Summary: Protamine P1

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Wikipedia: Protamine
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This is the Wikipedia entry entitled "Protamine". More...

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Protamine Edit Wikipedia article

Protamine P1

Identifiers

Symbol

Protamine_P1

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

protamine 1
Identifiers
Symbol	PRM1
Entrez	5619
HUGO	9447
OMIM	182880
RefSeq	NM_002761
UniProt	P04553
Other data
Locus	Chr. 16 p13.13

protamine 2
Identifiers
Symbol	PRM2
Entrez	5620
HUGO	9448
OMIM	182890
RefSeq	NM_002762
UniProt	P04554
Other data
Locus	Chr. 16 p13.13

Protamines are small, arginine-rich, nuclear proteins that replace histones late in the haploid phase of spermatogenesis and are believed essential for sperm head condensation and DNA stabilization. They may allow for denser packaging of DNA in spermatozoon than histones, but they must be decompressed before the genetic data can be used for protein synthesis. However, in humans and maybe other primates, 10-15% of the sperm's genome is packaged by histones thought to bind genes that are essential for early embryonic development.^[1]

[edit] Medical uses

When mixed with insulin, protamines slow down the onset and increase the duration of insulin action (see NPH insulin).^[2]

Protamine is used in cardiopulmonary bypass surgery to neutralize the anti-clotting effects of heparin. Adverse effects include increased pulmonary artery pressure and decrease peripheral blood pressure, myocardial oxygen consumption, cardiac output, and heart rate.^[3]

Protamine sulfate is an antidote for heparin overdose.^[4] A chain shortened version of protamine also acts as a potent heparin antagonist, but with markedly reduced antigenicity.^[5]

In gene therapy, protamine sulfate's ability to condense plasmid DNA along with its approval by the U.S. Food and Drug Administration (FDA) have made it an appealing candidate to increase transduction rates by both viral^[6] and nonviral (e.g. utilizing cationic liposomes)^[7] mediated delivery mechanisms.

[edit] Examples

Mice, humans, and certain fish have two or more different protamines, whereas the sperm of bull, boar, rat, rabbit, guinea pig, and ram have one form of protamine.

[edit] Human

The 2 human protamines are denoted PRM1 and PRM2.

[edit] Fish

Examples of protamines from fish are:

salmine from salmon
clupeine from herring sperm (Clupea)
iridine from rainbow trout
thinnine from tunafish (Thunnus)
stelline from starry sturgeon (Acipenser stellatus)
scylliorhinine from dogfish (Scylliorhinus)

[edit] Protamine structure

The secondary and tertiary structure of protamine is not known with certainty, but several proposals have been published.^[8]^[9]^[10]

[edit] References

^ Balhorn R (2007). "The protamine family of sperm nuclear proteins". Genome Biol 8 (9): 227. doi:10.1186/gb-2007-8-9-227. PMC 2375014. PMID 17903313. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2375014/.
^ Owens DR (June 2011). "Insulin preparations with prolonged effect". Diabetes Technol. Ther. 13 Suppl 1: S5–14. doi:10.1089/dia.2011.0068. PMID 21668337.
^ Carr JA, Silverman N (1999). "The heparin-protamine interaction. A review.". J Cardiovasc Surg (Torino) 40 (5): 659–66. PMID 10596998.
^ Weiler JM, Freiman P, Sharath MD, Metzger WJ, Smith JM, Richerson HB et al. (1985). "Serious adverse reactions to protamine sulfate: are alternatives needed?". J Allergy Clin Immunol 75 (2): 297–303. doi:10.1016/0091-6749(85)90061-2. PMID 2857186.
^ Byun Y, Chang LC, Lee LM, Han IS, Singh VK, Yang VC (2000). "Low molecular weight protamine: a potent but nontoxic antagonist to heparin/low molecular weight protamine". Asaio J. 46 (4): 435–9. doi:10.1097/00002480-200007000-00013. PMID 10926141.
^ Kenneth Cornetta, W.French Anderson (1989). "Protamine sulfate as an effective alternative to polybrene in retroviral-mediated gene-transfer: implications for human gene therapy". Journal of Virological Methods 23 (2): 187–194. http://www.sciencedirect.com/science/article/pii/0166093489901328.
^ Sorgi, F L., et. al (1997). "Protamine sulfate enhances lipid-mediated gene transfer". Gene Therapy 4 (9): 961–968. http://www.nature.com/gt/journal/v4/n9/pdf/3300484a.pdf.
^ Martins RP, Ostermeier GC, Krawetz SA (December 2004). "Nuclear matrix interactions at the human protamine domain: a working model of potentiation". J. Biol. Chem. 279 (50): 51862–8. doi:10.1074/jbc.M409415200. PMID 15452126.
^ Vilfan ID, Conwell CC, Hud NV (May 2004). "Formation of native-like mammalian sperm cell chromatin with folded bull protamine". J. Biol. Chem. 279 (19): 20088–95. doi:10.1074/jbc.M312777200. PMID 14990583.
^ Biegeleisen K (August 2006). "The probable structure of the protamine-DNA complex". J. Theor. Biol. 241 (3): 533–40. doi:10.1016/j.jtbi.2005.12.015. PMID 16442565.

[edit] External links

Protamines at the US National Library of Medicine Medical Subject Headings (MeSH)
V03AB14

Antidotes (V03AB)

Nervous
system

Nerve agent / Organophosphate poisoning	Atropine^# Biperiden Diazepam^# Oximes Obidoxime Pralidoxime see also: Cholinesterase

Barbiturate overdose	Bemegride Ethamivan

Benzodiazepine overdose	Cyprodenate Flumazenil

GHB overdose	Physostigmine SCH-50911

Opioid overdose	Diprenorphine Doxapram Nalmefene Nalorphine Naloxone^# Naltrexone

Reversal of neuromuscular blockade	Sugammadex

Cardiovascular

Beta blocker	Glucagon

Digoxin toxicity	Digoxin Immune Fab

Heparin	Protamine^#

Other

Arsenic poisoning	Dimercaprol^# Succimer

Cyanide poisoning	4-Dimethylaminophenol Hydroxocobalamin nitrite Amyl nitrite Sodium nitrite^# Sodium thiosulfate^#

Hydrofluoric acid	Calcium gluconate^#

Methanol / Ethylene glycol poisoning	Ethanol Fomepizole

Paracetamol toxicity (Acetaminophen)	Acetylcysteine^# Glutathione Methionine^#

Toxic metals (cadmium lead mercury thallium)	Dimercaprol^# Edetates Prussian blue^#

Other	iodine-131 Potassium iodide Methylthioninium chloride^# oxidizing agent Potassium permanganate Prednisolone/promethazine

Emetic

^#WHO-EM
^‡Withdrawn from market
Clinical trials:
- ^†Phase III
- ^§Never to phase III

M: TOX

gen / txn

pto

ant

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.

Protamine P1 Provide feedback

No Pfam abstract.

External database links

PANDIT:	PF00260
PROSITE:	PDOC00047
Pseudofam:	PF00260
SYSTERS:	Protamine_P1

This tab holds annotation information from the InterPro database.

InterPro entry IPR000221

Protamines are small, highly basic proteins, that substitute for histones in sperm chromatin during the haploid phase of spermatogenesis. They pack sperm DNA into a highly condensed, stable and inactive complex. There are two different types of mammalian protamine, called P1 and P2. P1 has been found in all species studied, while P2 is sometimes absent. There seems to be a single type of avian protamine whose sequence is closely related to that of mammalian P1 [PUBMED:2808336].

Gene Ontology

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

Cellular component	nucleus (GO:0005634)
Cellular component	nucleosome (GO:0000786)
Molecular function	DNA binding (GO:0003677)
Biological process	spermatogenesis (GO:0007283)

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
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
HTML: an HTML page showing the whole alignment.Please note: full Pfam alignments can be very large. These HTML views are extremely large and often cause problems for browsers. Please use either jalview or the Pfam viewer if you have trouble viewing the HTML version
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.
Pfam viewer: an HTML-based viewer that uses DAS to retrieve alignment fragments on request

Reformatting

You can download (or view in your browser) a text representation of a Pfam alignment in various formats:

Selex
Stockholm
FASTA
MSF

You can also change the order in which sequences are listed in the alignment, change how insertions are represented, alter the characters that are used to represent gaps in sequences and, finally, choose whether to download the alignment or to view it in your browser directly.

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 (14)	Full (147)	Representative proteomes				NCBI (97)	Meta (0)
	Seed (14)	Full (147)	RP15 (1)	RP35 (1)	RP55 (1)	RP75 (9)	NCBI (97)	Meta (0)
Jalview	View	View	View	View	View	View	View
HTML	View	View	View	View	View	View
PP/heatmap	₁	View	View	View	View	View
Pfam viewer	View	View

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

Key: available, not generated, — not available.

Format an alignment

	Seed (14)	Full (147)	Representative proteomes				NCBI (97)	Meta (0)
	Seed (14)	Full (147)	RP15 (1)	RP35 (1)	RP55 (1)	RP75 (9)	NCBI (97)	Meta (0)
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 (14)	Full (147)	Representative proteomes				NCBI (97)	Meta (0)
	Seed (14)	Full (147)	RP15 (1)	RP35 (1)	RP55 (1)	RP75 (9)	NCBI (97)	Meta (0)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download
Gzipped	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

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:

Prosite

Previous IDs:

protamine_P1;

Type:

Family

Author:

Finn RD

Number in seed:

14

Number in full:

147

Average length of the domain:

47.40 aa

Average identity of full alignment:

74 %

Average coverage of the sequence by the domain:

96.52 %

HMM information

HMM build commands:

build method: hmmbuild --amino -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	20.7	20.6
Noise cut-off	17.2	17.6

Model length:

51

Family (HMM) version:

15

Download:

download the raw HMM for this family

Species distribution

Sunburst
Tree

Sunburst controls

Show

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.

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:

superkingdom
kingdom
phylum
class
order
family
genus
species

Colouring and labels

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.

Anomalies in the taxonomy tree

There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.

Missing taxonomic levels

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.

Too many species/sequences

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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Tree controls

Hide

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:

show/hide the summary boxes
highlight species that are represented in the seed alignment
expand/collapse the tree or expand it to a given depth
select a sub-tree or a set of species within the tree and view them graphically or as an alignment
save a plain text representation of the tree

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Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: Protamine_P1 (PF00260)

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