3w1k: Difference between revisions

Latest revision as of 12:45, 8 November 2023

Crystal structure of the selenocysteine synthase SelA and tRNASec complex

Structural highlights

3w1k is a 10 chain structure with sequence from Aquifex aeolicus VF5 and Caldanaerobacter subterraneus subsp. tengcongensis MB4. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 7.5Å
Ligands:	LLP
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SELA_AQUAE Converts seryl-tRNA(Sec) to selenocysteinyl-tRNA(Sec) required for selenoprotein biosynthesis (By similarity).

Publication Abstract from PubMed

The 21st amino acid, selenocysteine (Sec), is synthesized on its cognate transfer RNA (tRNA(Sec)). In bacteria, SelA synthesizes Sec from Ser-tRNA(Sec), whereas in archaea and eukaryotes SepSecS forms Sec from phosphoserine (Sep) acylated to tRNA(Sec). We determined the crystal structures of Aquifex aeolicus SelA complexes, which revealed a ring-shaped homodecamer that binds 10 tRNA(Sec) molecules, each interacting with four SelA subunits. The SelA N-terminal domain binds the tRNA(Sec)-specific D-arm structure, thereby discriminating Ser-tRNA(Sec) from Ser-tRNA(Ser). A large cleft is created between two subunits and accommodates the 3'-terminal region of Ser-tRNA(Sec). The SelA structures together with in vivo and in vitro enzyme assays show decamerization to be essential for SelA function. SelA catalyzes pyridoxal 5'-phosphate-dependent Sec formation involving Arg residues nonhomologous to those in SepSecS. Different protein architecture and substrate coordination of the bacterial enzyme provide structural evidence for independent evolution of the two Sec synthesis systems present in nature.

Decameric SelA*tRNA(Sec) ring structure reveals mechanism of bacterial selenocysteine formation.,Itoh Y, Brocker MJ, Sekine S, Hammond G, Suetsugu S, Soll D, Yokoyama S Science. 2013 Apr 5;340(6128):75-8. doi: 10.1126/science.1229521. PMID:23559248^[1]

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

References

↑ Itoh Y, Brocker MJ, Sekine S, Hammond G, Suetsugu S, Soll D, Yokoyama S. Decameric SelA*tRNA(Sec) ring structure reveals mechanism of bacterial selenocysteine formation. Science. 2013 Apr 5;340(6128):75-8. doi: 10.1126/science.1229521. PMID:23559248 doi:10.1126/science.1229521

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Itoh Y, Brocker MJ, Sekine S, Hammond G, Suetsugu S, Soll D, Yokoyama S. Decameric SelA*tRNA(Sec) ring structure reveals mechanism of bacterial selenocysteine formation. Science. 2013 Apr 5;340(6128):75-8. doi: 10.1126/science.1229521. PMID:23559248 doi:10.1126/science.1229521

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='3w1k' size='340' side='right'caption='[[3w1k]], [[Resolution|resolution]] 7.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3w1k]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquae Aquae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W1K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3W1K FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3w1k]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus_VF5 Aquifex aeolicus VF5] and [https://en.wikipedia.org/wiki/Caldanaerobacter_subterraneus_subsp._tengcongensis_MB4 Caldanaerobacter subterraneus subsp. tengcongensis MB4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W1K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3W1K FirstGlance]. <br>
-</td></tr><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>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 7.5&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3w1h|3w1h]], [[3w1i|3w1i]], [[3w1j|3w1j]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">selA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224324 AQUAE])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/L-seryl-tRNA(Sec)_selenium_transferase L-seryl-tRNA(Sec) selenium transferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.9.1.1 2.9.1.1] </span></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=3w1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w1k OCA], [https://pdbe.org/3w1k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3w1k RCSB], [https://www.ebi.ac.uk/pdbsum/3w1k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3w1k ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/SELA_AQUAE SELA_AQUAE]] Converts seryl-tRNA(Sec) to selenocysteinyl-tRNA(Sec) required for selenoprotein biosynthesis (By similarity).
+[https://www.uniprot.org/uniprot/SELA_AQUAE SELA_AQUAE] Converts seryl-tRNA(Sec) to selenocysteinyl-tRNA(Sec) required for selenoprotein biosynthesis (By similarity).
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 29: / Line 27: @@
 __TOC__
 </StructureSection>
-[[Category: Aquae]]
+[[Category: Aquifex aeolicus VF5]]
+[[Category: Caldanaerobacter subterraneus subsp. tengcongensis MB4]]
 [[Category: Large Structures]]
-[[Category: Itoh, Y]]
+[[Category: Itoh Y]]
-[[Category: Sekine, S]]
+[[Category: Sekine S]]
-[[Category: Yokoyama, S]]
+[[Category: Yokoyama S]]
-[[Category: Homodecamer]]
-[[Category: Non-canonical trna]]
-[[Category: Pentamer of dimer]]
-[[Category: Protein-rna complex]]
-[[Category: Selenium metabolism]]
-[[Category: Selenocysteine synthesis]]
-[[Category: Transferase-rna complex]]

3w1k: Difference between revisions

Latest revision as of 12:45, 8 November 2023

Crystal structure of the selenocysteine synthase SelA and tRNASec complex

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools