3vn4

From Proteopedia

(Difference between revisions)

Revision as of 12:27, 8 November 2023

Crystal structure of the exosite-containing fragment of human ADAMTS13 (P475S mutant)

Structural highlights

3vn4 is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.8Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

ATS13_HUMAN Defects in ADAMTS13 are the cause of thrombotic thrombocytopenic purpura congenital (TTP) [MIM:274150; also known as Upshaw-Schulman syndrome (USS). A hematologic disease characterized by hemolytic anemia with fragmentation of erythrocytes, thrombocytopenia, diffuse and non-focal neurologic findings, decreased renal function and fever.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11] ^[12] ^[13] ^[14] ^[15] ^[16] ^[17] ^[18] ^[19] ^[20]

Function

ATS13_HUMAN Cleaves the vWF multimers in plasma into smaller forms.

References

↑ Levy GG, Nichols WC, Lian EC, Foroud T, McClintick JN, McGee BM, Yang AY, Siemieniak DR, Stark KR, Gruppo R, Sarode R, Shurin SB, Chandrasekaran V, Stabler SP, Sabio H, Bouhassira EE, Upshaw JD Jr, Ginsburg D, Tsai HM. Mutations in a member of the ADAMTS gene family cause thrombotic thrombocytopenic purpura. Nature. 2001 Oct 4;413(6855):488-94. PMID:11586351 doi:10.1038/35097008
↑ Kokame K, Matsumoto M, Soejima K, Yagi H, Ishizashi H, Funato M, Tamai H, Konno M, Kamide K, Kawano Y, Miyata T, Fujimura Y. Mutations and common polymorphisms in ADAMTS13 gene responsible for von Willebrand factor-cleaving protease activity. Proc Natl Acad Sci U S A. 2002 Sep 3;99(18):11902-7. Epub 2002 Aug 14. PMID:12181489 doi:10.1073/pnas.172277399
↑ Schneppenheim R, Budde U, Oyen F, Angerhaus D, Aumann V, Drewke E, Hassenpflug W, Haberle J, Kentouche K, Kohne E, Kurnik K, Mueller-Wiefel D, Obser T, Santer R, Sykora KW. von Willebrand factor cleaving protease and ADAMTS13 mutations in childhood TTP. Blood. 2003 Mar 1;101(5):1845-50. Epub 2002 Oct 17. PMID:12393505 doi:10.1182/blood-2002-08-2399
↑ Antoine G, Zimmermann K, Plaimauer B, Grillowitzer M, Studt JD, Lammle B, Scheiflinger F. ADAMTS13 gene defects in two brothers with constitutional thrombotic thrombocytopenic purpura and normalization of von Willebrand factor-cleaving protease activity by recombinant human ADAMTS13. Br J Haematol. 2003 Mar;120(5):821-4. PMID:12614216
↑ Assink K, Schiphorst R, Allford S, Karpman D, Etzioni A, Brichard B, van de Kar N, Monnens L, van den Heuvel L. Mutation analysis and clinical implications of von Willebrand factor-cleaving protease deficiency. Kidney Int. 2003 Jun;63(6):1995-9. PMID:12753286 doi:10.1046/j.1523-1755.63.6s.1.x
↑ Pimanda JE, Maekawa A, Wind T, Paxton J, Chesterman CN, Hogg PJ. Congenital thrombotic thrombocytopenic purpura in association with a mutation in the second CUB domain of ADAMTS13. Blood. 2004 Jan 15;103(2):627-9. Epub 2003 Sep 25. PMID:14512317 doi:10.1182/blood-2003-04-1346
↑ Matsumoto M, Kokame K, Soejima K, Miura M, Hayashi S, Fujii Y, Iwai A, Ito E, Tsuji Y, Takeda-Shitaka M, Iwadate M, Umeyama H, Yagi H, Ishizashi H, Banno F, Nakagaki T, Miyata T, Fujimura Y. Molecular characterization of ADAMTS13 gene mutations in Japanese patients with Upshaw-Schulman syndrome. Blood. 2004 Feb 15;103(4):1305-10. Epub 2003 Oct 16. PMID:14563640 doi:10.1182/blood-2003-06-1796
↑ Uchida T, Wada H, Mizutani M, Iwashita M, Ishihara H, Shibano T, Suzuki M, Matsubara Y, Soejima K, Matsumoto M, Fujimura Y, Ikeda Y, Murata M. Identification of novel mutations in ADAMTS13 in an adult patient with congenital thrombotic thrombocytopenic purpura. Blood. 2004 Oct 1;104(7):2081-3. Epub 2004 May 4. PMID:15126318 doi:10.1182/blood-2004-02-0715
↑ Veyradier A, Lavergne JM, Ribba AS, Obert B, Loirat C, Meyer D, Girma JP. Ten candidate ADAMTS13 mutations in six French families with congenital thrombotic thrombocytopenic purpura (Upshaw-Schulman syndrome). J Thromb Haemost. 2004 Mar;2(3):424-9. PMID:15009458
↑ Licht C, Stapenhorst L, Simon T, Budde U, Schneppenheim R, Hoppe B. Two novel ADAMTS13 gene mutations in thrombotic thrombocytopenic purpura/hemolytic-uremic syndrome (TTP/HUS). Kidney Int. 2004 Sep;66(3):955-8. PMID:15327386 doi:10.1111/j.1523-1755.2004.00841.x
↑ Plaimauer B, Fuhrmann J, Mohr G, Wernhart W, Bruno K, Ferrari S, Konetschny C, Antoine G, Rieger M, Scheiflinger F. Modulation of ADAMTS13 secretion and specific activity by a combination of common amino acid polymorphisms and a missense mutation. Blood. 2006 Jan 1;107(1):118-25. Epub 2005 Sep 13. PMID:16160007 doi:2005-06-2482
↑ Peyvandi F, Lavoretano S, Palla R, Valsecchi C, Merati G, De Cristofaro R, Rossi E, Mannuccio Mannucci P. Mechanisms of the interaction between two ADAMTS13 gene mutations leading to severe deficiency of enzymatic activity. Hum Mutat. 2006 Apr;27(4):330-6. PMID:16453338 doi:10.1002/humu.20267
↑ Tao Z, Anthony K, Peng Y, Choi H, Nolasco L, Rice L, Moake JL, Dong JF. Novel ADAMTS-13 mutations in an adult with delayed onset thrombotic thrombocytopenic purpura. J Thromb Haemost. 2006 Sep;4(9):1931-5. Epub 2006 Jun 22. PMID:16796708 doi:10.1111/j.1538-7836.2006.02098.x
↑ Shibagaki Y, Matsumoto M, Kokame K, Ohba S, Miyata T, Fujimura Y, Fujita T. Novel compound heterozygote mutations (H234Q/R1206X) of the ADAMTS13 gene in an adult patient with Upshaw-Schulman syndrome showing predominant episodes of repeated acute renal failure. Nephrol Dial Transplant. 2006 May;21(5):1289-92. Epub 2006 Jan 31. PMID:16449289 doi:gfk072
↑ Schneppenheim R, Kremer Hovinga JA, Becker T, Budde U, Karpman D, Brockhaus W, Hrachovinova I, Korczowski B, Oyen F, Rittich S, von Rosen J, Tjonnfjord GE, Pimanda JE, Wienker TF, Lammle B. A common origin of the 4143insA ADAMTS13 mutation. Thromb Haemost. 2006 Jul;96(1):3-6. PMID:16807643 doi:10.1160/TH05-12-0817
↑ Donadelli R, Banterla F, Galbusera M, Capoferri C, Bucchioni S, Gastoldi S, Nosari S, Monteferrante G, Ruggeri ZM, Bresin E, Scheiflinger F, Rossi E, Martinez C, Coppo R, Remuzzi G, Noris M. In-vitro and in-vivo consequences of mutations in the von Willebrand factor cleaving protease ADAMTS13 in thrombotic thrombocytopenic purpura. Thromb Haemost. 2006 Oct;96(4):454-64. PMID:17003922
↑ Meyer SC, Jeddi R, Meddeb B, Gouider E, Lammle B, Kremer Hovinga JA. A first case of congenital TTP on the African continent due to a new homozygous mutation in the catalytic domain of ADAMTS13. Ann Hematol. 2008 Aug;87(8):663-6. doi: 10.1007/s00277-008-0496-6. Epub 2008 Apr , 29. PMID:18443791 doi:10.1007/s00277-008-0496-6
↑ Fujimura Y, Matsumoto M, Kokame K, Isonishi A, Soejima K, Akiyama N, Tomiyama J, Natori K, Kuranishi Y, Imamura Y, Inoue N, Higasa S, Seike M, Kozuka T, Hara M, Wada H, Murata M, Ikeda Y, Miyata T, George JN. Pregnancy-induced thrombocytopenia and TTP, and the risk of fetal death, in Upshaw-Schulman syndrome: a series of 15 pregnancies in 9 genotyped patients. Br J Haematol. 2009 Mar;144(5):742-54. doi: 10.1111/j.1365-2141.2008.07515.x., Epub 2008 Nov 26. PMID:19055667 doi:10.1111/j.1365-2141.2008.07515.x
↑ Palla R, Lavoretano S, Lombardi R, Garagiola I, Karimi M, Afrasiabi A, Ramzi M, De Cristofaro R, Peyvandi F. The first deletion mutation in the TSP1-6 repeat domain of ADAMTS13 in a family with inherited thrombotic thrombocytopenic purpura. Haematologica. 2009 Feb;94(2):289-93. doi: 10.3324/haematol.13524. Epub 2008 Dec , 30. PMID:19116307 doi:10.3324/haematol.13524
↑ Lee SH, Park JH, Park SK, Lee EH, Choi JI, Visentin GP, Park TS, Oh SH, Kim SR. A novel homozygous missense ADAMTS13 mutation Y658C in a patient with recurrent thrombotic thrombocytopenic purpura. Ann Clin Lab Sci. 2011 Summer;41(3):273-6. PMID:22075512

1 Structural highlights
2 Disease
3 Function
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3vn4"

@@ Line 3: / Line 3: @@
 <StructureSection load='3vn4' size='340' side='right'caption='[[3vn4]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3vn4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VN4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VN4 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3vn4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VN4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VN4 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ghm|3ghm]], [[3ghn|3ghn]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ADAMTS13 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/ADAMTS13_endopeptidase ADAMTS13 endopeptidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.87 3.4.24.87] </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=3vn4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vn4 OCA], [https://pdbe.org/3vn4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vn4 RCSB], [https://www.ebi.ac.uk/pdbsum/3vn4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vn4 ProSAT]</span></td></tr>
 </table>
 == Disease ==
-[[https://www.uniprot.org/uniprot/ATS13_HUMAN ATS13_HUMAN]] Defects in ADAMTS13 are the cause of thrombotic thrombocytopenic purpura congenital (TTP) [MIM:[https://omim.org/entry/274150 274150]]; also known as Upshaw-Schulman syndrome (USS). A hematologic disease characterized by hemolytic anemia with fragmentation of erythrocytes, thrombocytopenia, diffuse and non-focal neurologic findings, decreased renal function and fever.<ref>PMID:11586351</ref> <ref>PMID:12181489</ref> <ref>PMID:12393505</ref> <ref>PMID:12614216</ref> <ref>PMID:12753286</ref> <ref>PMID:14512317</ref> <ref>PMID:14563640</ref> <ref>PMID:15126318</ref> <ref>PMID:15009458</ref> <ref>PMID:15327386</ref> <ref>PMID:16160007</ref> <ref>PMID:16453338</ref> <ref>PMID:16796708</ref> <ref>PMID:16449289</ref> <ref>PMID:16807643</ref> <ref>PMID:17003922</ref> <ref>PMID:18443791</ref> <ref>PMID:19055667</ref> <ref>PMID:19116307</ref> <ref>PMID:22075512</ref>
+[https://www.uniprot.org/uniprot/ATS13_HUMAN ATS13_HUMAN] Defects in ADAMTS13 are the cause of thrombotic thrombocytopenic purpura congenital (TTP) [MIM:[https://omim.org/entry/274150 274150]; also known as Upshaw-Schulman syndrome (USS). A hematologic disease characterized by hemolytic anemia with fragmentation of erythrocytes, thrombocytopenia, diffuse and non-focal neurologic findings, decreased renal function and fever.<ref>PMID:11586351</ref> <ref>PMID:12181489</ref> <ref>PMID:12393505</ref> <ref>PMID:12614216</ref> <ref>PMID:12753286</ref> <ref>PMID:14512317</ref> <ref>PMID:14563640</ref> <ref>PMID:15126318</ref> <ref>PMID:15009458</ref> <ref>PMID:15327386</ref> <ref>PMID:16160007</ref> <ref>PMID:16453338</ref> <ref>PMID:16796708</ref> <ref>PMID:16449289</ref> <ref>PMID:16807643</ref> <ref>PMID:17003922</ref> <ref>PMID:18443791</ref> <ref>PMID:19055667</ref> <ref>PMID:19116307</ref> <ref>PMID:22075512</ref>
 == Function ==
-[[https://www.uniprot.org/uniprot/ATS13_HUMAN ATS13_HUMAN]] Cleaves the vWF multimers in plasma into smaller forms.
+[https://www.uniprot.org/uniprot/ATS13_HUMAN ATS13_HUMAN] Cleaves the vWF multimers in plasma into smaller forms.
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-ADAMTS13 specifically cleaves plasma von Willebrand factor (VWF) and thereby controls VWF-mediated platelet thrombus formation. Severe deficiencies in ADAMTS13 can cause life-threatening thrombotic thrombocytopenic purpura. Here, we determined 2 crystal structures of ADAMTS13-DTCS (residues 287-685), an exosite-containing human ADAMTS13 fragment, at 2.6-A and 2.8-A resolution. The structures revealed folding similarities between the disintegrin-like (D) domain and the N-terminal portion of the cysteine-rich domain (designated the C(A) domain). The spacer (S) domain forms a globular functional unit with a 10-stranded beta-sandwich fold that has multiple interaction sites with the C(A) domain. We expressed 25 structure-based mutants of ADAMTS13-MDTCS (residues 75-685) and measured their enzymatic activity. We identified 3 VWF-binding exosites on the linearly aligned discontinuous surfaces of the D, C(A), and S domains traversing the W-shaped molecule. Since the MDTCS domains are conserved among ADAMTS family proteins, the structural framework of the multiple enzyme-substrate interactions identified in the ADAMTS13-VWF system provides the basis for a common substrate recognition mode in this class of proteinases.
-Crystal structures of the noncatalytic domains of ADAMTS13 reveal multiple discontinuous exosites for von Willebrand factor.,Akiyama M, Takeda S, Kokame K, Takagi J, Miyata T Proc Natl Acad Sci U S A. 2009 Nov 17;106(46):19274-9. Epub 2009 Oct 30. PMID:19880749<ref>PMID:19880749</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3vn4" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 30: / Line 19: @@
 __TOC__
 </StructureSection>
-[[Category: ADAMTS13 endopeptidase]]
+[[Category: Homo sapiens]]
-[[Category: Human]]
 [[Category: Large Structures]]
-[[Category: Akiyama, M]]
+[[Category: Akiyama M]]
-[[Category: Kokame, K]]
+[[Category: Kokame K]]
-[[Category: Miyata, T]]
+[[Category: Miyata T]]
-[[Category: Nakayama, D]]
+[[Category: Nakayama D]]
-[[Category: Takagi, J]]
+[[Category: Takagi J]]
-[[Category: Takeda, S]]
+[[Category: Takeda S]]
-[[Category: Hydrolase]]

3vn4

From Proteopedia

Revision as of 12:27, 8 November 2023

Crystal structure of the exosite-containing fragment of human ADAMTS13 (P475S mutant)

Structural highlights

Disease

Function

See Also

References

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