1ixa: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
Line 4: Line 4:
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1ixa]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IXA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IXA FirstGlance]. <br>
<table><tr><td colspan='2'>[[1ixa]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IXA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IXA FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR, 1 model</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ixa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ixa OCA], [https://pdbe.org/1ixa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ixa RCSB], [https://www.ebi.ac.uk/pdbsum/1ixa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ixa ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ixa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ixa OCA], [https://pdbe.org/1ixa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ixa RCSB], [https://www.ebi.ac.uk/pdbsum/1ixa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ixa ProSAT]</span></td></tr>
</table>
</table>
Line 16: Line 16:
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ix/1ixa_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ix/1ixa_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1ixa ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1ixa ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The three-dimensional structure of the first epidermal growth factor (EGF)-like module from human factor IX has been determined in solution using two-dimensional nuclear magnetic resonance (in the absence of calcium and at pH 4.5). The structure was found to resemble closely that of EGF and the homologous transforming growth factor-alpha (TGF-alpha). Residues 60-65 form an antiparallel beta-sheet with residues 68-73. In the C-terminal subdomain a type II beta-turn is found between residues 74 and 77 and a five-residue turn is found between residues 79 and 83. Glu 78 and Leu 84 pair in an antiparallel beta-sheet conformation. In the N-terminal region a loop is found between residues 50 and 55 such that the side chains of both are positioned above the face of the beta-sheet. Residues 56-60 form a turn that leads into the first strand of the beta-sheet. Whereas the global fold closely resembles that of EGF, the N-terminal residues of the module (46-49) do not form a beta-strand but are ill-defined in the structure, probably due to the local flexibility of this region. The structure is discussed with reference to recent site-directed mutagenesis data, which have identified certain conserved residues as ligands for calcium.
The three-dimensional structure of the first EGF-like module of human factor IX: comparison with EGF and TGF-alpha.,Baron M, Norman DG, Harvey TS, Handford PA, Mayhew M, Tse AG, Brownlee GG, Campbell ID Protein Sci. 1992 Jan;1(1):81-90. PMID:1304885<ref>PMID:1304885</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1ixa" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==

Latest revision as of 09:47, 30 October 2024

THE THREE-DIMENSIONAL STRUCTURE OF THE FIRST EGF-LIKE MODULE OF HUMAN FACTOR IX: COMPARISON WITH EGF AND TGF-ATHE THREE-DIMENSIONAL STRUCTURE OF THE FIRST EGF-LIKE MODULE OF HUMAN FACTOR IX: COMPARISON WITH EGF AND TGF-A

Structural highlights

1ixa is a 1 chain structure with sequence from Homo sapiens. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Solution NMR, 1 model
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

FA9_HUMAN Defects in F9 are the cause of recessive X-linked hemophilia B (HEMB) [MIM:306900; also known as Christmas disease.[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] Note=Mutations in position 43 (Oxford-3, San Dimas) and 46 (Cambridge) prevents cleavage of the propeptide, mutation in position 93 (Alabama) probably fails to bind to cell membranes, mutation in position 191 (Chapel-Hill) or in position 226 (Nagoya OR Hilo) prevent cleavage of the activation peptide. Defects in F9 are the cause of thrombophilia due to factor IX defect (THPH8) [MIM:300807. A hemostatic disorder characterized by a tendency to thrombosis.[37]

Function

FA9_HUMAN Factor IX is a vitamin K-dependent plasma protein that participates in the intrinsic pathway of blood coagulation by converting factor X to its active form in the presence of Ca(2+) ions, phospholipids, and factor VIIIa.

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 three-dimensional structure of the first epidermal growth factor (EGF)-like module from human factor IX has been determined in solution using two-dimensional nuclear magnetic resonance (in the absence of calcium and at pH 4.5). The structure was found to resemble closely that of EGF and the homologous transforming growth factor-alpha (TGF-alpha). Residues 60-65 form an antiparallel beta-sheet with residues 68-73. In the C-terminal subdomain a type II beta-turn is found between residues 74 and 77 and a five-residue turn is found between residues 79 and 83. Glu 78 and Leu 84 pair in an antiparallel beta-sheet conformation. In the N-terminal region a loop is found between residues 50 and 55 such that the side chains of both are positioned above the face of the beta-sheet. Residues 56-60 form a turn that leads into the first strand of the beta-sheet. Whereas the global fold closely resembles that of EGF, the N-terminal residues of the module (46-49) do not form a beta-strand but are ill-defined in the structure, probably due to the local flexibility of this region. The structure is discussed with reference to recent site-directed mutagenesis data, which have identified certain conserved residues as ligands for calcium.

The three-dimensional structure of the first EGF-like module of human factor IX: comparison with EGF and TGF-alpha.,Baron M, Norman DG, Harvey TS, Handford PA, Mayhew M, Tse AG, Brownlee GG, Campbell ID Protein Sci. 1992 Jan;1(1):81-90. PMID:1304885[38]

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

See Also

References

  1. ↑ de la Salle C, Charmantier JL, Ravanat C, Ohlmann P, Hartmann ML, Schuhler S, Bischoff R, Ebel C, Roecklin D, Balland A, et al.. The Arg-4 mutant factor IX Strasbourg 2 shows a delayed activation by factor XIa. Nouv Rev Fr Hematol. 1993;35(5):473-80. PMID:8295821
  2. ↑ Suehiro K, Kawabata S, Miyata T, Takeya H, Takamatsu J, Ogata K, Kamiya T, Saito H, Niho Y, Iwanaga S. Blood clotting factor IX BM Nagoya. Substitution of arginine 180 by tryptophan and its activation by alpha-chymotrypsin and rat mast cell chymase. J Biol Chem. 1989 Dec 15;264(35):21257-65. PMID:2592373
  3. ↑ Green PM, Bentley DR, Mibashan RS, Nilsson IM, Giannelli F. Molecular pathology of haemophilia B. EMBO J. 1989 Apr;8(4):1067-72. PMID:2743975
  4. ↑ Noyes CM, Griffith MJ, Roberts HR, Lundblad RL. Identification of the molecular defect in factor IX Chapel Hill: substitution of histidine for arginine at position 145. Proc Natl Acad Sci U S A. 1983 Jul;80(14):4200-2. PMID:6603618
  5. ↑ Bentley AK, Rees DJ, Rizza C, Brownlee GG. Defective propeptide processing of blood clotting factor IX caused by mutation of arginine to glutamine at position -4. Cell. 1986 May 9;45(3):343-8. PMID:3009023
  6. ↑ Davis LM, McGraw RA, Ware JL, Roberts HR, Stafford DW. Factor IXAlabama: a point mutation in a clotting protein results in hemophilia B. Blood. 1987 Jan;69(1):140-3. PMID:3790720
  7. ↑ Ware J, Davis L, Frazier D, Bajaj SP, Stafford DW. Genetic defect responsible for the dysfunctional protein: factor IXLong Beach. Blood. 1988 Aug;72(2):820-2. PMID:3401602
  8. ↑ Sugimoto M, Miyata T, Kawabata S, Yoshioka A, Fukui H, Takahashi H, Iwanaga S. Blood clotting factor IX Niigata: substitution of alanine-390 by valine in the catalytic domain. J Biochem. 1988 Dec;104(6):878-80. PMID:3243764
  9. ↑ Monroe DM, McCord DM, Huang MN, High KA, Lundblad RL, Kasper CK, Roberts HR. Functional consequences of an arginine180 to glutamine mutation in factor IX Hilo. Blood. 1989 May 1;73(6):1540-4. PMID:2713493
  10. ↑ Attree O, Vidaud D, Vidaud M, Amselem S, Lavergne JM, Goossens M. Mutations in the catalytic domain of human coagulation factor IX: rapid characterization by direct genomic sequencing of DNA fragments displaying an altered melting behavior. Genomics. 1989 Apr;4(3):266-72. PMID:2714791
  11. ↑ Koeberl DD, Bottema CD, Buerstedde JM, Sommer SS. Functionally important regions of the factor IX gene have a low rate of polymorphism and a high rate of mutation in the dinucleotide CpG. Am J Hum Genet. 1989 Sep;45(3):448-57. PMID:2773937
  12. ↑ Liddell MB, Peake IR, Taylor SA, Lillicrap DP, Giddings JC, Bloom AL. Factor IX Cardiff: a variant factor IX protein that shows abnormal activation is caused by an arginine to cysteine substitution at position 145. Br J Haematol. 1989 Aug;72(4):556-60. PMID:2775660
  13. ↑ Sakai T, Yoshioka A, Yamamoto K, Niinomi K, Fujimura Y, Fukui H, Miyata T, Iwanaga S. Blood clotting factor IX Kashihara: amino acid substitution of valine-182 by phenylalanine. J Biochem. 1989 May;105(5):756-9. PMID:2753873
  14. ↑ Ware J, Diuguid DL, Liebman HA, Rabiet MJ, Kasper CK, Furie BC, Furie B, Stafford DW. Factor IX San Dimas. Substitution of glutamine for Arg-4 in the propeptide leads to incomplete gamma-carboxylation and altered phospholipid binding properties. J Biol Chem. 1989 Jul 5;264(19):11401-6. PMID:2738071
  15. ↑ Chen SH, Thompson AR, Zhang M, Scott CR. Three point mutations in the factor IX genes of five hemophilia B patients. Identification strategy using localization by altered epitopes in their hemophilic proteins. J Clin Invest. 1989 Jul;84(1):113-8. PMID:2472424 doi:http://dx.doi.org/10.1172/JCI114130
  16. ↑ Wang NS, Zhang M, Thompson AR, Chen SH. Factor IX Chongqing: a new mutation in the calcium-binding domain of factor IX resulting in severe hemophilia B. Thromb Haemost. 1990 Feb 19;63(1):24-6. PMID:2339358
  17. ↑ Taylor SA, Liddell MB, Peake IR, Bloom AL, Lillicrap DP. A mutation adjacent to the beta cleavage site of factor IX (valine 182 to leucine) results in mild haemophilia Bm. Br J Haematol. 1990 Jun;75(2):217-21. PMID:2372509
  18. ↑ Bertina RM, van der Linden IK, Mannucci PM, Reinalda-Poot HH, Cupers R, Poort SR, Reitsma PH. Mutations in hemophilia Bm occur at the Arg180-Val activation site or in the catalytic domain of factor IX. J Biol Chem. 1990 Jul 5;265(19):10876-83. PMID:2162822
  19. ↑ Miyata T, Sakai T, Sugimoto M, Naka H, Yamamoto K, Yoshioka A, Fukui H, Mitsui K, Kamiya K, Umeyama H, et al.. Factor IX Amagasaki: a new mutation in the catalytic domain resulting in the loss of both coagulant and esterase activities. Biochemistry. 1991 Nov 26;30(47):11286-91. PMID:1958666
  20. ↑ Sarkar G, Cassady JD, Pyeritz RE, Gilchrist GS, Sommer SS. Isoleucine397 is changed to threonine in two females with hemophilia B. Nucleic Acids Res. 1991 Mar 11;19(5):1165. PMID:1902289
  21. ↑ Ludwig M, Sabharwal AK, Brackmann HH, Olek K, Smith KJ, Birktoft JJ, Bajaj SP. Hemophilia B caused by five different nondeletion mutations in the protease domain of factor IX. Blood. 1992 Mar 1;79(5):1225-32. PMID:1346975
  22. ↑ Taylor SA, Duffin J, Cameron C, Teitel J, Garvey B, Lillicrap DP. Characterization of the original Christmas disease mutation (cysteine 206----serine): from clinical recognition to molecular pathogenesis. Thromb Haemost. 1992 Jan 23;67(1):63-5. PMID:1615485
  23. ↑ David D, Rosa HA, Pemberton S, Diniz MJ, Campos M, Lavinha J. Single-strand conformation polymorphism (SSCP) analysis of the molecular pathology of hemophilia B. Hum Mutat. 1993;2(5):355-61. PMID:8257988 doi:http://dx.doi.org/10.1002/humu.1380020506
  24. ↑ Aguilar-Martinez P, Romey MC, Schved JF, Gris JC, Demaille J, Claustres M. Factor IX gene mutations causing haemophilia B: comparison of SSC screening versus systematic DNA sequencing and diagnostic applications. Hum Genet. 1994 Sep;94(3):287-90. PMID:8076946
  25. ↑ Aguilar-Martinez P, Romey MC, Gris JC, Schved JF, Demaille J, Claustres M. A novel mutation (Val-373 to Glu) in the catalytic domain of factor IX, resulting in moderately/severe hemophilia B in a southern French patient. Hum Mutat. 1994;3(2):156-8. PMID:8199596 doi:http://dx.doi.org/10.1002/humu.1380030211
  26. ↑ Caglayan SH, Vielhaber E, Gursel T, Aktuglu G, Sommer SS. Identification of mutations in four hemophilia B patients of Turkish origin, including a novel deletion of base 6411. Hum Mutat. 1994;4(2):163-5. PMID:7981722 doi:http://dx.doi.org/10.1002/humu.1380040214
  27. ↑ Wulff K, Schroder W, Wehnert M, Herrmann FH. Twenty-five novel mutations of the factor IX gene in haemophilia B. Hum Mutat. 1995;6(4):346-8. PMID:8680410 doi:10.1002/humu.1380060410
  28. ↑ Caglayan SH, Gokmen Y, Aktuglu G, Gurgey A, Sommer SS. Mutations associated with hemophilia B in Turkish patients. Hum Mutat. 1997;10(1):76-9. PMID:9222764 doi:<76::AID-HUMU11>3.0.CO;2-X 10.1002/(SICI)1098-1004(1997)10:1<76::AID-HUMU11>3.0.CO;2-X
  29. ↑ Chan V, Chan VW, Yip B, Chim CS, Chan TK. Hemophilia B in a female carrier due to skewed inactivation of the normal X-chromosome. Am J Hematol. 1998 May;58(1):72-6. PMID:9590153
  30. ↑ David D, Moreira I, Morais S, de Deus G. Five novel factor IX mutations in unrelated hemophilia B patients. Hum Mutat. 1998;Suppl 1:S301-3. PMID:9452115
  31. ↑ Heit JA, Thorland EC, Ketterling RP, Lind TJ, Daniels TM, Zapata RE, Ordonez SM, Kasper CK, Sommer SS. Germline mutations in Peruvian patients with hemophilia B: pattern of mutation in AmerIndians is similar to the putative endogenous germline pattern. Hum Mutat. 1998;11(5):372-6. PMID:9600455 doi:<372::AID-HUMU4>3.0.CO;2-M 10.1002/(SICI)1098-1004(1998)11:5<372::AID-HUMU4>3.0.CO;2-M
  32. ↑ Wulff K, Bykowska K, Lopaciuk S, Herrmann FH. Molecular analysis of hemophilia B in Poland: 12 novel mutations of the factor IX gene. Acta Biochim Pol. 1999;46(3):721-6. PMID:10698280
  33. ↑ Montejo JM, Magallon M, Tizzano E, Solera J. Identification of twenty-one new mutations in the factor IX gene by SSCP analysis. Hum Mutat. 1999;13(2):160-5. PMID:10094553 doi:<160::AID-HUMU9>3.0.CO;2-C 10.1002/(SICI)1098-1004(1999)13:2<160::AID-HUMU9>3.0.CO;2-C
  34. ↑ Vidal F, Farssac E, Altisent C, Puig L, Gallardo D. Factor IX gene sequencing by a simple and sensitive 15-hour procedure for haemophilia B diagnosis: identification of two novel mutations. Br J Haematol. 2000 Nov;111(2):549-51. PMID:11122099
  35. ↑ Onay UV, Kavakli K, Kilinc Y, Gurgey A, Aktuglu G, Kemahli S, Ozbek U, Caglayan SH. Molecular pathology of haemophilia B in Turkish patients: identification of a large deletion and 33 independent point mutations. Br J Haematol. 2003 Feb;120(4):656-9. PMID:12588353
  36. ↑ Espinos C, Casana P, Haya S, Cid AR, Aznar JA. Molecular analyses in hemophilia B families: identification of six new mutations in the factor IX gene. Haematologica. 2003 Feb;88(2):235-6. PMID:12604421
  37. ↑ Simioni P, Tormene D, Tognin G, Gavasso S, Bulato C, Iacobelli NP, Finn JD, Spiezia L, Radu C, Arruda VR. X-linked thrombophilia with a mutant factor IX (factor IX Padua). N Engl J Med. 2009 Oct 22;361(17):1671-5. doi: 10.1056/NEJMoa0904377. PMID:19846852 doi:10.1056/NEJMoa0904377
  38. ↑ Baron M, Norman DG, Harvey TS, Handford PA, Mayhew M, Tse AG, Brownlee GG, Campbell ID. The three-dimensional structure of the first EGF-like module of human factor IX: comparison with EGF and TGF-alpha. Protein Sci. 1992 Jan;1(1):81-90. PMID:1304885
Drag the structure with the mouse to rotate

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

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=1ixa&oldid=4195455"