6i58

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Allosteric activation of human prekallikrein by apple domain disc rotation

Structural highlights

6i58 is a 1 chain structure with sequence from Homo sapiens. This structure supersedes the now removed PDB entry 2f83. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.6Å
Ligands:CL, NAG, PEG
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

FA11_HUMAN Defects in F11 are the cause of factor XI deficiency (FA11D) [MIM:612416; also known as plasma thromboplastin antecedent deficiency or Rosenthal syndrome. It is a hemorrhagic disease characterized by reduced levels and activity of factor XI resulting in moderate bleeding symptoms, usually occurring after trauma or surgery. Patients usually do not present spontaneous bleeding but women can present with menorrhagia. Hemorrhages are usually moderate.[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20]

Function

FA11_HUMAN Factor XI triggers the middle phase of the intrinsic pathway of blood coagulation by activating factor IX.

Publication Abstract from PubMed

BACKGROUND: Plasma prekallikrein (PK) and Factor XI (FXI) are apple domain containing serine proteases which when activated to PKa and FXIa cleave substrates kininogen, Factor XII and Factor IX respectively directing plasma coagulation, bradykinin release, inflammation and thrombosis pathways. OBJECTIVE: To investigate the three-dimensional structure of full-length PKa and perform a comparison with FXI. METHODS: A series of recombinant full-length PKa and FXI constructs and variants were developed and the crystal structures determined. RESULTS AND CONCLUSIONS: A 1.3 A structure of full-length PKa reveals the protease domain positioned above a disc-shaped assemblage of four apple domains in an active conformation. A comparison with the homologous FXI structure reveals the intramolecular disulphide and structural differences in the apple 4 domain that prevents dimer formation in PKa as opposed to FXI. Two latch-like loops (LL1 and LL2) extend from the PKa protease domain to form interactions with the apple 1 and apple 3 domains respectively. A major unexpected difference in the PKa structure compared to FXI is the 180 masculine disc rotation of the apple domains relative to the protease domain. This results in a switched configuration of the latch loops such that LL2 interacts and buries portions of the apple 3 domain in the FXI zymogen whereas in PKa LL2 interacts with the apple 1 domain. Hydrogen-deuterium exchange mass spectrometry on plasma purified human PK and PKa determined that regions of the apple 3 domain have increased surface exposure in PKa compared to the zymogen PK suggesting conformational change upon activation. This article is protected by copyright. All rights reserved.

Plasma Kallikrein Structure Reveals Apple Domain Disc Rotated Conformation Compared to Factor XI.,Li C, Voos KM, Pathak M, Hall G, McCrae KR, Dreveny I, Li R, Emsley J J Thromb Haemost. 2019 Feb 23. doi: 10.1111/jth.14418. PMID:30801944[21]

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

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Citations
2 reviews cite this structure
Proteolytic activity of contact factor zymogens.
Shamanaev et al. (2021)
1 more
11 other articles
No citations found

See Also

References

  1. ↑ Asakai R, Chung DW, Ratnoff OD, Davie EW. Factor XI (plasma thromboplastin antecedent) deficiency in Ashkenazi Jews is a bleeding disorder that can result from three types of point mutations. Proc Natl Acad Sci U S A. 1989 Oct;86(20):7667-71. PMID:2813350
  2. ↑ Meijers JC, Davie EW, Chung DW. Expression of human blood coagulation factor XI: characterization of the defect in factor XI type III deficiency. Blood. 1992 Mar 15;79(6):1435-40. PMID:1547342
  3. ↑ Pugh RE, McVey JH, Tuddenham EG, Hancock JF. Six point mutations that cause factor XI deficiency. Blood. 1995 Mar 15;85(6):1509-16. PMID:7888672
  4. ↑ Imanaka Y, Lal K, Nishimura T, Bolton-Maggs PH, Tuddenham EG, McVey JH. Identification of two novel mutations in non-Jewish factor XI deficiency. Br J Haematol. 1995 Aug;90(4):916-20. PMID:7669672
  5. ↑ Wistinghausen B, Reischer A, Oddoux C, Ostrer H, Nardi M, Karpatkin M. Severe factor XI deficiency in an Arab family associated with a novel mutation in exon 11. Br J Haematol. 1997 Dec;99(3):575-7. PMID:9401068
  6. ↑ Martincic D, Zimmerman SA, Ware RE, Sun MF, Whitlock JA, Gailani D. Identification of mutations and polymorphisms in the factor XI genes of an African American family by dideoxyfingerprinting. Blood. 1998 Nov 1;92(9):3309-17. PMID:9787168
  7. ↑ Alhaq A, Mitchell M, Sethi M, Rahman S, Flynn G, Boulton P, Caeno G, Smith M, Savidge G. Identification of a novel mutation in a non-Jewish factor XI deficient kindred. Br J Haematol. 1999 Jan;104(1):44-9. PMID:10027710
  8. ↑ Mitchell M, Cutler J, Thompson S, Moore G, Jenkins Ap Rees E, Smith M, Savidge G, Alhaq A. Heterozygous factor XI deficiency associated with three novel mutations. Br J Haematol. 1999 Dec;107(4):763-5. PMID:10606881
  9. ↑ Zivelin A, Bauduer F, Ducout L, Peretz H, Rosenberg N, Yatuv R, Seligsohn U. Factor XI deficiency in French Basques is caused predominantly by an ancestral Cys38Arg mutation in the factor XI gene. Blood. 2002 Apr 1;99(7):2448-54. PMID:11895778
  10. ↑ Kravtsov DV, Wu W, Meijers JC, Sun MF, Blinder MA, Dang TP, Wang H, Gailani D. Dominant factor XI deficiency caused by mutations in the factor XI catalytic domain. Blood. 2004 Jul 1;104(1):128-34. Epub 2004 Mar 16. PMID:15026311 doi:10.1182/blood-2003-10-3530
  11. ↑ Dai L, Mitchell M, Carson P, Creagh D, Cutler J, Savidge G, Alhaq A. Severe factor XI deficiency caused by compound heterozygosity. Br J Haematol. 2004 Jun;125(6):817-8. PMID:15180874 doi:10.1111/j.1365-2141.2004.04979.x
  12. ↑ Hill M, McLeod F, Franks H, Gordon B, Dolan G. Genetic analysis in FXI deficiency: six novel mutations and the use of a polymerase chain reaction-based test to define a whole gene deletion. Br J Haematol. 2005 Jun;129(6):825-9. PMID:15953011 doi:10.1111/j.1365-2141.2005.05536.x
  13. ↑ Quelin F, Mathonnet F, Potentini-Esnault C, Trigui N, Peynet J, Bastenaire B, Guillon L, Bigel ML, Sauger A, Mazurier C, de Mazancourt P. Identification of five novel mutations in the factor XI gene (F11) of patients with factor XI deficiency. Blood Coagul Fibrinolysis. 2006 Jan;17(1):69-73. PMID:16607084 doi:10.1097/01.mbc.0000198054.50257.96
  14. ↑ Fard-Esfahani P, Lari GR, Ravanbod S, Mirkhani F, Allahyari M, Rassoulzadegan M, Ala F. Seven novel point mutations in the F11 gene in Iranian FXI-deficient patients. Haemophilia. 2008 Jan;14(1):91-5. Epub 2007 Nov 13. PMID:18005151 doi:10.1111/j.1365-2516.2007.01593.x
  15. ↑ Kim J, Song J, Lyu CJ, Kim YR, Oh SH, Choi YC, Yoo JH, Choi JR, Kim H, Lee KA. Population-specific spectrum of the F11 mutations in Koreans: evidence for a founder effect. Clin Genet. 2012 Aug;82(2):180-6. doi: 10.1111/j.1399-0004.2011.01732.x. Epub, 2011 Jun 30. PMID:21668437 doi:10.1111/j.1399-0004.2011.01732.x
  16. ↑ Dai L, Rangarajan S, Mitchell M. Three dominant-negative mutations in factor XI-deficient patients. Haemophilia. 2011 Sep;17(5):e919-22. doi: 10.1111/j.1365-2516.2011.02519.x. Epub , 2011 Apr 3. PMID:21457405 doi:10.1111/j.1365-2516.2011.02519.x
  17. ↑ Lee JH, Cho HS, Hyun MS, Kim HY, Kim HJ. A novel missense mutation Asp506Gly in Exon 13 of the F11 gene in an asymptomatic Korean woman with mild factor XI deficiency. Korean J Lab Med. 2011 Oct;31(4):290-3. doi: 10.3343/kjlm.2011.31.4.290. Epub, 2011 Oct 3. PMID:22016685 doi:10.3343/kjlm.2011.31.4.290
  18. ↑ Tirefort Y, Uhr MR, Neerman-Arbez M, de Moerloose P. Identification of a novel F11 missense mutation (Ile463Ser) in a family with congenital factor XI deficiency. Blood Coagul Fibrinolysis. 2012 Apr;23(3):251-2. doi:, 10.1097/MBC.0b013e32834ea02a. PMID:22322133 doi:10.1097/MBC.0b013e32834ea02a
  19. ↑ Girolami A, Scarparo P, Bonamigo E, Santarossa L, Cristiani A, Moro S, Lombardi AM. A cluster of factor XI-deficient patients due to a new mutation (Ile 436 Lys) in northeastern Italy. Eur J Haematol. 2012 Mar;88(3):229-36. doi: 10.1111/j.1600-0609.2011.01723.x., Epub 2011 Nov 17. PMID:21999818 doi:10.1111/j.1600-0609.2011.01723.x
  20. ↑ Gueguen P, Chauvin A, Quemener-Redon S, Pan-Petesch B, Ferec C, Abgrall JF, Le Marechal C. Revisiting the molecular epidemiology of factor XI deficiency: nine new mutations and an original large 4qTer deletion in western Brittany (France). Thromb Haemost. 2012 Jan;107(1):44-50. doi: 10.1160/TH11-06-0415. Epub 2011 Dec, 8. PMID:22159456 doi:10.1160/TH11-06-0415
  21. ↑ Li C, Voos KM, Pathak M, Hall G, McCrae KR, Dreveny I, Li R, Emsley J. Plasma Kallikrein Structure Reveals Apple Domain Disc Rotated Conformation Compared to Factor XI. J Thromb Haemost. 2019 Feb 23. doi: 10.1111/jth.14418. PMID:30801944 doi:http://dx.doi.org/10.1111/jth.14418

Contents


PDB ID 6i58

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