Summary: Pleckstrin homology domain

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Pleckstrin homology domain Edit Wikipedia article

PH domain of tyrosine-protein kinase BTK

Identifiers

Symbol

PH

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

Pleckstrin homology domain (PH domain) is a protein domain of approximately 120 amino acids that occurs in a wide range of proteins involved in intracellular signaling or as constituents of the cytoskeleton.^[1]^[2]^[3]^[4]^[5]^[6]^[7]

This domain can bind phosphatidylinositol lipids within biological membranes (such as phosphatidylinositol (3,4,5)-trisphosphate and phosphatidylinositol (4,5)-bisphosphate),^[8] and proteins such as the βγ-subunits of heterotrimeric G proteins,^[9] and protein kinase C.^[10] Through these interactions, PH domains play a role in recruiting proteins to different membranes, thus targeting them to appropriate cellular compartments or enabling them to interact with other components of the signal transduction pathways.

Lipid binding specificity

Individual PH domains possess specificities for phosphoinositides phosphorylated at different sites within the inositol ring, e.g., some bind phosphatidylinositol (4,5)-bisphosphate but not phosphatidylinositol (3,4,5)-trisphosphate or phosphatidylinositol (3,4)-bisphosphate, while others may possess the requisite affinity. This is important because it makes the recruitment of different PH domain containing proteins sensitive to the activities of enzymes that either phosphorylate or dephosphorylate these sites on the inositol ring, such as phosphoinositide 3-kinase or PTEN, respectively. Thus, such enzymes exert a part of their effect on cell function by modulating the localization of downstream signaling proteins that possess PH domains that are capable of binding their phospholipid products.

Structure

The 3D structure of several PH domains has been determined.^[11] All known cases have a common structure consisting of two perpendicular anti-parallel beta sheets, followed by a C-terminal amphipathic helix. The loops connecting the beta-strands differ greatly in length, making the PH domain relatively difficult to detect while providing the source of the domain's specificity. The only conserved residue among PH domains is a single tryptophan located within the alpha helix that serves to nucleate the core of the domain.

Proteins containing PH domain

PH domains can be found in many different proteins, such as OSBP or ARF. Recruitment to the Golgi in this case is dependent on both PtdIns and ARF. A large number of PH domains have poor affinity for phosphoinositides and are hypothesized to function as protein binding domains. A Genome-wide look in Saccharomyces cerevisiae showed that most of the 33 yeast PH domains are indeed promiscuous in binding to phosphoinositides, while only one (Num1-PH) behaved highly specific .^[12] Proteins reported to contain PH domains belong to the following families:

Pleckstrin, the protein where this domain was first detected, is the major substrate of protein kinase C in platelets. Pleckstrin is one of the rare proteins to contain two PH domains.
Ser/Thr protein kinases such as the Akt/Rac family, the beta-adrenergic receptor kinases, the mu isoform of PKC and the trypanosomal NrkA family.
Tyrosine protein kinases belonging to the Btk/Itk/Tec subfamily.
Insulin receptor substrate 1 (IRS-1).
Regulators of small G-proteins like guanine nucleotide releasing factor GNRP (Ras-GRF) (which contains 2 PH domains), guanine nucleotide exchange proteins like vav, dbl, SoS and S. cerevisiae CDC24, GTPase activating proteins like rasGAP and BEM2/IPL2, and the human break point cluster protein bcr.
Cytoskeletal proteins such as dynamin (see InterPro: IPR001401), Caenorhabditis elegans kinesin-like protein unc-104 (see InterPro: IPR001752), spectrin beta-chain, syntrophin (2 PH domains), and S. cerevisiae nuclear migration protein NUM1.
Mammalian phosphatidylinositol-specific phospholipase C (PI-PLC) (see InterPro: IPR000909) isoforms gamma and delta. Isoform gamma contains two PH domains, the second one is split into two parts separated by about 400 residues.
Oxysterol-binding proteins OSBP, S. cerevisiae OSH1 and YHR073w.
Mouse protein citron, a putative rho/rac effector that binds to the GTP-bound forms of rho and rac.
Several S. cerevisiae proteins involved in cell cycle regulation and bud formation like BEM2, BEM3, BUD4 and the BEM1-binding proteins BOI2 (BEB1) and BOI1 (BOB1).
C. elegans protein MIG-10.
Ceramide kinase, a lipid kinase that phosphorylates ceramides to ceramide-1-phosphate.^[13]

Subfamilies

Spectrin/pleckstrin-like InterPro: IPR001605

Examples

Human genes encoding proteins containing this domain include:

ABR, ADRBK1, ADRBK2, AFAP, AFAP1, AFAP1L1, AFAP1L2, AKAP13, AKT1, AKT2, AKT3, ANLN, APBB1IP, APPL1, APPL2, ARHGAP10, ARHGAP12, ARHGAP15, ARHGAP21, ARHGAP22, ARHGAP23, ARHGAP24, ARHGAP25, ARHGAP26, ARHGAP27, ARHGAP9, ARHGEF16, ARHGEF18, ARHGEF19, ARHGEF2, ARHGEF3, ARHGEF4, ARHGEF5, ARHGEF6, ARHGEF7, ARHGEF9, ASEF2,
BMX, BTK,
C20orf42, C9orf100, CADPS, CADPS2, CDC42BPA, CDC42BPB, CDC42BPG, CENTA1, CENTA2, CENTB1, CENTB2, CENTB5, CENTD1, CENTD2, CENTD3, CENTG1, CENTG2, CENTG3, CIT, CNKSR1, CNKSR2, COL4A3BP, CTGLF1, CTGLF2, CTGLF3, * CTGLF4, CTGLF5, CTGLF6,
DAB2IP, DAPP1, DDEF1, DDEF2, DDEFL1, DEF6, DEPDC2, DGKD, DGKH, DGKK, DNM1, DNM2, DNM3, DOCK10, DOCK11, DOCK9, DOK1, DOK2, DOK3, DOK4, DOK5, DOK6, DTGCU2,
EXOC8,
FAM109A, FAM109B, FARP1, FARP2, FGD1, FGD2, FGD3, FGD4, FGD5, FGD6,
GAB1, GAB2, GAB3, GAB4, GRB10, GRB14, GRB7,
IRS1, IRS2, IRS4, ITK, ITSN1, ITSN2,
KALRN, KIF1A, KIF1B, KIF1Bbeta,
MCF2, MCF2L, MCF2L2, MRIP, MYO10,
NET1, NGEF,
OBPH1, OBSCN, OPHN1, OSBP, OSBP2, OSBPL10, OSBPL11, OSBPL3, OSBPL5, OSBPL6, OSBPL7, OSBPL8, OSBPL9,
PHLDA2, PHLDA3, PHLDB1, PHLDB2, PHLPP, PIP3-E, PLCD1, PLCD4, PLCG1, PLCG2, PLCH1, PLCH2, PLCL1, PLCL2, PLD1, PLD2, PLEK, PLEK2, PLEKHA1, PLEKHA2, PLEKHA3, PLEKHA4, PLEKHA5, PLEKHA6, PLEKHA7, PLEKHA8, PLEKHB1, PLEKHB2, PLEKHC1, PLEKHF1, PLEKHF2, PLEKHG1, PLEKHG2, PLEKHG3, PLEKHG4, PLEKHG5, PLEKHG6, PLEKHH1, PLEKHH2, PLEKHH3, PLEKHJ1, PLEKHK1, PLEKHM1, PLEKHM2, PLEKHO1, PLEKHQ1, PREX1, PRKCN, PRKD1, PRKD2, PRKD3, PSCD1, PSCD2, PSCD3, PSCD4, PSD, PSD2, PSD3, PSD4, RALGPS1, RALGPS2, RAPH1,
RASA1, RASA2, RASA3, RASA4, RASAL1, RASGRF1, RGNEF, ROCK1, ROCK2, RTKN,
SBF1, SBF2, SCAP2, SGEF, SH2B, SH2B1, SH2B2, SH2B3, SH3BP2, SKAP1, SKAP2, SNTA1, SNTB1, SNTB2, SOS1, SOS2, SPATA13, SPNB4, SPTBN1, SPTBN2, SPTBN4, SPTBN5, STAP1, SWAP70, SYNGAP1,
TBC1D2, TEC, TIAM1, TRIO, TRIOBP, TYL,
URP1, URP2,
VAV1, VAV2, VAV3, VEPH1

References

^ Mayer, B. J.; Ren, R.; Clark, K. L.; Baltimore, D. (1993). "A putative modular domain present in diverse signaling proteins". Cell. 73 (4): 629–630. doi:10.1016/0092-8674(93)90244-K. PMID 8500161.
^ Haslam, R. J.; Koide, H. B.; Hemmings, B. A. (1993). "Pleckstrin domain homology". Nature. 363 (6427): 309–10. doi:10.1038/363309b0. PMID 8497315.
^ Musacchio, A.; Gibson, T.; Rice, P.; Thompson, J.; Saraste, M. (1993). "The PH domain: A common piece in the structural pathcwork of signalling proteins". Trends in Biochemical Sciences. 18 (9): 343–348. doi:10.1016/0968-0004(93)90071-T. PMID 8236453.
^ Gibson, T. J.; Hyvönen, M.; Musacchio, A.; Saraste, M.; Birney, E. (1994). "PH domain: The first anniversary". Trends in Biochemical Sciences. 19 (9): 349–353. doi:10.1016/0968-0004(94)90108-2. PMID 7985225.
^ Pawson, T. (1995). "Protein modules and signalling networks". Nature. 373 (6515): 573–580. doi:10.1038/373573a0. PMID 7531822.
^ Ingley, E.; Hemmings, B. A. (1994). "Pleckstrin homology (PH) domains in signal transducton". Journal of Cellular Biochemistry. 56 (4): 436–443. doi:10.1002/jcb.240560403. PMID 7890802.
^ Saraste, M.; Hyvönen, M. (1995). "Pleckstrin homology domains: A fact file". Current Opinion in Structural Biology. 5 (3): 403–408. doi:10.1016/0959-440X(95)80104-9. PMID 7583640.
^ Wang, D. S.; Shaw, G. (1995). "The Association of the C-Terminal Region of β1ΣII Spectrin to Brain Membranes is Mediated by a pH Domain, Does Not Require Membrane Proteins, and Coincides with a Inositol-1,4,5 Trisphosphate Binding Site". Biochemical and Biophysical Research Communications. 217 (2): 608–615. doi:10.1006/bbrc.1995.2818. PMID 7503742.
^ Wang, D. S.; Shaw, R.; Winkelmann, J. C.; Shaw, G. (1994). "Binding of PH Domains of β-Adrenergic-Receptor Kinase and β-Spectrin to WD40/β-Transducin Repeat Containing Regions of the β-Subunit of Trimeric G-Proteins". Biochemical and Biophysical Research Communications. 203 (1): 29–35. doi:10.1006/bbrc.1994.2144. PMID 8074669.
^ Yao, L.; Kawakami, Y.; Kawakami, T. (1994). "The pleckstrin homology domain of Bruton tyrosine kinase interacts with protein kinase C". Proceedings of the National Academy of Sciences. 91 (19): 9175–9179. doi:10.1073/pnas.91.19.9175.
^ Riddihough, G. (1994). "More meanders and sandwiches". Nature Structural Biology. 1 (11): 755–757. doi:10.1038/nsb1194-755. PMID 7634082.
^ Yu, J. W.; Mendrola, J. M.; Audhya, A.; Singh, S.; Keleti, D.; Dewald, D. B.; Murray, D.; Emr, S. D.; Lemmon, M. A. (2004). "Genome-Wide Analysis of Membrane Targeting by S. Cerevisiae Pleckstrin Homology Domains". Molecular Cell. 13 (5): 677–688. doi:10.1016/S1097-2765(04)00083-8. PMID 15023338.
^ Sugiura, M.; Kono, K.; Liu, H.; Shimizugawa, T.; Minekura, H.; Spiegel, S.; Kohama, T. (2002). "Ceramide Kinase, a Novel Lipid Kinase. MOLECULAR CLONING AND FUNCTIONAL CHARACTERIZATION". Journal of Biological Chemistry. 277 (26): 23294–23300. doi:10.1074/jbc.M201535200. PMID 11956206.

External links

Nash Lab Protein Interaction Domains - PH domain description
UMich Orientation of Proteins in Membranes families/superfamily-51 - Calculated orientations of PH domains in membranes

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Pleckstrin homology domain Provide feedback

This Pleckstrin homology domain is found in some fungal species.

Literature references

Gibson TJ, Hyvonen M, Musacchio A, Saraste M, Birney E; , Trends Biochem Sci 1994;19:349-353.: PH domain: the first anniversary. PUBMED:7985225 EPMC:7985225

Internal database links

SCOOP:	PH PH_2 PH_3 PH_6 PH_8 PH_9
Similarity to PfamA using HHSearch:	PH PH_8

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 PH (CL0266), which has the following description:

Members of this clan share a PH-like fold. Many families in this clan bind to short peptide motifs in proteins and are involved in signalling.

The clan contains the following 56 members:

BBL5 bPH_1 bPH_2 bPH_3 bPH_4 bPH_5 bPH_6 CARM1 DCP1 DUF1126 DUF1681 DUF3203 FERM_C Glycoprot_B_PH1 Glycoprot_B_PH2 GRAM hSac2 ICAP-1_inte_bdg INPP5B_PH IQ_SEC7_PH IRS Mcp5_PH Myosin_TH1 OCRL_clath_bd PH PH_10 PH_11 PH_12 PH_13 PH_2 PH_3 PH_4 PH_5 PH_6 PH_8 PH_9 PH_BEACH PH_TFIIH PID PID_2 POB3_N Proteasom_Rpn13 PTB Ran_BP1 Rtt106 Sec3-PIP2_bind Sharpin_PH SIN1_PH SPT16 SSrecog UCH_N Voldacs Vps36_ESCRT-II WH1 YcxB ZFYVE21_C

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

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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.

	Seed (7)	Full (475)	Representative proteomes				UniProt (596)	NCBI (3985)	Meta (1)
	Seed (7)	Full (475)	RP15 (38)	RP35 (171)	RP55 (324)	RP75 (408)	UniProt (596)	NCBI (3985)	Meta (1)
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 (7)	Full (475)	Representative proteomes				UniProt (596)	NCBI (3985)	Meta (1)
	Seed (7)	Full (475)	RP15 (38)	RP35 (171)	RP55 (324)	RP75 (408)	UniProt (596)	NCBI (3985)	Meta (1)
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 (7)	Full (475)	Representative proteomes				UniProt (596)	NCBI (3985)	Meta (1)
	Seed (7)	Full (475)	RP15 (38)	RP35 (171)	RP55 (324)	RP75 (408)	UniProt (596)	NCBI (3985)	Meta (1)
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.

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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:

PF00169

Previous IDs:

none

Type:

Domain

Author:

Coggill P

Number in seed:

7

Number in full:

475

Average length of the domain:

119.10 aa

Average identity of full alignment:

33 %

Average coverage of the sequence by the domain:

15.63 %

HMM information

HMM build commands:

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

search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	30.0	30.0
Trusted cut-off	30.0	30.0
Noise cut-off	29.9	29.9

Model length:

105

Family (HMM) version:

5

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Species distribution

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Colour assignments

Archea	Eukaryota
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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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kingdom
phylum
class
order
family
genus
species

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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.

As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.

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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.

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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For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.

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The tree shows the occurrence of this domain across different species. More...

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.

If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.

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.

We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

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.

You can use the tree controls to manipulate how the interactive tree is displayed:

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Interactions

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

FHA

v t e Protein domains

BAR BIR BZIP CARD C1 C2 DED ENTH FYVE HEAT Kringle LIM LRR NACHT PAS PDZ Pyrin PH PX SH2 SH3 SUN TRIO WD40 zinc finger

Family: PH_11 (PF15413)

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