1ggy
From Proteopedia
| Line 4: | Line 4: | ||
|PDB= 1ggy |SIZE=350|CAPTION= <scene name='initialview01'>1ggy</scene>, resolution 2.50Å | |PDB= 1ggy |SIZE=350|CAPTION= <scene name='initialview01'>1ggy</scene>, resolution 2.50Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=YB:YTTERBIUM (III) ION'>YB</scene> | + | |LIGAND= <scene name='pdbligand=YB:YTTERBIUM+(III)+ION'>YB</scene> |
| - | |ACTIVITY= [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] | + | |ACTIVITY= <span class='plainlinks'>[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] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ggy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ggy OCA], [http://www.ebi.ac.uk/pdbsum/1ggy PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ggy RCSB]</span> | ||
}} | }} | ||
| Line 14: | Line 17: | ||
==Overview== | ==Overview== | ||
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. | 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== | ||
| - | 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== | ==About this Structure== | ||
| Line 33: | Line 33: | ||
[[Category: Trong, I L.]] | [[Category: Trong, I L.]] | ||
[[Category: Yee, V C.]] | [[Category: Yee, V C.]] | ||
| - | [[Category: YB]] | ||
[[Category: blood coagulation]] | [[Category: blood coagulation]] | ||
[[Category: calcium]] | [[Category: calcium]] | ||
| Line 39: | Line 38: | ||
[[Category: ytterbium]] | [[Category: ytterbium]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 20:43:46 2008'' |
Revision as of 17:43, 30 March 2008
| |||||||
| , resolution 2.50Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | |||||||
| Activity: | Protein-glutamine gamma-glutamyltransferase, with EC number 2.3.2.13 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
HUMAN FACTOR XIII WITH YTTERBIUM BOUND IN THE ION SITE
Overview
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.
About this Structure
1GGY is a Single protein structure of sequence from Homo sapiens. Full crystallographic information is available from OCA.
Reference
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
Page seeded by OCA on Sun Mar 30 20:43:46 2008
