1ygc: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1ygc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YGC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YGC FirstGlance]. <br>
<table><tr><td colspan='2'>[[1ygc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YGC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YGC FirstGlance]. <br>
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=905:(R)-4-[2-(3-AMINO-BENZENESULFONYLAMINO)-1-(3,5-DIETHOXY-2-FLUOROPHENYL)-2-OXO-ETHYLAMINO]-2-HYDROXY-BENZAMIDINE'>905</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=905:(R)-4-[2-(3-AMINO-BENZENESULFONYLAMINO)-1-(3,5-DIETHOXY-2-FLUOROPHENYL)-2-OXO-ETHYLAMINO]-2-HYDROXY-BENZAMIDINE'>905</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1jbu|1jbu]], [[1kli|1kli]], [[1klj|1klj]], [[1dan|1dan]]</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1jbu|1jbu]], [[1kli|1kli]], [[1klj|1klj]], [[1dan|1dan]]</td></tr>
<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">F7 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">F7 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Coagulation_factor_VIIa Coagulation factor VIIa], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.21 3.4.21.21] </span></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Coagulation_factor_VIIa Coagulation factor VIIa], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.21 3.4.21.21] </span></td></tr>
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ygc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ygc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ygc RCSB], [http://www.ebi.ac.uk/pdbsum/1ygc PDBsum]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ygc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ygc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ygc RCSB], [http://www.ebi.ac.uk/pdbsum/1ygc PDBsum]</span></td></tr>
<table>
</table>
== Disease ==
== Disease ==
[[http://www.uniprot.org/uniprot/FA7_HUMAN FA7_HUMAN]] Defects in F7 are the cause of factor VII deficiency (FA7D) [MIM:[http://omim.org/entry/227500 227500]]. A hemorrhagic disease with variable presentation. The clinical picture can be very severe, with the early occurrence of intracerebral hemorrhages or repeated hemarthroses, or, in contrast, moderate with cutaneous-mucosal hemorrhages (epistaxis, menorrhagia) or hemorrhages provoked by a surgical intervention. Finally, numerous subjects are completely asymptomatic despite very low factor VII levels.<ref>PMID:8043443</ref> <ref>PMID:2070047</ref> <ref>PMID:1634227</ref> <ref>PMID:8364544</ref> <ref>PMID:8204879</ref> <ref>PMID:7981691</ref> <ref>PMID:7974346</ref> <ref>PMID:8652821</ref> <ref>PMID:8844208</ref> <ref>PMID:8940045</ref> <ref>PMID:8883260</ref> <ref>PMID:9414278</ref> <ref>PMID:9576180</ref> <ref>PMID:9452082</ref> <ref>PMID:11091194</ref> <ref>PMID:11129332</ref> <ref>PMID:10862079</ref> <ref>PMID:12472587</ref> <ref>PMID:14717781</ref> <ref>PMID:19751712</ref> <ref>PMID:18976247</ref> <ref>PMID:19432927</ref> <ref>PMID:21206266</ref> <ref>PMID:21372693</ref>   
[[http://www.uniprot.org/uniprot/FA7_HUMAN FA7_HUMAN]] Defects in F7 are the cause of factor VII deficiency (FA7D) [MIM:[http://omim.org/entry/227500 227500]]. A hemorrhagic disease with variable presentation. The clinical picture can be very severe, with the early occurrence of intracerebral hemorrhages or repeated hemarthroses, or, in contrast, moderate with cutaneous-mucosal hemorrhages (epistaxis, menorrhagia) or hemorrhages provoked by a surgical intervention. Finally, numerous subjects are completely asymptomatic despite very low factor VII levels.<ref>PMID:8043443</ref> <ref>PMID:2070047</ref> <ref>PMID:1634227</ref> <ref>PMID:8364544</ref> <ref>PMID:8204879</ref> <ref>PMID:7981691</ref> <ref>PMID:7974346</ref> <ref>PMID:8652821</ref> <ref>PMID:8844208</ref> <ref>PMID:8940045</ref> <ref>PMID:8883260</ref> <ref>PMID:9414278</ref> <ref>PMID:9576180</ref> <ref>PMID:9452082</ref> <ref>PMID:11091194</ref> <ref>PMID:11129332</ref> <ref>PMID:10862079</ref> <ref>PMID:12472587</ref> <ref>PMID:14717781</ref> <ref>PMID:19751712</ref> <ref>PMID:18976247</ref> <ref>PMID:19432927</ref> <ref>PMID:21206266</ref> <ref>PMID:21372693</ref>   
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[[Category: Coagulation factor VIIa]]
[[Category: Coagulation factor VIIa]]
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Artis, D R.]]
[[Category: Artis, D R]]
[[Category: Bunting, S.]]
[[Category: Bunting, S]]
[[Category: Eigenbrot, C.]]
[[Category: Eigenbrot, C]]
[[Category: Flygare, J.]]
[[Category: Flygare, J]]
[[Category: Goldsmith, R.]]
[[Category: Goldsmith, R]]
[[Category: Kirchhofer, D.]]
[[Category: Kirchhofer, D]]
[[Category: Olivero, A G.]]
[[Category: Olivero, A G]]
[[Category: Rawson, T.]]
[[Category: Rawson, T]]
[[Category: Refino, C.]]
[[Category: Refino, C]]
[[Category: Robarge, K.]]
[[Category: Robarge, K]]
[[Category: Hydrolase]]
[[Category: Hydrolase]]
[[Category: Inverted oxy-anion hole]]
[[Category: Inverted oxy-anion hole]]

Revision as of 12:27, 8 January 2015

Short Factor VIIa with a small molecule inhibitorShort Factor VIIa with a small molecule inhibitor

Structural highlights

1ygc is a 2 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:, ,
Gene:F7 (Homo sapiens)
Activity:Coagulation factor VIIa, with EC number 3.4.21.21
Resources:FirstGlance, OCA, RCSB, PDBsum

Disease

[FA7_HUMAN] Defects in F7 are the cause of factor VII deficiency (FA7D) [MIM:227500]. A hemorrhagic disease with variable presentation. The clinical picture can be very severe, with the early occurrence of intracerebral hemorrhages or repeated hemarthroses, or, in contrast, moderate with cutaneous-mucosal hemorrhages (epistaxis, menorrhagia) or hemorrhages provoked by a surgical intervention. Finally, numerous subjects are completely asymptomatic despite very low factor VII levels.[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24]

Function

[FA7_HUMAN] Initiates the extrinsic pathway of blood coagulation. Serine protease that circulates in the blood in a zymogen form. Factor VII is converted to factor VIIa by factor Xa, factor XIIa, factor IXa, or thrombin by minor proteolysis. In the presence of tissue factor and calcium ions, factor VIIa then converts factor X to factor Xa by limited proteolysis. Factor VIIa will also convert factor IX to factor IXa in the presence of tissue factor and calcium.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The serine protease factor VIIa (FVIIa) in complex with its cellular cofactor tissue factor (TF) initiates the blood coagulation reactions. TF.FVIIa is also implicated in thrombosis-related disorders and constitutes an appealing therapeutic target for treatment of cardiovascular diseases. To this end, we generated the FVIIa active site inhibitor G17905, which displayed great potency toward TF.FVIIa (Ki = 0.35 +/- 0.11 nM). G17905 did not appreciably inhibit 12 of the 14 examined trypsin-like serine proteases, consistent with its TF.FVIIa-specific activity in clotting assays. The crystal structure of the FVIIa.G17905 complex provides insight into the molecular basis of the high selectivity. It shows that, compared with other serine proteases, FVIIa is uniquely equipped to accommodate conformational disturbances in the Gln217-Gly219 region caused by the ortho-hydroxy group of the inhibitor's aminobenzamidine moiety located in the S1 recognition pocket. Moreover, the structure revealed a novel, nonstandard conformation of FVIIa active site in the region of the oxyanion hole, a "flipped" Lys192-Gly193 peptide bond. Macromolecular substrate activation assays demonstrated that G17905 is a noncompetitive, slow-binding inhibitor. Nevertheless, G17905 effectively inhibited thrombus formation in a baboon arterio-venous shunt model, reducing platelet and fibrin deposition by approximately 70% at 0.4 mg/kg + 0.1 mg/kg/min infusion. Therefore, the in vitro potency of G17905, characterized by slow binding kinetics, correlated with efficacious antithrombotic activity in vivo.

A selective, slow binding inhibitor of factor VIIa binds to a nonstandard active site conformation and attenuates thrombus formation in vivo.,Olivero AG, Eigenbrot C, Goldsmith R, Robarge K, Artis DR, Flygare J, Rawson T, Sutherlin DP, Kadkhodayan S, Beresini M, Elliott LO, DeGuzman GG, Banner DW, Ultsch M, Marzec U, Hanson SR, Refino C, Bunting S, Kirchhofer D J Biol Chem. 2005 Mar 11;280(10):9160-9. Epub 2005 Jan 4. PMID:15632123[25]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Bernardi F, Liney DL, Patracchini P, Gemmati D, Legnani C, Arcieri P, Pinotti M, Redaelli R, Ballerini G, Pemberton S, et al.. Molecular defects in CRM+ factor VII deficiencies: modelling of missense mutations in the catalytic domain of FVII. Br J Haematol. 1994 Mar;86(3):610-8. PMID:8043443
  2. ↑ O'Brien DP, Gale KM, Anderson JS, McVey JH, Miller GJ, Meade TW, Tuddenham EG. Purification and characterization of factor VII 304-Gln: a variant molecule with reduced activity isolated from a clinically unaffected male. Blood. 1991 Jul 1;78(1):132-40. PMID:2070047
  3. ↑ Marchetti G, Patracchini P, Gemmati D, DeRosa V, Pinotti M, Rodorigo G, Casonato A, Girolami A, Bernardi F. Detection of two missense mutations and characterization of a repeat polymorphism in the factor VII gene (F7). Hum Genet. 1992 Jul;89(5):497-502. PMID:1634227
  4. ↑ Marchetti G, Ferrati M, Patracchini P, Redaelli R, Bernardi F. A missense mutation (178Cys-->Tyr) and two neutral dimorphisms (115His and 333Ser) in the human coagulation factor VII gene. Hum Mol Genet. 1993 Jul;2(7):1055-6. PMID:8364544
  5. ↑ Chaing S, Clarke B, Sridhara S, Chu K, Friedman P, VanDusen W, Roberts HR, Blajchman M, Monroe DM, High KA. Severe factor VII deficiency caused by mutations abolishing the cleavage site for activation and altering binding to tissue factor. Blood. 1994 Jun 15;83(12):3524-35. PMID:8204879
  6. ↑ Bernardi F, Castaman G, Redaelli R, Pinotti M, Lunghi B, Rodeghiero F, Marchetti G. Topologically equivalent mutations causing dysfunctional coagulation factors VII (294Ala-->Val) and X (334Ser-->Pro). Hum Mol Genet. 1994 Jul;3(7):1175-7. PMID:7981691
  7. ↑ Ohiwa M, Hayashi T, Wada H, Minamikawa K, Shirakawa S, Suzuki K. Factor VII Mie: homozygous asymptomatic type I deficiency caused by an amino acid substitution of His (CAC) for Arg(247) (CGC) in the catalytic domain. Thromb Haemost. 1994 Jun;71(6):773-7. PMID:7974346
  8. ↑ Arbini AA, Mannucci M, Bauer KA. A Thr359Met mutation in factor VII of a patient with a hereditary deficiency causes defective secretion of the molecule. Blood. 1996 Jun 15;87(12):5085-94. PMID:8652821
  9. ↑ Bernardi F, Castaman G, Pinotti M, Ferraresi P, Di Iasio MG, Lunghi B, Rodeghiero F, Marchetti G. Mutation pattern in clinically asymptomatic coagulation factor VII deficiency. Hum Mutat. 1996;8(2):108-15. PMID:8844208 doi:<108::AID-HUMU2>3.0.CO;2-7 10.1002/(SICI)1098-1004(1996)8:2<108::AID-HUMU2>3.0.CO;2-7
  10. ↑ Bharadwaj D, Iino M, Kontoyianni M, Smith KJ, Foster DC, Kisiel W. Factor VII central. A novel mutation in the catalytic domain that reduces tissue factor binding, impairs activation by factor Xa, and abolishes amidolytic and coagulant activity. J Biol Chem. 1996 Nov 29;271(48):30685-91. PMID:8940045
  11. ↑ Tamary H, Fromovich Y, Shalmon L, Reich Z, Dym O, Lanir N, Brenner B, Paz M, Luder AS, Blau O, Korostishevsky M, Zaizov R, Seligsohn U. Ala244Val is a common, probably ancient mutation causing factor VII deficiency in Moroccan and Iranian Jews. Thromb Haemost. 1996 Sep;76(3):283-91. PMID:8883260
  12. ↑ Leonard BJ, Chen Q, Blajchman MA, Ofosu FA, Sridhara S, Yang D, Clarke BJ. Factor VII deficiency caused by a structural variant N57D of the first epidermal growth factor domain. Blood. 1998 Jan 1;91(1):142-8. PMID:9414278
  13. ↑ Ozawa T, Takikawa Y, Niiya K, Ejiri N, Suzuki K, Sato S, Sakuragawa N. Factor VII Morioka (FVII L-26P): a homozygous missense mutation in the signal sequence identified in a patient with factor VII deficiency. Br J Haematol. 1998 Apr;101(1):47-9. PMID:9576180
  14. ↑ Alshinawi C, Scerri C, Galdies R, Aquilina A, Felice AE. Two new missense mutations (P134T and A244V) in the coagulation factor VII gene. Hum Mutat. 1998;Suppl 1:S189-91. PMID:9452082
  15. ↑ Au WY, Lam CC, Chan EC, Kwong YL. Two novel factor VII gene mutations in a Chinese family with factor VII deficiency. Br J Haematol. 2000 Oct;111(1):143-5. PMID:11091194
  16. ↑ Millar DS, Kemball-Cook G, McVey JH, Tuddenham EG, Mumford AD, Attock GB, Reverter JC, Lanir N, Parapia LA, Reynaud J, Meili E, von Felton A, Martinowitz U, Prangnell DR, Krawczak M, Cooper DN. Molecular analysis of the genotype-phenotype relationship in factor VII deficiency. Hum Genet. 2000 Oct;107(4):327-42. PMID:11129332
  17. ↑ Wulff K, Herrmann FH. Twenty two novel mutations of the factor VII gene in factor VII deficiency. Hum Mutat. 2000;15(6):489-96. PMID:10862079 doi:<489::AID-HUMU1>3.0.CO;2-J 10.1002/1098-1004(200006)15:6<489::AID-HUMU1>3.0.CO;2-J
  18. ↑ Nagaizumi K, Inaba H, Suzuki T, Hatta Y, Hagiwara T, Amano K, Arai M, Fukutake K. Two double heterozygous mutations in the F7 gene show different manifestations. Br J Haematol. 2002 Dec;119(4):1052-8. PMID:12472587
  19. ↑ Takamiya O, Hino K. A patient homozygous for a Gly354Cys mutation in factor VII that results in severely impaired secretion of the molecule, but not complete deficiency. Br J Haematol. 2004 Feb;124(3):336-42. PMID:14717781
  20. ↑ Mota L, Shetty S, Idicula-Thomas S, Ghosh K. Phenotypic and genotypic characterization of Factor VII deficiency patients from Western India. Clin Chim Acta. 2009 Nov;409(1-2):106-11. doi: 10.1016/j.cca.2009.09.007. Epub, 2009 Sep 13. PMID:19751712 doi:10.1016/j.cca.2009.09.007
  21. ↑ Herrmann FH, Wulff K, Auerswald G, Schulman S, Astermark J, Batorova A, Kreuz W, Pollmann H, Ruiz-Saez A, De Bosch N, Salazar-Sanchez L. Factor VII deficiency: clinical manifestation of 717 subjects from Europe and Latin America with mutations in the factor 7 gene. Haemophilia. 2009 Jan;15(1):267-80. doi: 10.1111/j.1365-2516.2008.01910.x. Epub, 2008 Oct 30. PMID:18976247 doi:10.1111/j.1365-2516.2008.01910.x
  22. ↑ Landau D, Rosenberg N, Zivelin A, Staretz-Chacham O, Kapelushnik J. Familial factor VII deficiency with foetal and neonatal fatal cerebral haemorrhage associated with homozygosis to Gly180Arg mutation. Haemophilia. 2009 May;15(3):774-8. doi: 10.1111/j.1365-2516.2009.02004.x. PMID:19432927 doi:10.1111/j.1365-2516.2009.02004.x
  23. ↑ Kwon MJ, Yoo KY, Lee KO, Kim SH, Kim HJ. Recurrent mutations and genotype-phenotype correlations in hereditary factor VII deficiency in Korea. Blood Coagul Fibrinolysis. 2011 Mar;22(2):102-5. doi:, 10.1097/MBC.0b013e328343641a. PMID:21206266 doi:10.1097/MBC.0b013e328343641a
  24. ↑ Jiang M, Wang Z, Yu Z, Bai X, Su J, Cao L, Zhang W, Ruan C. A novel missense mutation close to the charge-stabilizing system in a patient with congenital factor VII deficiency. Blood Coagul Fibrinolysis. 2011 Jun;22(4):264-70. doi:, 10.1097/MBC.0b013e3283447388. PMID:21372693 doi:10.1097/MBC.0b013e3283447388
  25. ↑ Olivero AG, Eigenbrot C, Goldsmith R, Robarge K, Artis DR, Flygare J, Rawson T, Sutherlin DP, Kadkhodayan S, Beresini M, Elliott LO, DeGuzman GG, Banner DW, Ultsch M, Marzec U, Hanson SR, Refino C, Bunting S, Kirchhofer D. A selective, slow binding inhibitor of factor VIIa binds to a nonstandard active site conformation and attenuates thrombus formation in vivo. J Biol Chem. 2005 Mar 11;280(10):9160-9. Epub 2005 Jan 4. PMID:15632123 doi:10.1074/jbc.M409068200

1ygc, resolution 2.00Å

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