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New page: left|200px<br /> <applet load="1qrk" size="450" color="white" frame="true" align="right" spinBox="true" caption="1qrk, resolution 2.50Å" /> '''HUMAN FACTOR XIII W...
 
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[[Image:1qrk.gif|left|200px]]<br />
<applet load="1qrk" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1qrk, resolution 2.50&Aring;" />
'''HUMAN FACTOR XIII WITH STRONTIUM BOUND IN THE ION SITE'''<br />


==Overview==
==HUMAN FACTOR XIII WITH STRONTIUM BOUND IN THE ION SITE==
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.
<StructureSection load='1qrk' size='340' side='right'caption='[[1qrk]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
<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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</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='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>
== 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 ==
[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 ==
[[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/qr/1qrk_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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/main_output.php?pdb_ID=1qrk ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== 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.


==Disease==
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<ref>PMID:9988734</ref>
Known disease associated with this structure: Factor XIIIA deficiency OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=134570 134570]]


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
1QRK is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with SR as [http://en.wikipedia.org/wiki/ligand ligand]. This structure superseeds the now removed PDB entry 1BL2. Active as [http://en.wikipedia.org/wiki/Protein-glutamine_gamma-glutamyltransferase Protein-glutamine gamma-glutamyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.2.13 2.3.2.13] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1QRK OCA].
</div>
<div class="pdbe-citations 1qrk" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9988734 9988734]
*[[Factor XIII|Factor XIII]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Protein-glutamine gamma-glutamyltransferase]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[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: SR]]
[[Category: blood coagulation]]
[[Category: calcium]]
[[Category: strontium]]
[[Category: transglutaminase]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 18:55:55 2007''

Latest revision as of 13:05, 16 August 2023

HUMAN FACTOR XIII WITH STRONTIUM BOUND IN THE ION SITEHUMAN FACTOR XIII WITH STRONTIUM BOUND IN THE ION SITE

Structural highlights

1qrk is a 2 chain structure with sequence from Homo sapiens. This structure supersedes the now removed PDB entry 1bl2. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.5Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

  1. ↑ 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
  2. ↑ 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

1qrk, resolution 2.50Å

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