate synthase II Provide feedback

This family includes members of 3-dehydroquinate synthase II ( EC:1.4.1.24), encoded by aroB genes in M. maripaludis which is widely distributed in methanogens. In M. jannaschii, proteins ADTH synthase (AroA) and DHQ synthase II (AroB) are required to convert 6-deoxy-5-ketofructose-1-phosphate (DKFP) and aspartate semialdehyde to 3-dehydroquinate (DHQ) in vitro [1, 2].

Literature references

Porat I, Sieprawska-Lupa M, Teng Q, Bohanon FJ, White RH, Whitman WB;, Mol Microbiol. 2006;62:1117-1131.: Biochemical and genetic characterization of an early step in a novel pathway for the biosynthesis of aromatic amino acids and p-aminobenzoic acid in the archaeon Methanococcus maripaludis. PUBMED:17010158 EPMC:17010158
White RH;, Biochemistry. 2004;43:7618-7627.: L-Aspartate semialdehyde and a 6-deoxy-5-ketohexose 1-phosphate are the precursors to the aromatic amino acids in Methanocaldococcus jannaschii. PUBMED:15182204 EPMC:15182204

This tab holds annotation information from the InterPro database.

InterPro entry IPR002812

3-Dehydroquinate synthase (EC) is an enzyme in the common pathway of aromatic amino acid biosynthesis that catalyses the conversion of 3-deoxy-D-arabino-heptulosonic acid 7-phosphate (DAHP) into 3-dehydroquinic acid [PUBMED:11173489]. This synthesis of aromatic amino acids is an essential metabolic function for most prokaryotic as well as lower eukaryotic cells, including plants. The pathway is absent in humans; therefore, DHQS represents a potential target for the development of novel and selective antimicrobial agents. Owing to the threat posed by the spread of pathogenic bacteria resistant to many currently used antimicrobial drugs, there is clearly a need to develop new anti-infective drugs acting at novel targets. A further potential use for DHQS inhibitors is as herbicides [PUBMED:11412967].

Gene Ontology

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

Molecular function	3-dehydroquinate synthase activity (GO:0003856)
	oxidoreductase activity (GO:0016491)
Biological process	aromatic amino acid family biosynthetic process (GO:0009073)
	oxidation-reduction process (GO:0055114)

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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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, the UniProtKB sequence database, 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
UniProt: alignment generated by searching the UniProtKB sequence database using the family HMM
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

Viewing

You can see the alignments as HTML or in three different sequence viewers:

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PP/Heatmap: an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.

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Downloading

You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.

View options

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 (95)	Full (684)	Representative proteomes				UniProt (1648)	NCBI (1945)	Meta (104)
	Seed (95)	Full (684)	RP15 (175)	RP35 (429)	RP55 (635)	RP75 (832)	UniProt (1648)	NCBI (1945)	Meta (104)
Jalview	View	View	View	View	View	View	View	View	View
HTML	View	View
PP/heatmap	₁	View

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

Key: available, not generated, — not available.

Format an alignment

	Seed (95)	Full (684)	Representative proteomes				UniProt (1648)	NCBI (1945)	Meta (104)
	Seed (95)	Full (684)	RP15 (175)	RP35 (429)	RP55 (635)	RP75 (832)	UniProt (1648)	NCBI (1945)	Meta (104)
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 (95)	Full (684)	Representative proteomes				UniProt (1648)	NCBI (1945)	Meta (104)
	Seed (95)	Full (684)	RP15 (175)	RP35 (429)	RP55 (635)	RP75 (832)	UniProt (1648)	NCBI (1945)	Meta (104)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download	Download	Download
Gzipped	Download	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.

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

Seed source:

Enright A

Previous IDs:

DUF109;

Type:

Family

Sequence Ontology:

SO:0100021

Author:

Enright A

, Ouzounis C

, Bateman A

, El-Gebali S

Number in seed:

95

Number in full:

684

Average length of the domain:

326.70 aa

Average identity of full alignment:

37 %

Average coverage of the sequence by the domain:

91.75 %

HMM information

HMM build commands:

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

search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	22.2	22.2
Trusted cut-off	22.7	22.3
Noise cut-off	21.5	21.5

Model length:

352

Family (HMM) version:

16

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Species distribution

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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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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.

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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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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.

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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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Family: DHQS (PF01959)

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