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[[Image:3bc8.jpg|left|200px]]


{{Structure
==Crystal structure of mouse selenocysteine synthase==
|PDB= 3bc8 |SIZE=350|CAPTION= <scene name='initialview01'>3bc8</scene>, resolution 1.65&Aring;
<StructureSection load='3bc8' size='340' side='right'caption='[[3bc8]], [[Resolution|resolution]] 1.65&Aring;' 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>
== Structural highlights ==
|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>
<table><tr><td colspan='2'>[[3bc8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. The August 2008 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Selenocysteine Synthase''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2008_8 10.2210/rcsb_pdb/mom_2008_8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BC8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BC8 FirstGlance]. <br>
|ACTIVITY=  
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
|GENE= Sepsecs, D5Ertd135e ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus])
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>
|DOMAIN=
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3bca|3bca]], [[3bcb|3bcb]]</div></td></tr>
|RELATEDENTRY=[[3bca|3BCA]], [[3bcb|3BCB]]
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Sepsecs, D5Ertd135e ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</td></tr>
|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>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3bc8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bc8 OCA], [https://pdbe.org/3bc8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bc8 RCSB], [https://www.ebi.ac.uk/pdbsum/3bc8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bc8 ProSAT]</span></td></tr>
}}
</table>
== Function ==
[[https://www.uniprot.org/uniprot/SPCS_MOUSE SPCS_MOUSE]] Converts O-phosphoseryl-tRNA(Sec) to selenocysteinyl-tRNA(Sec) required for selenoprotein biosynthesis (By similarity).
== 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/bc/3bc8_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=3bc8 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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 1.65 A 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.


'''Crystal structure of mouse selenocysteine synthase'''
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<ref>PMID:18093968</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3bc8" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
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.
*[[Selenocysteine synthase|Selenocysteine synthase]]
 
== References ==
==About this Structure==
<references/>
3BC8 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BC8 OCA].
__TOC__
 
</StructureSection>
==Reference==
[[Category: Large Structures]]
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:[http://www.ncbi.nlm.nih.gov/pubmed/18093968 18093968]
[[Category: Lk3 transgenic mice]]
[[Category: Mus musculus]]
[[Category: RCSB PDB Molecule of the Month]]
[[Category: Single protein]]
[[Category: Selenocysteine Synthase]]
[[Category: Ganichkin, O M.]]
[[Category: Ganichkin, O M]]
[[Category: Wahl, M C.]]
[[Category: Wahl, M C]]
[[Category: Crystal structure]]
[[Category: Cytoplasm]]
[[Category: Disorder-order transition]]
[[Category: Disorder-order transition]]
[[Category: Phosphate-loop]]
[[Category: Phosphate-loop]]
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[[Category: Selenium]]
[[Category: Selenium]]
[[Category: Transferase]]
[[Category: Transferase]]
[[Category: X-ray crystallography]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat Apr  5 19:14:19 2008''

Latest revision as of 14:30, 5 January 2022

Crystal structure of mouse selenocysteine synthaseCrystal structure of mouse selenocysteine synthase

Structural highlights

3bc8 is a 1 chain structure with sequence from Lk3 transgenic mice. The August 2008 RCSB PDB Molecule of the Month feature on Selenocysteine Synthase by David Goodsell is 10.2210/rcsb_pdb/mom_2008_8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:,
NonStd Res:
Gene:Sepsecs, D5Ertd135e (LK3 transgenic mice)
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[SPCS_MOUSE] Converts O-phosphoseryl-tRNA(Sec) to selenocysteinyl-tRNA(Sec) required for selenoprotein biosynthesis (By similarity).

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

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 1.65 A 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.

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[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Ganichkin OM, Xu XM, Carlson BA, Mix H, Hatfield DL, Gladyshev VN, Wahl MC. Structure and catalytic mechanism of eukaryotic selenocysteine synthase. J Biol Chem. 2008 Feb 29;283(9):5849-65. Epub 2007 Dec 19. PMID:18093968 doi:10.1074/jbc.M709342200

3bc8, resolution 1.65Å

Drag the structure with the mouse to rotate

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