Summary: Choline/ethanolamine kinase

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Wikipedia: Choline/ethanolamine kinase family
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This is the Wikipedia entry entitled "Choline/ethanolamine kinase family". More...

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Choline/ethanolamine kinase family Edit Wikipedia article

Choline_kinase

crystal structure of choline kinase

Identifiers

Symbol

Choline_kinase

Pfam clan

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

In molecular biology, the choline/ethanolamine kinase family includes choline kinase(EC 2.7.1.32) and ethanolamine kinase (EC 2.7.1.82).

Ethanolamine and choline are major membrane phospholipids, in the form of glycerophosphoethanolamine and glycerophosphocholine. Ethanolamine is also a component of the glycosylphosphatidylinositol (GPI) anchor, which is necessary for cell-surface protein attachment.^[1] The de novo synthesis of these phospholipids begins with the creation of phosphoethanolamine and phosphocholine by ethanolamine and choline kinases in the first step of the CDP-ethanolamine pathway.^[2]^[3] There are two putative choline/ethanolamine kinases (C/EKs) in the Trypanosoma brucei genome.

Ethanolamine kinase has no choline kinase activity ^[1] and its activity is inhibited by ADP.^[3] Inositol supplementation represses ethanolamine kinase, decreasing the incorporation of ethanolamine into the CDP-ethanolamine pathway and into phosphatidylethanolamine and phosphatidylcholine.^[4]

References

^ ^a ^b Gibellini F, Hunter WN, Smith TK (October 2008). "Biochemical characterization of the initial steps of the Kennedy pathway in Trypanosoma brucei: the ethanolamine and choline kinases". Biochem. J. 415 (1): 135–44. doi:10.1042/BJ20080435. PMC 2552378. PMID 18489261.
^ Tian Y, Jackson P, Gunter C, Wang J, Rock CO, Jackowski S (September 2006). "Placental thrombosis and spontaneous fetal death in mice deficient in ethanolamine kinase 2". J. Biol. Chem. 281 (38): 28438–49. doi:10.1074/jbc.M605861200. PMID 16861741.
^ ^a ^b Kim KH, Voelker DR, Flocco MT, Carman GM (March 1998). "Expression, purification, and characterization of choline kinase, product of the CKI gene from Saccharomyces cerevisiae". J. Biol. Chem. 273 (12): 6844–52. doi:10.1074/jbc.273.12.6844. PMID 9506987.
^ Kersting MC, Choi HS, Carman GM (August 2004). "Regulation of the yeast EKI1-encoded ethanolamine kinase by inositol and choline". J. Biol. Chem. 279 (34): 35353–9. doi:10.1074/jbc.M405704200. PMID 15201274.

This article incorporates text from the public domain Pfam and InterPro IPR002573

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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.

Choline/ethanolamine kinase Provide feedback

Choline kinase catalyses the committed step in the synthesis of phosphatidylcholine by the CDP-choline pathway [1]. This alignment covers the protein kinase portion of the protein. The divergence of this family makes it very difficult to create a model that specifically predicts choline/ethanolamine kinases only. However if [add Pfam ID here for Choline_kinase_C] is also present then it is definitely a member of this family.

Literature references

Kim KH, Voelker DR, Flocco MT, Carman GM; , J Biol Chem 1998;273:6844-6852.: Expression, purification, and characterization of choline kinase, product of the CKI gene from Saccharomyces cerevisiae. PUBMED:9506987 EPMC:9506987

Internal database links

SCOOP:	APH APH_6_hur DUF1679 EcKinase Fructosamin_kin Kdo Kinase-like PK_Tyr_Ser-Thr Pkinase Pkinase_fungal RIO1
Similarity to PfamA using HHSearch:	APH EcKinase

This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

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 PKinase (CL0016), which has the following description:

This superfamily includes the Serine/Threonine- and Tyrosine- protein kinases as well as related kinases that act on non-protein substrates.

The clan contains the following 38 members:

ABC1 AceK Act-Frag_cataly Alpha_kinase APH APH_6_hur Choline_kinase CotH DUF1679 DUF2252 DUF4135 EcKinase Fam20C Fructosamin_kin FTA2 Haspin_kinase HipA_C Ins_P5_2-kin IPK IucA_IucC Kdo Kinase-like Kinase-PolyVal KIND Pan3_PK PI3_PI4_kinase PIP49_C PIP5K PK_Tyr_Ser-Thr Pkinase Pkinase_fungal Pox_ser-thr_kin RIO1 Seadorna_VP7 UL97 WaaY YrbL-PhoP_reg YukC

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:

jalview: a Java applet developed at the University of Dundee. You will need Java installed before running jalview
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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 (31)	Full (4855)	Representative proteomes				UniProt (11371)	NCBI (47421)	Meta (1530)
	Seed (31)	Full (4855)	RP15 (785)	RP35 (2210)	RP55 (3740)	RP75 (5555)	UniProt (11371)	NCBI (47421)	Meta (1530)
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 (31)	Full (4855)	Representative proteomes				UniProt (11371)	NCBI (47421)	Meta (1530)
	Seed (31)	Full (4855)	RP15 (785)	RP35 (2210)	RP55 (3740)	RP75 (5555)	UniProt (11371)	NCBI (47421)	Meta (1530)
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 (31)	Full (4855)	Representative proteomes				UniProt (11371)	NCBI (47421)	Meta (1530)
	Seed (31)	Full (4855)	RP15 (785)	RP35 (2210)	RP55 (3740)	RP75 (5555)	UniProt (11371)	NCBI (47421)	Meta (1530)
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:

Pfam-B_1165 (release 4.1)

Previous IDs:

none

Type:

Family

Sequence Ontology:

SO:0100021

Author:

Bateman A

Number in seed:

31

Number in full:

4855

Average length of the domain:

197.60 aa

Average identity of full alignment:

23 %

Average coverage of the sequence by the domain:

48.81 %

HMM information

HMM build commands:

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

search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	20.7	20.7
Trusted cut-off	20.7	20.7
Noise cut-off	20.6	20.6

Model length:

213

Family (HMM) version:

21

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Species distribution

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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 adjacent tab. 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.

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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.

So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".

Sub-species

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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Species trees

We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.

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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Interactions

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

Choline_kinase

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 Choline_kinase domain has been found. There are 56 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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Family: Choline_kinase (PF01633)

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Summary: Choline/ethanolamine kinase

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Choline/ethanolamine kinase family Edit Wikipedia article

References

Choline/ethanolamine kinase Provide feedback

Literature references

Internal database links

Domain organisation

Pfam Clan

Alignments

Alignment types

Viewing

Reformatting

Downloading

View options

Format an alignment

Download options

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

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