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<StructureSection load='1ppb' size='350' side='right' scene='' caption='Human thrombin large (red) and small ( | <StructureSection load='1ppb' size='350' side='right' scene='' caption='Human thrombin large (red) and small (green) subunits complex with prolinamide derivative (PDB code [[1ppb]])'> | ||
__TOC__ | |||
==Introduction== | ==Introduction== | ||
'''Thrombin''' (Thr) is a serine protease. '''Prothrombin''' (PThr) is cleaved to form Thr in the coagulation cascade. The first step of the cleavage is at residue R320 and produces '''meizothrombin''' (MThr). Thr catalyzes the conversion of fibrinogen to the insoluble fibrin. Thr is composed of heavy chain (HC) and light chain (LC). Prethrombin-1 lacks 155 N-terminal residues of PThr and is composed of a single polypeptide chain. '''Prethrombin-2''' is the product of proteolysis of '''prethrombin-1''' by trypsin or by active factor X. P-PACK Thr is a | '''Thrombin''' (Thr) is a serine protease. '''Prothrombin''' (PThr) is cleaved by prothrombinase at 2 cleavage sites to form the 2 chains of Thr in the coagulation cascade<ref>PMID:23809130</ref>. The first step of the cleavage is at residue R320 and produces '''meizothrombin''' (MThr)<ref>PMID:22815477</ref>. Thr catalyzes the conversion of fibrinogen to the insoluble fibrin. Thr is composed of heavy chain (HC) and light chain (LC). '''Prethrombin-1''' lacks 155 N-terminal residues of PThr and is composed of a single polypeptide chain. '''Prethrombin-2''' is the product of proteolysis of '''prethrombin-1''' by trypsin or by active factor X. P-PACK Thr is a chemically modified Thr with inactivated catalytic site and active anion binding site. [[Hirudin]] is the most potent natural inhibitor of Thr ([[Sean Swale/Human Thrombin Inhibitor]]). For some more details see [[Serine Proteases]]. Prothrombin cleavage results in the creation of thrombin, a coagulative agent in plasma and is connected to fibrinolysis and platelet activation. During this process several peptides involved in the conversion are released into the plasma, and the remaining protein splits into two portions(http://www.uniprot.org/citations/3759958). It has been shown that prothrombin has a statistically significant connection to the occurrence of ischemic stroke with the presence of the G20210A mutation, though the cause was not isolated to prothrombin alone (http://www.uniprot.org/citations/15534175) (these links added by Connor Gramazio). Some additional details in<br /> | ||
* [[Ann Taylor 115]]<br /> | * [[Ann Taylor 115]]<br /> | ||
* [[Sean Swale/Human Thrombin Inhibitor]]<br /> | * [[Sean Swale/Human Thrombin Inhibitor]]<br /> | ||
* [[Thrombin heavy chain]]<br /> | * [[Thrombin heavy chain]]<br /> | ||
* [[Thrombin light chain]]<br /> | * [[Thrombin light chain]]<br /> | ||
* [[Thrombin (hebrew)]]<br /> | |||
<scene name='58/583418/Thombin_main_secondary/2'>Thrombin</scene> catalyzes the penultimate step in blood coagulation. It is activated from its [http://en.wikipedia.org/wiki/Zymogen zymogen], prothrombin, at the site of tissue injury by [[Factor_Xa | Factor Xa (FXa)]] and its cofactor [http://en.wikipedia.org/wiki/Factor_V FVa] in the presence of phospholipid membrane and calcium. Thrombin is then able to catalyze the cleavage of [[Fibrinogen | fibrinogen]] to | <scene name='58/583418/Thombin_main_secondary/2'>Thrombin</scene> catalyzes the penultimate step in blood coagulation. It is activated from its [http://en.wikipedia.org/wiki/Zymogen zymogen], prothrombin, at the site of tissue injury by [[Factor_Xa | Factor Xa (FXa)]] and its cofactor [http://en.wikipedia.org/wiki/Factor_V FVa] in the presence of phospholipid membrane and calcium. Thrombin is then able to catalyze the cleavage of [[Fibrinogen | fibrinogen]] to insoluble fibrin which spontaneously polymerizes to form a stable clot.<ref name="zero">PMID: 7023326</ref><ref name="one">PMID: 11001069</ref> Thrombin also acts as a procoagulant by: | ||
* Activating platelets through their [http://en.wikipedia.org/wiki/Protease-activated_receptor protease activated receptors (PARs)]<ref name="one"/> | * Activating platelets through their [http://en.wikipedia.org/wiki/Protease-activated_receptor protease activated receptors (PARs)]<ref name="one"/> | ||
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By balancing substrate specificity, activity, and inhibition thrombin plays a central role in the blood coagulation cascade. <ref name="three"/> | By balancing substrate specificity, activity, and inhibition thrombin plays a central role in the blood coagulation cascade. <ref name="three"/> | ||
[[Image:Substrates.png| | [[Image:Substrates.png|450px|center|thumb| Coagulation related substrates of thrombin, excluding serpin inhibitors.]] | ||
{{Clear}} | |||
==The Thrombin Life Cycle== | ==The Thrombin Life Cycle== | ||
Upon tissue damage [http://en.wikipedia.org/wiki/Tissue_factor tissue factor (TF)] is released by subendothelial cells. This interacts with circulating [[Factor_VII| FVIIa]], a zymogen-like serine protease, significantly increasing its activity. '''The FVIIa-TF complex (extrinsic Xase) activates FVII, FIX, and FX'''. The now active '''FXa cleaves prothrombin''' bound to membranes through its [http://en.wikipedia.org/wiki/Gla_domain gamma-carboxyglutamyl (Gla) domain], activating it to thrombin. | Upon tissue damage [http://en.wikipedia.org/wiki/Tissue_factor tissue factor (TF)] is released by subendothelial cells. This interacts with circulating [[Factor_VII| FVIIa]], a zymogen-like serine protease, significantly increasing its activity. '''The FVIIa-TF complex (extrinsic Xase) activates FVII, FIX, and FX'''. The now active '''FXa cleaves prothrombin''' bound to membranes through its [http://en.wikipedia.org/wiki/Gla_domain gamma-carboxyglutamyl (Gla) domain], activating it to thrombin. | ||
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==Prothrombin Activation== | ==Prothrombin Activation== | ||
[[Image:Prothrombin activation scheme_3.png| | [[Image:Prothrombin activation scheme_3.png|450px|left|thumb| Activation scheme of in vivo activation of prothrombin by FXa in the absence of FVa.]] | ||
[[Image:Prothrombin activation scheme_nofva3.png| | {{Clear}} | ||
[[Image:Prothrombin activation scheme_nofva3.png|450px|left|thumb| Activation scheme of in vivo activation of prothrombin by the prothrombinase complex in presence of calcium and a phospholipid bilayer]] | |||
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Prothrombin is the zymogen form of thrombin. From N-terminal to C-terminal it consists of a Gla domain, two kringle domains, and a catalytic domain. The Gla domain is formed by vitamin K dependent carboxylation of glutamate residues.<ref>PMID: 18374193</ref> | Prothrombin is the zymogen form of thrombin. From N-terminal to C-terminal it consists of a Gla domain, two kringle domains, and a catalytic domain. The Gla domain is formed by vitamin K dependent carboxylation of glutamate residues.<ref>PMID: 18374193</ref> | ||
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==Structure and Function== | ==Structure and Function== | ||
[[Image:Electrostatic labeled.png| | [[Image:Electrostatic labeled.png|450px|right|thumb| Thrombin (1PPB) overlayed with electrostatic surface. Structural features 60-loop, γ-loop, exosite I, and exosite II labeled]] | ||
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Thrombin is a α/β heterodimer composed of a 36 amino acid A chain and 259 amino acid B chain connected by a <scene name='58/583418/Disulfides_nospin/1'>disufide</scene> bridge between Cys1 and Cys122, in addition to 3 other intrachain disulfide bonds.<ref name='eight'>PMID: 2583108</ref> Its overall fold is similar to trypsin and chymotrypsin and it belongs to the [http://merops.sanger.ac.uk/cgi-bin/famsum?family=s1 peptidase S1 protease family]<ref>PMID: 18768474</ref>. It is an overall spherical protein with approximate dimensions of 45 Å X 45 Å X 50 Å.<ref name='eight'/> | Thrombin is a α/β heterodimer composed of a 36 amino acid A chain and 259 amino acid B chain connected by a <scene name='58/583418/Disulfides_nospin/1'>disufide</scene> bridge between Cys1 and Cys122, in addition to 3 other intrachain disulfide bonds.<ref name='eight'>PMID: 2583108</ref> Its overall fold is similar to trypsin and chymotrypsin and it belongs to the [http://merops.sanger.ac.uk/cgi-bin/famsum?family=s1 peptidase S1 protease family]<ref>PMID: 18768474</ref>. It is an overall spherical protein with approximate dimensions of 45 Å X 45 Å X 50 Å.<ref name='eight'/> | ||
Important structural features include: | Important structural features include: | ||
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The <scene name='58/583418/Sodium_binding_loop/1'>sodium binding site</scene> is formed by the 180s- and 220s- loops. Na+ is bound by the backbone oxygens of Arg221a and Lys224 in addition to four water molecules in a classic [http://chemwiki.ucdavis.edu/Inorganic_Chemistry/Crystal_Field_Theory/High_Spin_and_Low_Spin_Complexes#Octahedral_Geometry octahedral geometry]<ref>PMID: 9108691</ref>. Through the covelent disulfide linkage between Cys220 and Cys 191 the sodium binding site is linked to Ser195 and the oxyanion hole. | The <scene name='58/583418/Sodium_binding_loop/1'>sodium binding site</scene> is formed by the 180s- and 220s- loops. Na+ is bound by the backbone oxygens of Arg221a and Lys224 in addition to four water molecules in a classic [http://chemwiki.ucdavis.edu/Inorganic_Chemistry/Crystal_Field_Theory/High_Spin_and_Low_Spin_Complexes#Octahedral_Geometry octahedral geometry]<ref>PMID: 9108691</ref>. Through the covelent disulfide linkage between Cys220 and Cys 191 the sodium binding site is linked to Ser195 and the oxyanion hole. | ||
'''Thrombin''' is a "trypsin-like" serine protease. Its structure (PDB code [[1ppb]]) is shown here with a peptide chloroketone inhibitor (PPACK). The thrombin A chain (cleaved N terminal fragement) is shown in cyan and the B chain is shown in red. The <scene name='Serine_Protease/Active_site/2'>Active site</scene> is made up of a catalytic triad of Ser195, His57 and Asp102, backed up by Ser214. The peptide chloroketone inhibitor (PPACK) is shown in purple. A closeup shows the <scene name='Serine_Protease/Activation_site/2'>activation site</scene> at which the sidechain of Asp194 makes a salt link with the N-terminus at residue 16, newly formed when the A chain is cleaved in the zymogen-to-enzyme activation process. The specificity pocket is on one side of the throat of the domain 2 beta barrel, and the activation site is close next to it. | |||
The B chain consists of <scene name='Serine_Protease/Domains/1'>two domains</scene>. As is true for all of the "trypsin-like" serine proteases, each of the two thrombin domains consists mainly of a 6-stranded, antiparallel beta barrel. The specificity pocket (here filled with the Lys sidechain of the PPACK inhibitor) is in one side of the throat of the domain 2beta barrel, and the activation site is close next to it. | |||
==Allostery== | ==Allostery== | ||
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[[Image:Capping.png|450px|center|thumb| “Capping box” motif in alpha thrombin (PDB: 1PPB) represented by His230 (Ncap) side chain and main chain hydrogen bonded with the backbone nitrogen of Arg233 (N3). An additional feature is a weak hydrophobic interaction between Thr229 (N’) and Val234 (N4) termed the “hydrophobic staple.” This motif derives it’s name from the box shaped hydrogen bonding pattern.]] | [[Image:Capping.png|450px|center|thumb| “Capping box” motif in alpha thrombin (PDB: 1PPB) represented by His230 (Ncap) side chain and main chain hydrogen bonded with the backbone nitrogen of Arg233 (N3). An additional feature is a weak hydrophobic interaction between Thr229 (N’) and Val234 (N4) termed the “hydrophobic staple.” This motif derives it’s name from the box shaped hydrogen bonding pattern.]] | ||
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[[Image:Cation pi.png|450px|center|thumb| A cation-π interaction between Trp128 and Arg 129 in alpha thrombin (PDB: 2BDY). The guanidinium carbon is 3.6 angstroms from the top edge of the Trp. It is expected that the epsilon nitrogen forms the primary cation-π interaction. The electrostatic and Van der Waals interaction energies were calculated to be -3.29 kcal/mol and -3.08 kcal/mol respectively by the CaPTURE program (http://capture.caltech.edu/result.cgi).]] | [[Image:Cation pi.png|450px|center|thumb| A cation-π interaction between Trp128 and Arg 129 in alpha thrombin (PDB: 2BDY). The guanidinium carbon is 3.6 angstroms from the top edge of the Trp. It is expected that the epsilon nitrogen forms the primary cation-π interaction. The electrostatic and Van der Waals interaction energies were calculated to be -3.29 kcal/mol and -3.08 kcal/mol respectively by the CaPTURE program (http://capture.caltech.edu/result.cgi).]] | ||
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== 3D Structures of thrombin== | == 3D Structures of thrombin== | ||
[[Thrombin 3D Structures]] | |||
</StructureSection> | |||
== References == | == References == | ||
<references/> | <references/> | ||
With participation by [[User:Cody Couperus]] | |||
[[Category:Topic Page]] | [[Category:Topic Page]] | ||