Summary: Staphylokinase/Streptokinase family

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Wikipedia: Streptokinase
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Streptokinase Edit Wikipedia article

Streptokinase C

Complex of Catalytic Domain of Human Plasmin and Streptokinase; structure derived from PDB file 1BML.
Identifiers
Symbol	skc
Entrez	8110746
PDB	1BML
UniProt	P00779
Other data
EC number	3.4.24.29

Staphylokinase/Streptokinase family

Structure of staphylokinase, a plasminogen activator.^[1]

Identifiers

Symbol

Staphylokinase

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

Streptokinase (SK), a protein secreted by several species of streptococci can bind and activate human plasminogen. SK is used as an effective and inexpensive thrombolysis medication in some cases of myocardial infarction (heart attack)^[2] and pulmonary embolism.^[3] Streptokinase belongs to a group of medications known as fibrinolytics, and complexes of streptokinase with human plasminogen can hydrolytically activate other unbound plasminogen by activating through bond cleavage to produce plasmin. There are three domains to Streptokinase, denoted α (residues 1–150), β (residues 151–287), and γ (residues 288–414). Each domain binds plasminogen, although none can activate plasminogen independently.^[4]

[edit] Mechanism of action

Proposed counterion for Asp740 is Lys698 create salt-bridge; structure derived from PDB file 1BML

Youtube Substrate Enzyme Mechanism Movie

Plasmin is produced in the blood to break down fibrin, the major constituent of blood thrombi, therefore dissolving clots once they have fulfilled their purpose in stopping bleeding. Extra production of plasmin caused by streptokinase breaks down unwanted blood clots, for example, in the lungs (pulmonary embolism). The usual activation of Plasminogen (Plgn) is by proteolysis of the Arg561—Val562 bond.^[5] The amino group of Val562 then forms a salt-bridge with Asp740, which triggers a conformational change producing the active protease Plasmin (Pm). When (SK) is present, it binds to Plgn to form a complex (SK. Plgn) that converts substrate Plgn to Pm. Residues 1–59 of SK regulate its capacity to induce an active site in bound Pg by a nonproteolytic mechanism and to activate substrate Pg in a fibrin-independent manner. This complex subsequently rearranges to an active complex although the Arg561–Val562 bond remains intact. Therefore another residue must substitute for the free amino group of Val562 and provide a counterion for Asp740 in this active complex.^[6] Two candidates for this counterion have been suggested: Ile1 of streptokinase and Lys698 of Plgn. Deletion of Ile1 of SK markedly inhibits its capacity to induce an active site in plasminogen, which supports the hypothesis that establishment of a salt bridge between Ile1 of SK and Asp740 of plasminogen is necessary for SK to induce an active site in plasminogen by a nonproteolytic mechanism.^[7] In contrast with the Ile1 substitutions, the Lys698 mutations also decreased the dissociation constant of the SK complex by 15 to 50 fold. These observations suggest that Lys698 is involved in formation of the initial SK·Plgn complex.^[8]

[edit] Administration

It is given intravenously as soon as possible after the onset of a heart attack to dissolve clots in the arteries of the heart wall. Thus it reduces the amount of damage to the heart muscle. As Streptokinase is a bacterial product, the body has the ability to build up an immunity to it. Therefore, it is recommended that this medication should not be used again after four days from the first administration, as it may not be as effective and can also cause an allergic reaction. For this reason, it is usually given only for a person's first heart attack. Further thrombotic events could be treated with Tissue plasminogen activator (tPA). Overdose of streptokinase or tPA can be treated with aminocaproic acid.

Laboratory findings in various platelet and coagulation disorders (V - T)
Condition	Prothrombin time	Partial thromboplastin time	Bleeding time	Platelet count
Vitamin K deficiency or warfarin	Prolonged	Normal or mildly prolonged	Unaffected	Unaffected
Disseminated intravascular coagulation	Prolonged	Prolonged	Prolonged	Decreased
Von Willebrand disease	Unaffected	Prolonged	Prolonged	Unaffected
Hemophilia	Unaffected	Prolonged	Unaffected	Unaffected
Aspirin	Unaffected	Unaffected	Prolonged	Unaffected
Thrombocytopenia	Unaffected	Unaffected	Prolonged	Decreased
Liver failure, early	Prolonged	Unaffected	Unaffected	Unaffected
Liver failure, end-stage	Prolonged	Prolonged	Prolonged	Decreased
Uremia	Unaffected	Unaffected	Prolonged	Unaffected
Congenital afibrinogenemia	Prolonged	Prolonged	Prolonged	Unaffected
Factor V deficiency	Prolonged	Prolonged	Unaffected	Unaffected
Factor X deficiency as seen in amyloid purpura	Prolonged	Prolonged	Unaffected	Unaffected
Glanzmann's thrombasthenia	Unaffected	Unaffected	Prolonged	Unaffected
Bernard-Soulier syndrome	Unaffected	Unaffected	Prolonged	Decreased or unaffected
Factor XII deficiency	Unaffected	Prolonged	Unaffected	Unaffected

[edit] Current research applications

Streptokinase may find a use in helping to prevent postoperative adhesions, a common complication of surgery, especially abdominal surgery (appendectomy, gall stones, hysterectomy, etc.) One study using animal models (rats) found that when used with a PHBV membrane drug-delivery system, it was 90 percent effective in preventing adhesions.^[9]

[edit] Marketing

It is marketed in Chile as Streptase by Alpes Selection, under license of ZLB Behring from Marburg, Germany.

Available in Viet Nam under the name Mutose. Available in Cuba, Venezuela, Ecuador and other Latin American countries under the trademark Heberkinasa, commercialized by Heber Biotech, Havana, Cuba. Available in India under the name STPase by Cadila Pharmaceuticals Limited.

[edit] References

^ Rabijns A, De Bondt HL, De Ranter C (May 1997). "Three-dimensional structure of staphylokinase, a plasminogen activator with therapeutic potential". Nat. Struct. Biol. 4 (5): 357–60. doi:10.1038/nsb0597-357. PMID 9145104.
^ Sikri N, Bardia A (2007). "A history of streptokinase use in acute myocardial infarction". Tex Heart Inst J 34 (3): 318–27. PMC 1995058. PMID 17948083. //www.ncbi.nlm.nih.gov/pmc/articles/PMC1995058/.
^ Meneveau N, Schiele F, Vuillemenot A, et al. (July 1997). "Streptokinase vs alteplase in massive pulmonary embolism. A randomized trial assessing right heart haemodynamics and pulmonary vascular obstruction". Eur. Heart J. 18 (7): 1141–8. PMID 9243149. http://eurheartj.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=9243149.
^ Mundada L, Prorok, M (2003). "Structure-Function Analysis of Streptokinase Amino Terminus". Journal of Biological Chemistry 278 (3): 24421–24427. doi:10.1074/jbc.M301825200. PMID 5746739. http://www.jbc.org/content/278/27/24421.full.
^ Young, K Shi, G (1997). "Plasminogen Activation by Streptokinase iva a Unique Mechanism". Texas Heart Institute journal / from the Texas Heart Institute of St. Luke's Episcopal Hospital, Texas Children's Hospital 34 (3): 1–13. PMID 5643782. http://www.jbs.org/content/273/5/3/3110.full.^{[dead link]}
^ Loy, J, Lin,X (2001). "Domain Interactions between Streptokinase and Human Plasminogen". Biochemistry 48 (3): 14686–14695. doi:10.1021/bio11309d. PMID 45675. http://pubs.acs.org/doi/full/10.1021/bio11309d?cookieSet=1.
^ Wang, S, Reed, GL, Hedstrom, L (1999). "Deletion of Ile1 changes the mechanism of streptokinase: evidence for the molecular sexuality hypothesis". Biochemistry 38 (16): 5232–5240. doi:10.1021/bi981915h. PMID 10213631. http://pubs.acs.org/doi/abs/10.1021/bi981915h.
^ Wang X, Lin X (1998). "Crystal Structure of Catalytic Domain of Human Plasmin Complexed with Streptokinase". Science Magazine 281 (3): 1662–1665. PMID 76543. http://www.sciencemag.org/cgi/content/full/281/5383/1662.
^ A. Yagmurlu, M. Barlas, I. Gursel, I.H. Gokcora (2003). "Reduction of Surgery-Induced Peritoneal Adhesions by Continuous Release of Streptokinase from a Drug Delivery System". Eur Surg Res 35 (1): 46–49. doi:10.1159/000067035. PMID 12566787.

Antithrombotics (thrombolytics, anticoagulants and antiplatelet drugs) (B01)

Antiplatelet drugs

Glycoprotein IIb/IIIa inhibitors	Abciximab Eptifibatide Tirofiban

ADP receptor/P2Y₁₂ inhibitors	thienopyridines Clopidogrel Prasugrel Ticlopidine nucleotide/nucleoside analogs Cangrelor Elinogrel Ticagrelor

Prostaglandin analogue (PGI2)	Beraprost Iloprost Prostacyclin Treprostinil

COX inhibitors	Acetylsalicylic acid/Aspirin^# Aloxiprin Carbasalate calcium Indobufen Triflusal

Thromboxane inhibitors	thromboxane synthase inhibitors Dipyridamole Picotamide receptor antagonist Terutroban^†

Phosphodiesterase inhibitors	Cilostazol Dipyridamole Triflusal

Other	Cloricromen Ditazole

Anticoagulants

Vitamin K antagonists
(inhibit II, VII, IX, X)

Factor Xa inhibitors
(with some II inhibition)

Heparin group/ glycosaminoglycans/ (bind antithrombin)	low molecular weight heparin Bemiparin Certoparin Dalteparin Enoxaparin Nadroparin Parnaparin Reviparin Tinzaparin oligosaccharides Fondaparinux Idraparinux heparinoid Danaparoid Dermatan sulfate Sulodexide

Direct Xa inhibitors	xabans Apixaban Betrixaban Edoxaban Otamixaban Rivaroxaban

Direct thrombin (II) inhibitors

Other

Thrombolytic drugs/
fibrinolytics

Non-medicinal

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

M: MYL

cell/phys (coag, heme, immu, gran), csfs

rbmg/mogr/tumr/hist, sysi/epon, btst

drug (B1/2/3+5+6), btst, trns

Endopeptidases: serine proteases/serine endopeptidases (EC 3.4.21)

Digestive enzymes

Coagulation

factors: Thrombin
Factor VIIa
Factor IXa
Factor Xa
Factor XIa
Factor XIIa
Kallikrein
- PSA
- KLK1
- KLK2
- KLK3
- KLK4
- KLK5
- KLK6
- KLK7
- KLK8
- KLK9
- KLK10
- KLK11
- KLK12
- KLK13
- KLK14
- KLK15

Complement system

Other immune system

Venombin

Other

B
enzm
1.1
- 2
- 3
- 4
- 5
- 6
- 7
- 8
- 10
- 11
- 13
- 14
- 15-18
2.1
- 2
- 3
- 4
- 5
- 6
- 7
- 8
2.7.10
2.7.11-12
3.1
- - 3.1.3.48
- 2
- 3
- 4
  - 3.4.21
- 5
- 6
- 7
- 22
- 23
- 24
4.1
- 2
- 3
- 4
- 5
- 6
5.1
- 2
- 3
- 4
- 99
6.1-3
- 4
- 5-6

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.

Staphylokinase/Streptokinase family Provide feedback

No Pfam abstract.

Literature references

Rabijns A, De Bondt HL, De Ranter C; , Nat Struct Biol 1997;4:357-360.: Three-dimensional structure of staphylokinase, a plasminogen activator with therapeutic potential. PUBMED:9145104 EPMC:9145104

External database links

PANDIT:	PF02821
Pseudofam:	PF02821
SCOP:	2sak
SYSTERS:	Staphylokinase

This tab holds annotation information from the InterPro database.

InterPro entry IPR004093

Staphylokinases and streptokinases are not proteases. They are involved in plasminogen activation. The three-dimensional structure of streptokinase is believed to contain two independently folded domains, each homologous to serine proteases [PUBMED:6760891].

Gene Ontology

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

Molecular function

serine-type endopeptidase activity (GO:0004252)

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:

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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

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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 (11)	Full (458)	Representative proteomes				NCBI (340)	Meta (0)
	Seed (11)	Full (458)	RP15 (1)	RP35 (4)	RP55 (7)	RP75 (11)	NCBI (340)	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 (11)	Full (458)	Representative proteomes				NCBI (340)	Meta (0)
	Seed (11)	Full (458)	RP15 (1)	RP35 (4)	RP55 (7)	RP75 (11)	NCBI (340)	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 (11)	Full (458)	Representative proteomes				NCBI (340)	Meta (0)
	Seed (11)	Full (458)	RP15 (1)	RP35 (4)	RP55 (7)	RP75 (11)	NCBI (340)	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:

PDB

Previous IDs:

none

Type:

Domain

Author:

Bateman A, Griffiths-Jones SR

Number in seed:

11

Number in full:

458

Average length of the domain:

122.40 aa

Average identity of full alignment:

32 %

Average coverage of the sequence by the domain:

79.68 %

HMM information

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	21.7	21.7
Trusted cut-off	21.9	31.2
Noise cut-off	21.5	21.1

Model length:

125

Family (HMM) version:

11

Download:

download the raw HMM for this family

Species distribution

Sunburst
Tree

Sunburst controls

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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.

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

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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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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 are 2 interactions for this family. More...

Staphylokinase Trypsin

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 Staphylokinase domain has been found. There are 31 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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Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: Staphylokinase (PF02821)

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