3vn4

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==Crystal structure of the exosite-containing fragment of human ADAMTS13 (P475S mutant)==
==Crystal structure of the exosite-containing fragment of human ADAMTS13 (P475S mutant)==
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<StructureSection load='3vn4' size='340' side='right' caption='[[3vn4]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
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<StructureSection load='3vn4' size='340' side='right'caption='[[3vn4]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3vn4]] 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=3VN4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VN4 FirstGlance]. <br>
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<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>
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</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=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>
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</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>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ghm|3ghm]], [[3ghn|3ghn]]</td></tr>
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<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=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
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<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>
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<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>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/ADAMTS13_endopeptidase ADAMTS13 endopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.87 3.4.24.87] </span></td></tr>
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<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=3vn4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vn4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vn4 RCSB], [http://www.ebi.ac.uk/pdbsum/3vn4 PDBsum]</span></td></tr>
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</table>
</table>
== Disease ==
== Disease ==
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[[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>
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[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 ==
== Function ==
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[[http://www.uniprot.org/uniprot/ATS13_HUMAN ATS13_HUMAN]] Cleaves the vWF multimers in plasma into smaller forms.
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[https://www.uniprot.org/uniprot/ATS13_HUMAN ATS13_HUMAN] Cleaves the vWF multimers in plasma into smaller forms.
<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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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.
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BACKGROUND: An East Asian-specific P475S polymorphism in the gene encoding ADAMTS-13 causes an approximately 16% reduction in plasma ADAMTS-13 activity. OBJECTIVES: To demonstrate the impact of this dysfunctional polymorphism by characterizing the structure and activity of the P475S mutant protein. METHODS: We determined the crystal structure of the P475S mutant of ADAMTS-13-DTCS (DTCS-P475S, residues 287-685) and compared it with the wild-type structure. We determined the enzymatic parameters of ADAMTS-13-MDTCS (residues 75-685) and MDTCS-P475S, and further examined the effects of denaturants and reaction temperature on their activity. We also examined the cleavage of shear-treated von Willebrand factor (VWF) by MDTCS-P475S. RESULTS: MDTCS-P475S showed a reaction rate similar to that of wild-type MDTCS, but showed two-fold lower affinity for the peptidyl substrate, indicating that the Pro475-containing V-loop (residues 474-481) in the CA domain is a substrate-binding exosite. Structural analysis showed that the conformation of the V-loop was significantly different in DTCS-P475S and the wild type, where no obvious interactions of Ser475 with other residues were observed. This explains the higher susceptibility of the enzymatic activity of MDTCS-P475S to reaction environments such as denaturants and high temperature. MDTCS-P475S can moderately cleave shear-treated VWF. CONCLUSIONS: We have provided structural evidence that the P475S polymorphism in ADAMTS-13 leads to increased local structural instability, resulting in lowered affinity for the substrate without changing the reaction rate. The moderate activity of ADAMTS-13-P475S for shear-treated VWF is sufficient to prevent thrombotic thrombocytopenic purpura (TTP) onset.
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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>
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Crystal structure and enzymatic activity of an ADAMTS-13 mutant with the East Asian-specific P475S polymorphism.,Akiyama M, Nakayama D, Takeda S, Kokame K, Takagi J, Miyata T J Thromb Haemost. 2013 Jul;11(7):1399-406. doi: 10.1111/jth.12279. PMID:23621748<ref>PMID:23621748</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 3vn4" style="background-color:#fffaf0;"></div>
==See Also==
==See Also==
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*[[A Disintegrin And Metalloproteinase|A Disintegrin And Metalloproteinase]]
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*[[A Disintegrin And Metalloproteinase 3D structures|A Disintegrin And Metalloproteinase 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: ADAMTS13 endopeptidase]]
 
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Akiyama, M]]
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[[Category: Large Structures]]
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[[Category: Kokame, K]]
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[[Category: Akiyama M]]
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[[Category: Miyata, T]]
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[[Category: Kokame K]]
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[[Category: Nakayama, D]]
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[[Category: Miyata T]]
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[[Category: Takagi, J]]
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[[Category: Nakayama D]]
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[[Category: Takeda, S]]
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[[Category: Takagi J]]
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[[Category: Hydrolase]]
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[[Category: Takeda S]]

Current revision

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

PDB ID 3vn4

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