3BC8

Crystal structure of mouse selenocysteine synthase

PDB DOI: 10.2210/pdb3BC8/pdb

Classification: TRANSFERASE
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-11-12 Released: 2007-12-18
Deposition Author(s): Ganichkin, O.M., Wahl, M.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.199
R-Value Work: 0.168
R-Value Observed: 0.169

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structure and catalytic mechanism of eukaryotic selenocysteine synthase.

Ganichkin, O.M., Xu, X.M., Carlson, B.A., Mix, H., Hatfield, D.L., Gladyshev, V.N., Wahl, M.C.

(2008) J Biol Chem 283: 5849-5865

PubMed: 18093968 Search on PubMed
DOI: 10.1074/jbc.M709342200
Primary Citation of Related Structures:
3BC8, 3BCA, 3BCB

PubMed Abstract:

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.

Organizational Affiliation:

Max-Planck-Institut für Biophysikalische Chemie, Zelluläre Biochemie/Makromolekulare Röntgenkristallographie, Am Fassberg 11, D-37077 Göttingen, Germany.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-phosphoseryl-tRNA(Sec) selenium transferase	A	450	Mus musculus	Mutation(s): 0 Gene Names: Sepsecs, D5Ertd135e EC: 2.9.1 (PDB Primary Data), 2.9.1.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P6M7 (Mus musculus) Explore Q6P6M7 Go to UniProtKB: Q6P6M7
IMPC: MGI:1098791
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6P6M7
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Ligand Interaction
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Ligand Interaction