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Factor IX: Difference between revisions

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<StructureSection load='3lc3' size='350' side='right' scene='' caption='Human factor IX residues 133-188 (green), residues 227-461 (grey) complex with benzothiophene inhibitor and Ca+2 ions (green) (PDB code [[3lc3]])'>
<StructureSection load='3lc3' size='350' side='right' scene='' caption='Human factor IX residues 133-188 (green), residues 227-461 (grey) complex with benzothiophene inhibitor and Ca+2 ions (green) (PDB code [[3lc3]])'>
== Function==


<span style="color:Brown">'''<scene name='Factor_IX/Ixstructure/4'>Factor IX</scene>'''</span> ('''plasma thromboplastin component''', '''Christmas factor''', or '''hemophilia B factor''') is a 57-kDa vitamin K-dependent procoagulant glycoprotein. It is synthesized by the liver hepatocyte as a [[pre-prozymogen]] that requires extensive posttranslational modification<ref>PMID:2169923</ref>. The [[pre-prozymogen]] contains a pre-peptide (hydrophobic signal peptide) at its amino terminal that transports the growing polypeptide into the lumen of the Endoplasmic Reticulum. Once inside the ER, this signal peptide is cleaved by a signal peptidase.   
<span style="color:Brown">'''<scene name='Factor_IX/Ixstructure/4'>Factor IX</scene>'''</span> ('''plasma thromboplastin component''', '''Christmas factor''', or '''hemophilia B factor''') is a 57-kDa vitamin K-dependent procoagulant glycoprotein. It is synthesized by the liver hepatocyte as a [[pre-prozymogen]] that requires extensive posttranslational modification<ref>PMID:2169923</ref>. The [[pre-prozymogen]] contains a pre-peptide (hydrophobic signal peptide) at its amino terminal that transports the growing polypeptide into the lumen of the Endoplasmic Reticulum. Once inside the ER, this signal peptide is cleaved by a signal peptidase.   
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The first cleavage is at Arg145, generating an inactive FIXα. The second cleavage is at Arg180 results in a catalytically active molecule FIXaβ. This resulting heterodimer is held by a disulfide bridge at Cys132-Cys289. The serine protease contains a catalytic triad of <scene name='Factor_IX/Ixstructure_catalytictriad/3'>His221, Asp269, and Ser365</scene><ref>PMID:9374470</ref>. Upon cleave at Arg180, Val181 can form a salt bridge with Asp364, which is a characteristic of active serine proteases. The active FIXa, can then interact with its cofactor, FVIIIa, to form a membrane-bound Xase complex, which activated FX to FXa.
The first cleavage is at Arg145, generating an inactive FIXα. The second cleavage is at Arg180 results in a catalytically active molecule FIXaβ. This resulting heterodimer is held by a disulfide bridge at Cys132-Cys289. The serine protease contains a catalytic triad of <scene name='Factor_IX/Ixstructure_catalytictriad/3'>His221, Asp269, and Ser365</scene><ref>PMID:9374470</ref>. Upon cleave at Arg180, Val181 can form a salt bridge with Asp364, which is a characteristic of active serine proteases. The active FIXa, can then interact with its cofactor, FVIIIa, to form a membrane-bound Xase complex, which activated FX to FXa.


See [[Colored & Bioluminescent Protein]].
For activated factor IX see [[Factor IXa]].
__TOC__
 
See [[Colored & Bioluminescent Protein]].<br />
[[Mg-8 may contribute to the binding to factors VIIa and X]]<br />
[[Conformation-specific anti-Factor IX antibodies]].




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== γ-Carboxyglutamic Acid (Gla) Domain ==
== γ-Carboxyglutamic Acid (Gla) Domain ==
   
   
The Gla domain is situated at the N-terminus of coagulation factor IX, and is evolutionary conserved in other vitamin K dependent proteins such as factor VII, X, and prothrombin. A <scene name='Factor_IX/Gladomain_glamgca/3'>Gla domain</scene> is made up of 10-13 of γ-carboxyglutamic acid residues and requires both <scene name='Factor_IX/Gladomain_1/8'>Ca2+ and Mg2+ </scene> ions for membrane association and stabilization of its active three dimensional conformation <ref>PMID:3511981</ref>.  
The Gla domain is situated at the N-terminus of coagulation factor IX, and is evolutionary conserved in other vitamin K dependent proteins such as factor VII, X, and prothrombin. A <scene name='Factor_IX/Gladomain_glamgca/3'>Gla domain</scene> is made up of 10-13 of γ-carboxyglutamic acid residues and requires both <scene name='Factor_IX/Gladomain_1/8'>Ca2+ and Mg2+ </scene> ions for membrane association and stabilization of its active three dimensional conformation <ref>PMID:3511981</ref>.  
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This structure emphasizes the possible role of magnesium in Gla domain binding to membrane surfaces. However upon examination of the calcium bound Factor IX-(1-46) complex revealed that the calcium coordination within this FIX Gla domain structure differs from other vitamin K-dependent proteins (prothrombin, Factor VII, and Factor X). This deviation may be explained by the interaction of the snake venom FIX-bp interaction.
This structure emphasizes the possible role of magnesium in Gla domain binding to membrane surfaces. However upon examination of the calcium bound Factor IX-(1-46) complex revealed that the calcium coordination within this FIX Gla domain structure differs from other vitamin K-dependent proteins (prothrombin, Factor VII, and Factor X). This deviation may be explained by the interaction of the snake venom FIX-bp interaction.


To further probe into the structure of FIX Gla domain, [[conformation-specific anti-Factor IX antibodies]] were utilized. Using an  
To further probe into the structure of FIX Gla domain, [[conformation-specific anti-Factor IX antibodies]] were utilized. Using an  
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== Serine Protease Domain ==  
== Serine Protease Domain ==  


The serine protease domain of FIX is required for blood coagulation<ref>PMID:10467178</ref>. FIX circulates in plasma as a single-chain zymogen at a concentration of 2.5-5 mg/ml and a half life is approximately 24 hours. The zymogen is activated by either FVII–tissue-factor complex or Factor XIa (FXIa). During activation the peptide bonds between Arg145–Ala146 and Arg180–Val181 are cleaved releasing an 11 kDa activation peptide from the Factor IX. This cleavage allows the exposure of the serine protease site on the heavy chain which can then activate Factor X in the presence of Factor VIII, calcium and phospholipid surface. This enzyme belongs to the family of trypsin-like serine proteases.The mechanism of these serine proteases involves the catalytic triad, which is found in the enzymes active site and is composed of three amino acids.  
The serine protease domain of FIX is required for blood coagulation<ref>PMID:10467178</ref>. FIX circulates in plasma as a single-chain zymogen at a concentration of 2.5-5 mg/ml and a half life is approximately 24 hours. The zymogen is activated by either FVII–tissue-factor complex or Factor XIa (FXIa). During activation the peptide bonds between Arg145–Ala146 and Arg180–Val181 are cleaved releasing an 11 kDa activation peptide from the Factor IX. This cleavage allows the exposure of the serine protease site on the heavy chain which can then activate Factor X in the presence of Factor VIII, calcium and phospholipid surface. This enzyme belongs to the family of trypsin-like serine proteases.The mechanism of these serine proteases involves the catalytic triad, which is found in the enzymes active site and is composed of three amino acids.  


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The catalytic domain of FIX is composed of two β-<scene name='Factor_IX/Rfnscene/3'>barrel</scene> subdomains that form an active site at their interface. The active site is located at the junction of these β-barrels. The EGF-2 domain is connected to the catalytic domain through a disulfide bridge and is opposite to the active site. There are three disulfide bonds, and the C-terminus contains helical structures that run across the N-terminus of the β-barrel. The catalytic domain contains a calcium binding site that exposes the <scene name='Factor_IX/Rfnscene_5/1'>148-loop</scene> for proteolytic cleavage. This calcium ion is stabilized by Glu-70, Glu-77, Glu-80 and a main chain oxygens of Asn-72 and Glu-75. This site seems to be preformed, unlike the calcium binding sites that are generated in the Gla domain upon calcium binding.  
The catalytic domain of FIX is composed of two β-<scene name='Factor_IX/Rfnscene/3'>barrel</scene> subdomains that form an active site at their interface. The active site is located at the junction of these β-barrels. The EGF-2 domain is connected to the catalytic domain through a disulfide bridge and is opposite to the active site. There are three disulfide bonds, and the C-terminus contains helical structures that run across the N-terminus of the β-barrel. The catalytic domain contains a calcium binding site that exposes the <scene name='Factor_IX/Rfnscene_5/1'>148-loop</scene> for proteolytic cleavage. This calcium ion is stabilized by Glu-70, Glu-77, Glu-80 and a main chain oxygens of Asn-72 and Glu-75. This site seems to be preformed, unlike the calcium binding sites that are generated in the Gla domain upon calcium binding.  
</StructureSection>
 
==3D structures of factor IX==
==3D structures of factor IX==
[[Factor IX 3D structures]]


Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
</StructureSection>
{{#tree:id=OrganizedByTopic|openlevels=0|
 
*Factor IX
 
**[[1mgx]], [[1cfi]], [[1cfh]] - hIX GLA domain – human – NMR<br />
**[[1edm]] – hIX EGF-like domain<br />
**[[1ixa]] - hIX EGF-like domain - NMR
 
*Factor IX complexes
 
**[[3lc3]], [[3lc5]] – hIXa light+heavy chain + benzothiophene inhibitor<br />
**[[3kcg]] - hIXa light+heavy chains + antithrombin-III+ pentasaccharide<br />
**[[2wph]], [[2wpi]], [[2wpj]], [[2wpk]], [[2wpl]] - hIXa light+heavy chains (mutant) + FPR-chloromethyl ketone<br />
**[[2wpm]] - hIXa light+heavy chains (mutant) + EGR-chloromethyl ketone<br />
**[[1x7a]] - pIXa light+heavy chains + inhibitor – pig<br />
**[[1nl0]] – hIX GLA domain + anti-factor IX antibody<br />
**[[1j34]], [[1j35]] - hIX GLA domain + IX-binding protein – bovine<br />
**[[1rfn]] - hIXa light+heavy chains EGF2-catalytic domain + inhibitor<br />
**[[1pfx]] – pIXa +FPR<br />
**[[4yzu]], [[4z0k]], [[5tno]] – hIX peptidase S1 and EGF-like 2 domains + inhibitor <br />
**[[4zae]], [[5egm]], [[5jb8]], [[5jb9]], [[5jba]], [[5jbb]], [[5jbc]], [[5tnt]] – hIX peptidase S1 and EGF-like 2 domains (mutant) + inhibitor <br />
**[[4wm0]] – hIX residues 92-130 + xyloside gxylosyltransferase + glucopyranose derivative<br />
**[[4wma]] – hIX residues 92-130 + xyloside gxylosyltransferase + UDP-glucose <br />
**[[4wnh]] – hIX residues 92-130 + xyloside gxylosyltransferase + UDP-xylose <br />
**[[4wmb]] – hIX residues 92-130 + xyloside gxylosyltransferase + UDP <br />
**[[4wmi]], [[4wmk]], [[4wn2]] – hIX residues 92-130 + xyloside gxylosyltransferase + glucopyranose derivative + UDP<br />
**[[5fm6]] – hIX residues 92-130 + glucosyltransferase <br />
**[[5fm4]] – hIX residues 92-130 + glucosyltransferase + UDP-glucose <br />
**[[5fm5]] – hIX residues 92-130 + glucosyltransferase + UDP <br />
}}


==Additional Resources==
==Additional Resources==

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Nadia Dorochko, Alexander Berchansky, David Canner, Michal Harel
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