Summary: Hydroxyethylthiazole kinase family
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Hydroxyethylthiazole kinase Edit Wikipedia article
|PDB structures||RCSB PDB PDBe PDBsum|
|Gene Ontology||AmiGO / QuickGO|
|Hydroxyethylthiazole kinase family|
crystal structure of native thiazole kinase in the monoclinic form
|SCOPe||1c3q / SUPFAM|
- ATP + 4-methyl-5-(2-hydroxyethyl)thiazole ADP + 4-methyl-5-(2-phosphonooxyethyl)thiazole
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is ATP:4-methyl-5-(2-hydroxyethyl)thiazole 2-phosphotransferase. Other names in common use include hydroxyethylthiazole kinase (phosphorylating), and 4-methyl-5-(beta-hydroxyethyl)thiazole kinase. This enzyme participates in thiamine metabolism. Thiamine pyrophosphate (TPP), a required cofactor for many enzymes in the cell, is synthesised de novo in Salmonella typhimurium.
- Petersen LA, Downs DM (August 1997). "Identification and characterization of an operon in Salmonella typhimurium involved in thiamine biosynthesis". J. Bacteriol. 179 (15): 4894â€“900. PMC 179339. PMID 9244280.
- Nosaka K, Nishimura H, Kawasaki Y, Tsujihara T, Iwashima A (December 1994). "Isolation and characterization of the THI6 gene encoding a bifunctional thiamin-phosphate pyrophosphorylase/hydroxyethylthiazole kinase from Saccharomyces cerevisiae". J. Biol. Chem. 269 (48): 30510â€“6. PMID 7982968.
- Lewin LM & Brown GM (1961). "The biosynthesis of thiamine. III. Mechanism of enzymatic formation of the pyrophosphate ester of 2-methyl-4-amino-5-hydroxymethylpyrimidine". J. Biol. Chem. 236: 2768â€“2771.
|This EC 2.7 enzyme-related article is a stub. You can help Wikipedia by expanding it.|
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No Pfam abstract.
Internal database links
|SCOOP:||Carb_kinase PfkB Phos_pyr_kin|
|Similarity to PfamA using HHSearch:||Carb_kinase Phos_pyr_kin|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR000417
Most microorganisms and plants can synthesise thiamin de novo [PUBMED:19348578]. In this de novo pathway, the thiazole and pyrimidine moieties of thiamin are made separately and coupled together to form thiamin phosphate. For the thiazole moiety, 4-methyl-5-(2-hydroxyethyl)thiazole (THZ), the key salvage step is phosphorylation to give 4-methyl-5-(2-phosphonooxyethyl)thiazole (THZ-P). The enzyme hydoxyethylthiazole kinase (EC) is responsible for this step. Hydoxyethylthiazole kinase is encoded by thiM in Escherichia coli [PUBMED:2542220] and other bacteria, and by the C-terminal region of bifunctional proteins in some cases, such as Saccharomyces cerevisiae, in which the N-terminal domain corresponds to the bacterial thiamine-phosphate pyrophosphorylase (EC), ThiE [PUBMED:7982968, PUBMED:20968298].
The Arabidopsis and maize genomes encode homologues of ThiM [PUBMED:23816351].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||hydroxyethylthiazole kinase activity (GO:0004417)|
|Biological process||thiamine biosynthetic process (GO:0009228)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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All of these enzymes are phosphotransferases that have an alcohol group as an acceptor (EC:2.7.1.-). However, 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase (HMPP kinase) catalyses two phosphorylation reactions: one to a hydroxymethyl group of hydroxymethyl pyrimidine (HMP) and the second to the phosphomethyl group of HMPP . The common structural feature for the enzymes in this superfamily is a central eight-stranded sheet that is flanked by eight structurally conserved helices, five on one side and three on the other . The active site is located in a shallow groove along one edge of the sheet, with the phosphate acceptor hydroxyl group and -phosphate of ATP close together in the middle of the groove, and substrate and ATP binding at the ends .
The clan contains the following 5 members:ADP_PFK_GK Carb_kinase HK PfkB Phos_pyr_kin
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We make a range of alignments for each Pfam-A family:
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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.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
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.
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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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|Author:||Mian N , Bateman A|
|Number in seed:||8|
|Number in full:||3194|
|Average length of the domain:||238.00 aa|
|Average identity of full alignment:||36 %|
|Average coverage of the sequence by the domain:||75.59 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||16|
|Download:||download the raw HMM for this family|
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
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.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
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Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
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Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
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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The tree shows the occurrence of this domain across different species. More...
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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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There are 2 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 HK domain has been found. There are 76 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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