3ghm

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of the exosite-containing fragment of human ADAMTS13 (form-1)

Structural highlights

3ghm 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 2.6Å
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.

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

ADAMTS13 is a reprolysin-type metalloproteinase belonging to the ADAMTS (a disintegrin and metalloproteinase with thrombospondin type 1 motif) family. It specifically cleaves plasma von Willebrand factor (VWF) and regulates platelet adhesion and aggregation. ADAMTS13 is a multi-domain enzyme. In addition to the N-terminal metalloproteinase domain, the ancillary domains, including a disintegrin-like domain, a thrombospondin-1 type 1 repeat, a Cys-rich domain and a spacer domain, are required for VWF recognition and cleavage. In the present study, a fragment of the ADAMTS13 ancillary domains (ADAMTS13-DTCS; residues 287-685) was expressed using CHO Lec cells, purified and crystallized. Diffraction data sets were collected using the SPring-8 beamline. Two ADAMTS13-DTCS crystals with distinct unit-cell parameters generated data sets to 2.6 and 2.8 A resolution, respectively.

Production, crystallization and preliminary crystallographic analysis of an exosite-containing fragment of human von Willebrand factor-cleaving proteinase ADAMTS13.,Akiyama M, Takeda S, Kokame K, Takagi J, Miyata T Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Jul 1;65(Pt, 7):739-42. Epub 2009 Jun 30. PMID:019574655^[21]

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

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
↑ Akiyama M, Takeda S, Kokame K, Takagi J, Miyata T. Production, crystallization and preliminary crystallographic analysis of an exosite-containing fragment of human von Willebrand factor-cleaving proteinase ADAMTS13. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Jul 1;65(Pt, 7):739-42. Epub 2009 Jun 30. PMID:19574655 doi:10.1107/S1744309109023410

1 Structural highlights
2 Disease
3 Function
4 Evolutionary Conservation
5 Publication Abstract from PubMed
6 See Also
7 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 1: / Line 1: @@
 ==Crystal structure of the exosite-containing fragment of human ADAMTS13 (form-1)==
-<StructureSection load='3ghm' size='340' side='right' caption='[[3ghm]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+<StructureSection load='3ghm' size='340' side='right'caption='[[3ghm]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3ghm]] is a 1 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=3GHM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GHM FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3ghm]] 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=3GHM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GHM FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</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]] 2.6&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ghn|3ghn]]</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=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 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=3ghm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ghm OCA], [https://pdbe.org/3ghm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ghm RCSB], [https://www.ebi.ac.uk/pdbsum/3ghm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ghm ProSAT]</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=3ghm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ghm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ghm RCSB], [http://www.ebi.ac.uk/pdbsum/3ghm PDBsum]</span></td></tr>
 </table>
 == Disease ==
-[[http://www.uniprot.org/uniprot/ATS13_HUMAN ATS13_HUMAN]] Defects in ADAMTS13 are the cause of thrombotic thrombocytopenic purpura congenital (TTP) [MIM:[http://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 ==
-[[http://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.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gh/3ghm_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gh/3ghm_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>
   </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/chain_selection.php?pdb_ID=2ata 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=3ghm ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 26: / Line 26: @@
 ADAMTS13 is a reprolysin-type metalloproteinase belonging to the ADAMTS (a disintegrin and metalloproteinase with thrombospondin type 1 motif) family. It specifically cleaves plasma von Willebrand factor (VWF) and regulates platelet adhesion and aggregation. ADAMTS13 is a multi-domain enzyme. In addition to the N-terminal metalloproteinase domain, the ancillary domains, including a disintegrin-like domain, a thrombospondin-1 type 1 repeat, a Cys-rich domain and a spacer domain, are required for VWF recognition and cleavage. In the present study, a fragment of the ADAMTS13 ancillary domains (ADAMTS13-DTCS; residues 287-685) was expressed using CHO Lec cells, purified and crystallized. Diffraction data sets were collected using the SPring-8 beamline. Two ADAMTS13-DTCS crystals with distinct unit-cell parameters generated data sets to 2.6 and 2.8 A resolution, respectively.
-Production, crystallization and preliminary crystallographic analysis of an exosite-containing fragment of human von Willebrand factor-cleaving proteinase ADAMTS13.,Akiyama M, Takeda S, Kokame K, Takagi J, Miyata T Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Jul 1;65(Pt, 7):739-42. Epub 2009 Jun 30. PMID:19574655<ref>PMID:19574655</ref>
+Production, crystallization and preliminary crystallographic analysis of an exosite-containing fragment of human von Willebrand factor-cleaving proteinase ADAMTS13.,Akiyama M, Takeda S, Kokame K, Takagi J, Miyata T Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Jul 1;65(Pt, 7):739-42. Epub 2009 Jun 30. PMID:019574655<ref>PMID:019574655</ref>
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3ghm" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[A Disintegrin And Metalloproteinase|A Disintegrin And Metalloproteinase]]
+*[[A Disintegrin And Metalloproteinase 3D structures|A Disintegrin And Metalloproteinase 3D structures]]
 == References ==
 <references/>
@@ Line 38: / Line 39: @@
 </StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Akiyama, M]]
+[[Category: Large Structures]]
-[[Category: Kokame, K]]
+[[Category: Akiyama M]]
-[[Category: Miyata, T]]
+[[Category: Kokame K]]
-[[Category: Takagi, J]]
+[[Category: Miyata T]]
-[[Category: Takeda, S]]
+[[Category: Takagi J]]
-[[Category: Beta sandwich]]
+[[Category: Takeda S]]
-[[Category: Hydrolase]]
-[[Category: Thrombospondin type-1 motif]]

3ghm

From Proteopedia

Current revision

Crystal structure of the exosite-containing fragment of human ADAMTS13 (form-1)

Structural highlights

Disease

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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