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| | <StructureSection load='1qrk' size='340' side='right'caption='[[1qrk]], [[Resolution|resolution]] 2.50Å' scene=''> | | <StructureSection load='1qrk' size='340' side='right'caption='[[1qrk]], [[Resolution|resolution]] 2.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1qrk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1bl2 1bl2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QRK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QRK FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1qrk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1bl2 1bl2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QRK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QRK FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SR:STRONTIUM+ION'>SR</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]] 2.5Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ggt|1ggt]], [[1fie|1fie]], [[1ggu|1ggu]], [[1ggy|1ggy]]</div></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Protein-glutamine_gamma-glutamyltransferase Protein-glutamine gamma-glutamyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.2.13 2.3.2.13] </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=1qrk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qrk OCA], [https://pdbe.org/1qrk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qrk RCSB], [https://www.ebi.ac.uk/pdbsum/1qrk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qrk 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=1qrk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qrk OCA], [https://pdbe.org/1qrk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qrk RCSB], [https://www.ebi.ac.uk/pdbsum/1qrk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qrk 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>
| + | [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.
| + | [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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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Human]] | + | [[Category: Homo sapiens]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Protein-glutamine gamma-glutamyltransferase]] | + | [[Category: Bishop PD]] |
| - | [[Category: Bishop, P D]] | + | [[Category: Fox BA]] |
| - | [[Category: Fox, B A]] | + | [[Category: Le Trong I]] |
| - | [[Category: Pederson, L C]] | + | [[Category: Pederson LC]] |
| - | [[Category: Stenkamp, R E]] | + | [[Category: Stenkamp RE]] |
| - | [[Category: Teller, D C]] | + | [[Category: Teller DC]] |
| - | [[Category: Trong, I Le]]
| + | [[Category: Yee VC]] |
| - | [[Category: Yee, V C]] | + | |
| - | [[Category: Blood coagulation]]
| + | |
| - | [[Category: Calcium]]
| + | |
| - | [[Category: Strontium]]
| + | |
| - | [[Category: Transferase]]
| + | |
| - | [[Category: Transglutaminase]]
| + | |
| Structural highlights
Disease
F13A_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]
Function
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
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 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 Also
References
- ↑ Board P, Coggan M, Miloszewski K. Identification of a point mutation in factor XIII A subunit deficiency. Blood. 1992 Aug 15;80(4):937-41. PMID:1353995
- ↑ Fox BA, Yee VC, Pedersen LC, Le Trong I, Bishop PD, Stenkamp RE, Teller DC. Identification of the calcium binding site and a novel ytterbium site in blood coagulation factor XIII by x-ray crystallography. J Biol Chem. 1999 Feb 19;274(8):4917-23. PMID:9988734
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