Modomics - A Database of RNA Modifications

ID Card:

Full name: Selenide,water dikinase
Synonym: FdhB
GI: 134423
Orf: b1764
COG: COG0709
UniProt: P16456
Structures: | 3U0O |
Alpha Fold Predicted Structure: AF-P16456-F1
Enzyme type: selenophosphate synthase


PDB Structures:


3U0O

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

Selenophosphate synthetase (SPS) catalyzes the synthesis of selenophosphate, the selenium donor for the biosynthesis of selenocysteine and 2-selenouridine residues in seleno-tRNA. Selenocysteine, known as the 21st amino acid, is then incorporated into proteins during translation to form selenoproteins which serve a variety of cellular processes. SPS activity is dependent on both Mg(2+) and K(+) and uses ATP, selenide, and water to catalyze the formation of AMP, orthophosphate, and selenophosphate. In this reaction, the gamma phosphate of ATP is transferred to the selenide to form selenophosphate, while ADP is hydrolyzed to form orthophosphate and AMP. Most of what is known about the function of SPS has derived from studies investigating Escherichia coli SPS (EcSPS) as a model system. Here we report the crystal structure of the C17S mutant of SPS from E. coli (EcSPS(C17S)) in apo form (without ATP bound). EcSPS(C17S) crystallizes as a homodimer, which was further characterized by analytical ultracentrifugation experiments. The glycine-rich N-terminal region (residues 1 through 47) was found in the open conformation and was mostly ordered in both structures, with a magnesium cofactor bound at the active site of each monomer involving conserved aspartate residues. Mutating these conserved residues (D51, D68, D91, and D227) along with N87, also found at the active site, to alanine completely abolished AMP production in our activity assays, highlighting their essential role for catalysis in EcSPS. Based on the structural and biochemical analysis of EcSPS reported here and using information obtained from similar studies done with SPS orthologs from Aquifex aeolicus and humans, we propose a catalytic mechanism for EcSPS-mediated selenophosphate synthesis.

Download RCSB-PDB Structures:

Pdb Files   3U0O.pdb  
Pdbx/mmCIF Files   3U0O.cif  


Protein sequence:

MSENSIRLTQYSHGAGCGCKISPKVLETILHSEQAKFVDPNLLVGNETRDDAAVYDLGNGTSVISTTDFFMPIVDNPFDFGRIAATNAISDIFAMGGKPIMAIAILGWPINKLSPEIAREVTEGGRYACRQAGIALAGGHSIDAPEPIFGLAVTGIVPTERVKKNSTAQAGCKLFLTKPLGIGVLTTAEKKSLLKPEHQGLATEVMCRMNIAGASFANIEGVKAMTDVTGFGLLGHLSEMCQGAGVQARVDYEAIPKLPGVEEYIKLGAVPGGTERNFASYGHLMGEMPREVRDLLCDPQTSGGLLLAVMPEAENEVKATAAEFGIELTAIGELVPARGGRAMVEIR

Comments:

Selenium donor protein. It catalyzes the magnesium-dependent synthesis of a labile selenium donor compound from selenide and ATP (formation of mono-selenophosphate). selD gene product also is essential for an entirely different process, a posttranscriptional tRNA modification involving the substitution of selenium for sulfur. This compound is required both for the incorporation of selenium into the wobble uridine-34 of several mnm5s2U-containing tRNAs and for the biosynthesis of selenocysteine from an L-serine residue ester bonded to unique tRNA-Ser (anticodon UCA). The exchange of sulfur in mnm5s2U-tRNA into mnm5se2U-tRNA is catalyzed by SelU. Certain Eukarya SelD-like protein lacks the selenide-dependent monophosphate synthetase activity and catalyses only the biosynthesis of selenocysteine.





Alpha Fold Predicted Structure:






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Protein sequence:

M S E N S I R L T Q Y S H G A G C G C K I S P K V L E T I L H S E Q A K F V D P N L L V G N E T R D D A A V Y D L G N G T S V I S T T D F F M P I V D N P F D F G R I A A T N A I S D I F A M G G K P I M A I A I L G W P I N K L S P E I A R E V T E G G R Y A C R Q A G I A L A G G H S I D A P E P I F G L A V T G I V P T E R V K K N S T A Q A G C K L F L T K P L G I G V L T T A E K K S L L K P E H Q G L A T E V M C R M N I A G A S F A N I E G V K A M T D V T G F G L L G H L S E M C Q G A G V Q A R V D Y E A I P K L P G V E E Y I K L G A V P G G T E R N F A S Y G H L M G E M P R E V R D L L C D P Q T S G G L L L A V M P E A E N E V K A T A A E F G I E L T A I G E L V P A R G G R A M V E I R

Secondary Structure Alphabet

  • G: 3-turn helix (310helix)
  • H: α-helix
  • I: 𝝅-helix (5 - turn helix)
  • T: Hydrogen Bonded Turn
  • B: β-sheet
  • S: Bend
  • C: Coil (residues not present in any of the above conformations)
  • N: Not assigned

Download PDB Structures & DSSP Secondary Structures:

Alpha Fold Pdb Files   AF-P16456-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P16456-F1.cif  
DSSP Secondary Structures   P16456.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
In vitro synthesis of selenocysteinyl-tRNA(UCA) from seryl-tRNA(UCA): involvement and characterization of the selD gene product. Leinfelder W, Forchhammer K, Veprek B, Zehelein E, Bock A Proc Natl Acad Sci U S A [details] 2405383 -
Escherichia coli mutant SELD enzymes. The cysteine 17 residue is essential for selenophosphate formation from ATP and selenide. Kim IY, Veres Z, Stadtman TC... J Biol Chem [details] 1527085 -
Selenophosphate synthetase. Enzyme properties and catalytic reaction. Veres Z, Kim IY, Scholz TD, Stadtman TC... J Biol Chem [details] 8144648 -
Biosynthesis of selenophosphate. Lacourciere GM... Biofactors [details] 10609888 -

Links:

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