2YYE

Crystal structure of selenophosphate synthetase from Aquifex aeolicus complexed with AMPCPP

Summary for 2YYE

• Entry DOI: 10.2210/pdb2yye/pdb
• Related: 2E0B 2ZAU 2ZOD
• Descriptor: Selenide, water dikinase, COBALT (II) ION, DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER, ... (5 entities in total)
• Functional Keywords: full-length selenophosphate synthetase complex with atp-analog, structural genomics, nppsfa, national project on protein structural and functional analyses, riken structural genomics/proteomics initiative, rsgi, transferase
• Biological source: Aquifex aeolicus
• Total number of polymer chains: 2
• Total formula weight: 77089.34

Authors

Itoh, Y.,Sekine, S.,Matsumoto, E.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2007-04-29, release date: 2008-04-29, Last modification date: 2024-11-06)

Primary citation

Itoh, Y.,Sekine, S.,Matsumoto, E.,Akasaka, R.,Takemoto, C.,Shirouzu, M.,Yokoyama, S.
Structure of selenophosphate synthetase essential for selenium incorporation into proteins and RNAs
J.Mol.Biol., 385:1456-1469, 2009

PubMed Abstract: Selenophosphate synthetase (SPS) catalyzes the activation of selenide with adenosine 5'-triphosphate (ATP) to generate selenophosphate, the essential reactive selenium donor for the formation of selenocysteine (Sec) and 2-selenouridine residues in proteins and RNAs, respectively. Many SPS are themselves Sec-containing proteins, in which Sec replaces Cys in the catalytically essential position (Sec/Cys). We solved the crystal structures of Aquifex aeolicus SPS and its complex with adenosine 5'-(alpha,beta-methylene) triphosphate (AMPCPP). The ATP-binding site is formed at the subunit interface of the homodimer. Four Asp residues coordinate four metal ions to bind the phosphate groups of AMPCPP. In the free SPS structure, the two loop regions in the ATP-binding site are not ordered, and no enzyme-associated metal is observed. This suggests that ATP binding, metal binding, and the formation of their binding sites are interdependent. To identify the amino-acid residues that contribute to SPS activity, we prepared six mutants of SPS and examined their selenide-dependent ATP consumption. Mutational analyses revealed that Sec/Cys13 and Lys16 are essential. In SPS.AMPCPP, the N-terminal loop, including the two residues, assumes different conformations ("open" and "closed") between the two subunits. The AMPCPP gamma-phosphate group is solvent-accessible, suggesting that a putative nucleophile could attack the ATP gamma-phosphate group to generate selenophosphate and adenosine 5'-diphosphate (ADP). Selenide attached to Sec/Cys13 as -Se-Se(-)/-S-Se(-) could serve as the nucleophile in the "closed" conformation. A water molecule, fixed close to the beta-phosphate group, could function as the nucleophile in subsequent ADP hydrolysis to orthophosphate and adenosine 5'-monophosphate.

PubMed: 18773910
DOI: 10.1016/j.jmb.2008.08.042

Experimental method

X-RAY DIFFRACTION (2.1 Å)