3bc8
From Proteopedia
| Line 4: | Line 4: | ||
|PDB= 3bc8 |SIZE=350|CAPTION= <scene name='initialview01'>3bc8</scene>, resolution 1.65Å | |PDB= 3bc8 |SIZE=350|CAPTION= <scene name='initialview01'>3bc8</scene>, resolution 1.65Å | ||
|SITE= <scene name='pdbsite=AC1:Cl+Binding+Site+For+Residue+A+501'>AC1</scene> and <scene name='pdbsite=AC2:Edo+Binding+Site+For+Residue+A+502'>AC2</scene> | |SITE= <scene name='pdbsite=AC1:Cl+Binding+Site+For+Residue+A+501'>AC1</scene> and <scene name='pdbsite=AC2:Edo+Binding+Site+For+Residue+A+502'>AC2</scene> | ||
| - | |LIGAND= <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene> | + | |LIGAND= <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=LLP:2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)'>LLP</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= Sepsecs, D5Ertd135e ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus]) | |GENE= Sepsecs, D5Ertd135e ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[3bca|3BCA]], [[3bcb|3BCB]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3bc8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bc8 OCA], [http://www.ebi.ac.uk/pdbsum/3bc8 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=3bc8 RCSB]</span> | ||
}} | }} | ||
| Line 24: | Line 27: | ||
[[Category: Ganichkin, O M.]] | [[Category: Ganichkin, O M.]] | ||
[[Category: Wahl, M C.]] | [[Category: Wahl, M C.]] | ||
| - | [[Category: CL]] | ||
| - | [[Category: EDO]] | ||
[[Category: crystal structure]] | [[Category: crystal structure]] | ||
[[Category: cytoplasm]] | [[Category: cytoplasm]] | ||
| Line 39: | Line 40: | ||
[[Category: x-ray crystallography]] | [[Category: x-ray crystallography]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:25:04 2008'' |
Revision as of 02:25, 31 March 2008
| |||||||
| , resolution 1.65Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | and | ||||||
| Ligands: | , , | ||||||
| Gene: | Sepsecs, D5Ertd135e (Mus musculus) | ||||||
| Related: | 3BCA, 3BCB
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of mouse selenocysteine synthase
Overview
In eukaryotes and Archaea, selenocysteine synthase (SecS) converts O-phospho-l-seryl-tRNA([Ser]Sec) into selenocysteyl-tRNA([Ser]Sec) using selenophosphate as the selenium donor compound. The molecular mechanisms underlying SecS activity are presently unknown. We have delineated a 450-residue core of mouse SecS, which retained full selenocysteyl-tRNA([Ser]Sec) synthesis activity, and determined its crystal structure at 1.65A resolution. SecS exhibits three domains that place it in the fold type I family of pyridoxal phosphate (PLP)-dependent enzymes. Two SecS monomers interact intimately and together build up two identical active sites around PLP in a Schiff-base linkage with lysine 284. Two SecS dimers further associate to form a homotetramer. The N terminus, which mediates tetramer formation, and a large insertion that remodels the active site set SecS aside from other members of the family. The active site insertion contributes to PLP binding and positions a glutamate next to the PLP, where it could repel substrates with a free alpha-carboxyl group, suggesting why SecS does not act on free O-phospho-l-serine. Upon soaking crystals in phosphate buffer, a previously disordered loop within the active site insertion contracted to form a phosphate binding site. Residues that are strictly conserved in SecS orthologs but variant in related enzymes coordinate the phosphate and upon mutation corrupt SecS activity. Modeling suggested that the phosphate loop accommodates the gamma-phosphate moiety of O-phospho-l-seryl-tRNA([Ser]Sec) and, after phosphate elimination, binds selenophosphate to initiate attack on the proposed aminoacrylyl-tRNA([Ser]Sec) intermediate. Based on these results and on the activity profiles of mechanism-based inhibitors, we offer a detailed reaction mechanism for the enzyme.
About this Structure
3BC8 is a Single protein structure of sequence from Mus musculus. Full crystallographic information is available from OCA.
Reference
Structure and catalytic mechanism of eukaryotic selenocysteine synthase., Ganichkin OM, Xu XM, Carlson BA, Mix H, Hatfield DL, Gladyshev VN, Wahl MC, J Biol Chem. 2008 Feb 29;283(9):5849-65. Epub 2007 Dec 19. PMID:18093968
Page seeded by OCA on Mon Mar 31 05:25:04 2008
Categories: Mus musculus | Single protein | Ganichkin, O M. | Wahl, M C. | Crystal structure | Cytoplasm | Disorder-order transition | Phosphate-loop | Protein biosynthesis | Pyridoxal phosphate | Selenium | Selenocysteine synthase (sec | Sepsecs) | Soluble liver antigen/liver and pancreas antigen (sla/lp) | Transferase | X-ray crystallography
