1ggy: Difference between revisions
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==HUMAN FACTOR XIII WITH YTTERBIUM BOUND IN THE ION SITE== | ==HUMAN FACTOR XIII WITH YTTERBIUM BOUND IN THE ION SITE== | ||
<StructureSection load='1ggy' size='340' side='right' caption='[[1ggy]], [[Resolution|resolution]] 2.50Å' scene=''> | <StructureSection load='1ggy' size='340' side='right'caption='[[1ggy]], [[Resolution|resolution]] 2.50Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1ggy]] is a 2 chain structure with sequence from [ | <table><tr><td colspan='2'>[[1ggy]] is a 2 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=1GGY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GGY FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=YB:YTTERBIUM+(III)+ION'>YB</scene></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ggy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ggy OCA], [https://pdbe.org/1ggy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ggy RCSB], [https://www.ebi.ac.uk/pdbsum/1ggy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ggy ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Disease == | == Disease == | ||
[ | [https://www.uniprot.org/uniprot/F13A_HUMAN F13A_HUMAN] Defects in F13A1 are the cause of factor XIII subunit A deficiency (FA13AD) [MIM:[https://omim.org/entry/613225 613225]. FA13AD is an autosomal recessive disorder characterized by a life-long bleeding tendency, impaired wound healing and spontaneous abortion in affected women.<ref>PMID:1353995</ref> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/F13A_HUMAN F13A_HUMAN] Factor XIII is activated by thrombin and calcium ion to a transglutaminase that catalyzes the formation of gamma-glutamyl-epsilon-lysine cross-links between fibrin chains, thus stabilizing the fibrin clot. Also cross-link alpha-2-plasmin inhibitor, or fibronectin, to the alpha chains of fibrin. | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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</div> | </div> | ||
<div class="pdbe-citations 1ggy" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 1ggy" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Factor XIII|Factor XIII]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Homo sapiens]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Bishop | [[Category: Bishop PD]] | ||
[[Category: Fox | [[Category: Fox BA]] | ||
[[Category: Pederson | [[Category: Pederson LC]] | ||
[[Category: Stenkamp | [[Category: Stenkamp RE]] | ||
[[Category: Teller | [[Category: Teller DC]] | ||
[[Category: Trong | [[Category: Trong IL]] | ||
[[Category: Yee | [[Category: Yee VC]] | ||
Latest revision as of 09:11, 9 August 2023
HUMAN FACTOR XIII WITH YTTERBIUM BOUND IN THE ION SITEHUMAN FACTOR XIII WITH YTTERBIUM BOUND IN THE ION SITE
Structural highlights
DiseaseF13A_HUMAN Defects in F13A1 are the cause of factor XIII subunit A deficiency (FA13AD) [MIM:613225. FA13AD is an autosomal recessive disorder characterized by a life-long bleeding tendency, impaired wound healing and spontaneous abortion in affected women.[1] FunctionF13A_HUMAN Factor XIII is activated by thrombin and calcium ion to a transglutaminase that catalyzes the formation of gamma-glutamyl-epsilon-lysine cross-links between fibrin chains, thus stabilizing the fibrin clot. Also cross-link alpha-2-plasmin inhibitor, or fibronectin, to the alpha chains of fibrin. 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 PubMedThe presence or absence of calcium determines the activation, activity, oligomerization, and stability of blood coagulation factor XIII. To explore these observed effects, we have determined the x-ray crystal structure of recombinant factor XIII A2 in the presence of calcium, strontium, and ytterbium. The main calcium binding site within each monomer involves the main chain oxygen atom of Ala-457, and also the side chains from residues Asn-436, Asp-438, Glu-485, and Glu-490. Calcium and strontium bind in the same location, while ytterbium binds several angstroms removed. A novel ytterbium binding site is also found at the dimer two-fold axis, near residues Asp-270 and Glu-272, and this site may be related to the reported inhibition by lanthanide metals (Achyuthan, K. E., Mary, A., and Greenberg, C. S. (1989) Biochem. J. 257, 331-338). The overall structure of ion-bound factor XIII is very similar to the previously determined crystal structures of factor XIII zymogen, likely due to the constraints of this monoclinic crystal form. We have merged the three independent sets of water molecules in the structures to determine which water molecules are conserved and possibly structurally significant. Identification of the calcium binding site and a novel ytterbium site in blood coagulation factor XIII by x-ray crystallography.,Fox BA, Yee VC, Pedersen LC, Le Trong I, Bishop PD, Stenkamp RE, Teller DC J Biol Chem. 1999 Feb 19;274(8):4917-23. PMID:9988734[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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