1qrk: Difference between revisions
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 /> | [[Image:1qrk.gif|left|200px]]<br /><applet load="1qrk" size="350" color="white" frame="true" align="right" spinBox="true" | ||
<applet load="1qrk" size=" | |||
caption="1qrk, resolution 2.50Å" /> | caption="1qrk, resolution 2.50Å" /> | ||
'''HUMAN FACTOR XIII WITH STRONTIUM BOUND IN THE ION SITE'''<br /> | '''HUMAN FACTOR XIII WITH STRONTIUM BOUND IN THE ION SITE'''<br /> | ||
==Overview== | ==Overview== | ||
The presence or absence of calcium determines the activation, activity, oligomerization, and stability of blood coagulation factor XIII. To | 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== | ==Disease== | ||
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==About this Structure== | ==About this Structure== | ||
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 | 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 <scene name='pdbligand=SR:'>SR</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. This structure supersedes 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://oca.weizmann.ac.il/oca-bin/ocashort?id=1QRK OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: Protein-glutamine gamma-glutamyltransferase]] | [[Category: Protein-glutamine gamma-glutamyltransferase]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Bishop, P | [[Category: Bishop, P D.]] | ||
[[Category: Fox, B | [[Category: Fox, B A.]] | ||
[[Category: Pederson, L | [[Category: Pederson, L C.]] | ||
[[Category: Stenkamp, R | [[Category: Stenkamp, R E.]] | ||
[[Category: Teller, D | [[Category: Teller, D C.]] | ||
[[Category: Trong, I | [[Category: Trong, I Le.]] | ||
[[Category: Yee, V | [[Category: Yee, V C.]] | ||
[[Category: SR]] | [[Category: SR]] | ||
[[Category: blood coagulation]] | [[Category: blood coagulation]] | ||
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[[Category: transglutaminase]] | [[Category: transglutaminase]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:42:58 2008'' | ||
Revision as of 15:42, 21 February 2008
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HUMAN FACTOR XIII WITH STRONTIUM BOUND IN THE ION SITE
OverviewOverview
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.
DiseaseDisease
Known disease associated with this structure: Factor XIIIA deficiency OMIM:[134570]
About this StructureAbout this Structure
1QRK is a Single protein structure of sequence from Homo sapiens with as ligand. This structure supersedes the now removed PDB entry 1BL2. Active as Protein-glutamine gamma-glutamyltransferase, with EC number 2.3.2.13 Full crystallographic information is available from OCA.
ReferenceReference
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
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