5x0k

Free serine kinase (E30Q mutant) in complex with AMP

spinqualitylabelsall models 5x0k, resolution 1.65Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 5x0k is a 1 chain structure with sequence from Thermococcus kodakarensis KOD1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.65Å Ligands: AMP Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function SERK_THEKO Free serine kinase that uses ADP to phosphorylate L-serine to yield O-phospho-L-serine and AMP. Publication Abstract from PubMed A free serine kinase (SerK) is involved in L-cysteine biosynthesis in the hyperthermophilic archaeon Thermococcus kodakarensis. The enzyme converts ADP and L-serine (Ser) into AMP and O-phospho-L-serine (Sep), which is a precursor of L-cysteine. SerK is the first identified enzyme that phosphorylates free serine, while serine/threonine protein kinases have been well studied. SerK displays low sequence similarities to known kinases, suggesting that its reaction mechanism is different from those of known kinases. Here, we determined the crystal structures of SerK from T. kodakarensis (Tk-SerK). The overall structure is divided into two domains. A large cleft is found between the two domains in the AMP complex and in the ADP complex. The cleft is closed in the ternary product complex (Sep, AMP, and Tk-SerK), and may also be in the ternary substrate complex (Ser, ADP, and Tk-SerK). The closure may reorient the carboxyl group of E30 near to the Ogamma atom of Ser. The Ogamma atom is considered to be deprotonated by E30 and to attack the beta-phosphate of ADP to form Sep. The substantial decrease in the activity of the E30A mutant is consistent with this mechanism. Our structures also revealed the residues that contribute to the ligand binding. The conservation of these residues in uncharacterized proteins from bacteria may raise the possibility of the presence of free Ser kinases not only in archaea but also in bacteria. Structural Study on the Reaction Mechanism of a Free Serine Kinase Involved in Cysteine Biosynthesis.,Nagata R, Fujihashi M, Kawamura H, Sato T, Fujita T, Atomi H, Miki K ACS Chem Biol. 2017 Mar 30. doi: 10.1021/acschembio.7b00064. PMID:28358477 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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