Factor XIa: Difference between revisions

==Coagulation Factor XIa==

===Introduction===

'''Factor XIa''' is unique protease derived from the activation of the coagulation zymogen, factor XI. Factor XIa partcipates in the procoagulant response via contact activation pathway. Synthesized by the liver similar to most vitamin K-dependent coagulation proteins, the zymogen, factor XI circulates in plasma as a 160 kDa disulfide-linked homodimer in complex with high molecular weight kininogen (HK)<ref>PMID:915004</ref>. Studies show that factor XI is a substrate for various plasma proteins such as  factor XIIa, thrombin, meizothrombin and factor XIa (via autoactivation). Proteolysis of the <scene name='Sandbox/Arg369-ile370/1'> Arg369-Ile370</scene> bond generates the active enzyme factor XIa which in turn cleaves its substrate factor IX to produce the serine protease factor IXa.

'''Factor XIa''' is a <scene name='Sandbox/Disulfides/1'>disulfide</scene> linked-dimer of similar amino acid composition of approximately 625 residues. The first 18 amino acid residues constitute the signal peptide whereas residues 19-387 and 388-625 represents the heavy- and light- chains of the factor XIa molecule respectively. The protein forms five main distinct domains. Beginning from the N-terminus,each dimeric subunit contains 4 apple domains (<scene name='Sandbox/A1_domain/1'>A1</scene>, <scene name='Sandbox/A2_domain/1'>A2</scene>, <scene name='Sandbox/A3_domain/1'>A3</scene> and <scene name='Sandbox/A4_domain/2'>A4</scene>) which are characterized by approximately 90 or 91 amino acid residues. Protein-protein interactions are thought to be the primary role of the apple domains. The <scene name='Sandbox/A3_domain/1'>A3 domain</scene> is reported to mediate binding to platelet glycoprotein Ib (GPIb)<ref>PMID:15317813</ref> as well as interactions with exosite I of thrombin, and kringle 2 domain of prothrombin. The <scene name='Sandbox/A1_domain/1'>A1 domain</scene> is the main site of factor XI protein-protein interaction when in complex with high molecular weight kininogen<ref>PMID:7686159</ref>. The C-terminus (heavy chain) of factor XIa contain a trypsin-like catalytic domain <ref>PMID:893417</ref>. Together with Prekallikrein (PK) a monomeric homolog of factor XIa, they belong to the PAN (plasminogen, apple, nematode) module family which all have a conserved N-terminal apple domain found in hepatocyte growth factor and plasminogen <ref>PMID:10561497</ref>.  

'''β-turn'''

[[Image:Beta_turn.jpg | thumb |400px| β-turn in factor XIa]]

The globular and compact nature of factor XIa as opposed to an elongated form (prevalent in vitamin K-dependent serine proteases) could in part be attributed to the abundance of β-turns in the protein. β-turns are characterized by a hydrogen bond involving carbonyl oxygen (C=O) of residue (i) and amide hydrogen (NH) of residue (i+3). The heavy chain has ~4 β-turns and one such β-turn (residues 566-568) is found in the light chain of factor XIa (see figure on the right). This β-turn based on distance between Cαi-Cαi+3 (5.4Å) and the measured dihedral angles: φ(i+1)=50.5°, ψ(i+1)=47.2° and φ(i+2)=90° and ψ(i+2)=15.8°could be classified as '''Type I′''' according to Hutchinson and Thornton (1994)<ref>PMID:7756980</ref>.

'''α-Helix'''

[[Image:Ncap.png | thumb |400px| N-terminal capping motif in factor XIa]]

In addition to β-sheets, factor XIa folds into a number of α-helices. The heavy chain region has ~8 helix repeats while about 5 helix repeats are present in the light chain region of the protein. Helices that are capped at either the N or C-terminals forming a capping motif. '''''Helix Capping Motif''''' display a unique hydrogen bonding pattern in addition to hydrophobic interactions. Factor XIa has an N-terminal capping motif in the light chain: residues 523-531 form an α-helix (see the figure on the right). Thr-532 is the Ncap and Glu-526 is found at the N3 position of the helix. The N-terminal capping motif shown in the figure (right hand side of page) appears to belong  to the '''capping box''' classification. Thus the side chain of Thr-523 forms a H-bond with the backbone of the N3 however, H-bonding between the side chain of N3 and backbone of Ncap is absent. Next to the C-terminal Cys356 of the <scene name='Sandbox/A4_domain/2'>A4</scene> domain,factor XI assumes an interesting helical element the <scene name='Sandbox/310_helix_of_a4_domain/1'>3-10 helical structure</scene>. Originally classified as a type III turn, the <scene name='Sandbox/310_helix_of_a4_domain/1'>3-10 helical structure</scene> is tight and contains 3 residues (357-360) per turn.  

===Active Site Residues===

Similar to other members of the serine protease family, factor XIa bears the two β-barrels topology unique to chymotrypsin-like proteases which are linked through a central loop. Thus cleavage at <scene name='Sandbox/Arg369-ile370/1'> Arg369-Ile370</scene> of the zymogen generates a functional enzyme. the [http://en.wikipedia.org/wiki/Catalytic_triad catalytic triad] residues Ser-557, Asp-462 and His-413 constitute the <scene name='Sandbox/Active_site/2'>active site</scene> of factor XIa.

Thus, the Nε2 of His57 acts a the general base to enhance the nucleophilicity of the catalytic Ser195-OH by abstracting its proton. The acylation phase occurs with the attack of the carbonyl of the scissile bond generation the transition state intermediate. Also known as the tetrahedral intermediate, the negative oxygen ion in this structure is thought to be stabilized by the oxyanion hole formed by the amide backbone hydrogens of Ser195 and Gly193. The collapse of this intermediate involves the abstraction of the Nε2-H of His57 (general acid) by the leaving group P1' nitrogen of the substrate forming the first product and an acylenzyme intermediate<ref>PMID:332063</ref>.

===The Charge Relay Mechanism of serine proteases===

Blow and colleagues crystallized chymotrypsin in the presence of K2PtCL4 at a resolution of 5.8 Å and proposed a hydrogen bonding network between Asp102, His57 and Ser195<ref>PMID:5764436</ref>. Popularly known as the charge relay mechanism, Blow and colleagues proposed that, a two concerted proton transfers must occur in the transition state for the tetrahedral intermediate to be formed. Thus inaddition to His57, Asp102 acts a base to abstract a proton from the Nδ1-H of His57. On the contrary, later studies refuted the role of Asp102 as a base. Neutron diffraction studies<ref>PMID:7030393</ref> and NMR data<ref>PMID:31898</ref>revealed His57 as the only base and the presence of positive charge on the imidazole ring respectively.

===The LBHB-mediated General Base Mechanism of serine proteases===

===The His Flip Mechanism of Serine Proteases===

Studies on the central role of His57 and its orientation as regards functioning as the general base and general acid, led to the proposal of the '''His Moving''' mechanism. Earlier kinetics studies using subtilisin as the model organism revealed that, whereas the kcat for ester hydrolysis in 50% N,N-dimethylformamide (DMF) remains unchanged, hydrolysis of amides was 2-fold lower.

Amino acid substitutions such as Phe283Leu<ref>PMID:17257616</ref> and Gly350Glu<ref>PMID:15026311 </ref> in the heavy chain results in an increased dimer dissociation and absence of dimer formation respectively. Some mutations in the factor XI A4 domain and catalytic domains are inherited as autosomal recessive bleeding diathesis however, other amino acid substitutions are exert a dominant negative effect on the normal monomer subunit affecting protein secretion. Studies suggest that dimerization is not affected under dominant negative mutations but the mutant subunit traps the normal subunit in the cell preventing its secretion. Majority of these missense mutations:Ser225Phe, Cys398Tyr, Gly400Val and Trp569Ser which produce a dominant negative effect involves residues found in the catalytic domain<ref>PMID:15026311 </ref>.

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==References==

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