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25  structures 3378  species 0  interactions 7254  sequences 132  architectures

Family: DAGK_cat (PF00781)

Summary: Diacylglycerol kinase catalytic domain

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This is the Wikipedia entry entitled "Diacylglycerol kinase". More...

Diacylglycerol kinase Edit Wikipedia article

Prokaryotic diacylglycerol kinase
Soluble diacylglycerol kinase DgkB from Staphylococcus aureus.png
DgkB, soluble DAGK from Staphylococcus aureus. α-helices in red, β-strands in yellow, coils in green.
Identifiers
Symbol DAGK_prokar
Pfam PF01219
InterPro IPR000829
PROSITE PDOC00820
OPM superfamily 217
OPM protein 2kdc
Diacylglycerol kinase catalytic domain
Identifiers
Symbol DAGK_cat
Pfam PF00781
Pfam clan CL0240
InterPro IPR001206
SMART DAGKc
Diacylglycerol kinase accessory domain
Identifiers
Symbol DAGK_acc
Pfam PF00609
InterPro IPR000756
SMART DAGKa

Diacylglycerol kinase (DGK or DAGK) is a family of enzymes that catalyzes the conversion of diacylglycerol (DAG) to phosphatidic acid (PA) utilizing ATP as a source of the phosphate. In non-stimulated cells, DGK activity is low allowing DAG to be used for glycerophospholipid biosynthesis but on receptor activation of the phosphoinositide pathway, DGK activity increases driving the conversion of DAG to PA. As both lipids are thought to function as bioactive lipid signaling molecules with distinct cellular targets, DGK therefore occupies an important position, effectively serving as a switch by terminating the signalling of one lipid while simultaneously activating signalling by another.[1]

In bacteria, DGK is very small (13 to 15 kD) membrane protein which seems to contain three transmembrane domains.[2] The best conserved region is a stretch of 12 residues which are located in a cytoplasmic loop between the second and third transmembrane domains. Some Gram-positive bacteria also encode a soluble diacylglycerol kinase capable of reintroducing DAG into the phospholipid biosynthesis pathway. DAG accumulates in Gram-positive bacteria as a result of the transfer of glycerol-1-phosphate moieties from phosphatidylglycerol to lipotechoic acid.[3]

Mammalian DGK Isoforms

Currently, nine members of the DGK family have been cloned and identified. Although all family members have conserved catalytic domains and two cysteine rich domains, they are further classified into five groups according to the presence of additional functional domains and substrate specificity.[4] These are as follows:

  • Type 1 - DGK-α, DGK-β, DGK-γ - contain EF-hand motifs and a recoverin homology domain
  • Type 2 - DGK-δ, DGK-η - contain a pleckstrin homology domain
  • Type 3 - DGK-ε - has specificity for arachidonate-containing DAG
  • Type 4 - DGK-ζ, DGK-ι - contain a MARCKS homology domain, ankyrin repeats, a C-terminal nuclear localisation signal, and a PDZ-binding motif.
  • Type 5 - DGK-θ - contains a third cysteine-rich domain, a pleckstrin homology domain and a proline rich region

References

  1. ^ Merida I, Avila-Flores A, Merino E (2008). "Diacylglycerol kinases: at the hub of cell signalling.". Biochem. J. 409 (1): 1–18. doi:10.1042/BJ20071040. PMID 18062770. 
  2. ^ Smith RL, O'Toole JF, Maguire ME, Sanders CR (September 1994). "Membrane topology of Escherichia coli diacylglycerol kinase". J. Bacteriol. 176 (17): 5459–65. PMC 196734. PMID 8071224. 
  3. ^ Miller DJ, Jerga A, Rock CO, White SW (July 2008). "Analysis of the Staphylococcus aureus DgkB structure reveals a common catalytic mechanism for the soluble diacylglycol kinases". Structure 16 (7): 1036–46. doi:10.1016/j.str.2008.03.019. PMC 2847398. PMID 18611377. 
  4. ^ Van Blitterswijk, WJ, and Houssa, B (2000). "Properties and functions of diacylglycerol kinases.". Cellular Signaling 1 (9-10): 595–605. PMID 11080611. 

External links

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.

Diacylglycerol kinase catalytic domain Provide feedback

Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. The catalytic domain is assumed from the finding of bacterial homologues. YegS is the Escherichia coli protein in this family whose crystal structure reveals an active site in the inter-domain cleft formed by four conserved sequence motifs, revealing a novel metal-binding site. The residues of this site are conserved across the family [5].

Literature references

  1. Sakane F, Yamada K, Kanoh H, Yokoyama C, Tanabe T; , Nature 1990;344:345-348.: Porcine diacylglycerol kinase sequence has zinc finger and E-F hand motifs. PUBMED:2156169 EPMC:2156169

  2. Sakane F, Imai S, Kai M, Wada I, Kanoh H; , J Biol Chem 1996;271:8394-8401.: Molecular cloning of a novel diacylglycerol kinase isozyme with a pleckstrin homology domain and a C-terminal tail similar to those of the EPH family of protein-tyrosine kinases. PUBMED:8626538 EPMC:8626538

  3. Schaap D, de Widt J, van der Wal J, Vandekerckhove J, van Damme J, Gussow D, Ploegh HL, van Blitterswijk WJ, van der Bend RL; , FEBS Lett 1990;275:151-158.: Purification, cDNA-cloning and expression of human diacylglycerol kinase. PUBMED:2175712 EPMC:2175712

  4. Kanoh H, Yamada K, Sakane F; , Trends Biochem Sci 1990;15:47-50.: Diacylglycerol kinase: a key modulator of signal transduction? PUBMED:2159661 EPMC:2159661

  5. Bakali HM, Herman MD, Johnson KA, Kelly AA, Wieslander A, Hallberg BM, Nordlund P; , J Biol Chem. 2007;282:19644-19652.: Crystal structure of YegS, a homologue to the mammalian diacylglycerol kinases, reveals a novel regulatory metal binding site. PUBMED:17351295 EPMC:17351295


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001206

The DAG-kinase catalytic domain or DAGKc domain is present in mammalian lipid kinases, such as diacylglycerol (DAG), ceramide and sphingosine kinases, as well as in related bacterial proteins [PUBMED:8626538, PUBMED:17351295]. Eukaryotic DAG-kinase (EC) catalyses the phosphorylation of DAG to phosphatidic acid, thus modulating the balance between the two signaling lipids. At least ten different isoforms have been identified in mammals, which form 5 groups characterised by different functional domains, such as the calcium-binding EF hand (see PROSITEDOC), PH (see PROSITEDOC), SAM (see PROSITEDOC) , DAG/PE-binding C1 domain (see PROSITEDOC) and ankyrin repeats (see PROSITEDOC) [PUBMED:17512245].

In bacteria, an integral membrane DAG kinase forms a homotrimeric protein that lacks the DAGKc domain (see PROSITEDOC). In contrast, the bacterial yegS protein is a soluble cytosolic protein that contains the DAGKc domain in the N-terminal part. YegS is a lipid kinase with two structural domains, wherein the active site is located in the interdomain cleft, C-terminal to the DAGKc domain which forms an alpha/beta fold [PUBMED:17351295]. The tertiary structure resembles that of NAD kinases and contains a metal-binding site in the C-terminal region [PUBMED:17351295, PUBMED:19112175].

This domain is usually associated with an accessory domain (see INTERPRO).

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 PFK (CL0240), which has the following description:

This clan includes two SCOP superfamilies. Strong similarities between NAD kinases, DAG kinase, sphingosine kinase and PFK have previously been shown[1].

The clan contains the following 3 members:

DAGK_cat NAD_kinase PFK

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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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.

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(125)
Full
(7254)
Representative proteomes NCBI
(5666)
Meta
(830)
RP15
(772)
RP35
(1353)
RP55
(1927)
RP75
(2390)
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Format an alignment

  Seed
(125)
Full
(7254)
Representative proteomes NCBI
(5666)
Meta
(830)
RP15
(772)
RP35
(1353)
RP55
(1927)
RP75
(2390)
Alignment:
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Order:
Sequence:
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  Seed
(125)
Full
(7254)
Representative proteomes NCBI
(5666)
Meta
(830)
RP15
(772)
RP35
(1353)
RP55
(1927)
RP75
(2390)
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.

HMM logo

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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 View help on the curation process

Seed source: Alignment kindly provided by SMART
Previous IDs: DAGKc;
Type: Family
Author: SMART, Coggill PC
Number in seed: 125
Number in full: 7254
Average length of the domain: 128.70 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 30.86 %

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 20.5 20.5
Trusted cut-off 20.5 20.5
Noise cut-off 20.4 20.4
Model length: 130
Family (HMM) version: 19
Download: download the raw HMM for this family

Species distribution

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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 DAGK_cat domain has been found. There are 25 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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