Crystallization and preliminary crystallographic analysis of human serine dehydratase

Sun, Lei; Li, Xuemei; Dong, Yuhui; Yang, Maojun; Liu, Yiwei; Han, Xiaoyang; Zhang, Xian-En; Pang, Hai; Rao, Zihe

doi:10.1107/s0907444903020110

Cited by 6 publications

(2 citation statements)

References 28 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The closest structural homologs of Sp SR and hSR are the degradative threonine dehydratase from Salmonella enterica subsp. enterica serovar Typhimiurium ( St TdcB) 26 (pdb code: 2GN2) and human serine dehydratase (hSDH) 27 , 28 (pdb code: 1P5J) 14 . SR, TdcB and SDH are all able to catalyse the cleavage of the Cβ-O bond of either serine or threonine with formation of an α-aminoacrylate/α-aminocrotonate that spontaneously hydrolyses to pyruvate/α-ketobutyrate and ammonia (Fig.…”

Section: Resultsmentioning

confidence: 99%

Glutamine 89 is a key residue in the allosteric modulation of human serine racemase activity by ATP

Canosa

Faggiano

Marchetti

et al. 2018

Sci Rep

View full text Add to dashboard Cite

Serine racemase (SR) catalyses two reactions: the reversible racemisation of L-serine and the irreversible dehydration of L- and D-serine to pyruvate and ammonia. SRs are evolutionarily related to serine dehydratases (SDH) and degradative threonine deaminases (TdcB). Most SRs and TdcBs – but not SDHs – are regulated by nucleotides. SR binds ATP cooperatively and the nucleotide allosterically stimulates the serine dehydratase activity of the enzyme. A H-bond network comprising five residues (T52, N86, Q89, E283 and N316) and water molecules connects the active site with the ATP-binding site. Conservation analysis points to Q89 as a key residue for the allosteric communication, since its mutation to either Met or Ala is linked to the loss of control of activity by nucleotides. We verified this hypothesis by introducing the Q89M and Q89A point mutations in the human SR sequence. The allosteric communication between the active site and the allosteric site in both mutants is almost completely abolished. Indeed, the stimulation of the dehydratase activity by ATP is severely diminished and the binding of the nucleotide is no more cooperative. Ancestral state reconstruction suggests that the allosteric control by nucleotides established early in SR evolution and has been maintained in most eukaryotic lineages.

show abstract

Section: Resultsmentioning

confidence: 99%

Glutamine 89 is a key residue in the allosteric modulation of human serine racemase activity by ATP

Canosa

Faggiano

Marchetti

et al. 2018

Sci Rep

View full text Add to dashboard Cite

show abstract

“…The expression of hSDH in E. coli , the purification of the expressed enzyme and the crystallization of the purified enzyme have been reported elsewhere (Sun et al 2003). Briefly, recombinant hSDH was crystallized by the hanging‐drop vapor diffusion method.…”

Section: Methodsmentioning

confidence: 99%

Crystal structure of the pyridoxal‐5′‐phosphate‐dependent serine dehydratase from human liver

et al. 2005

View full text Add to dashboard Cite

L-serine dehydratase (SDH), a member of the ␤-family of pyridoxal phosphate-dependent (PLP) enzymes, catalyzes the deamination of L-serine and L-threonine to yield pyruvate or 2-oxobutyrate. The crystal structure of L-serine dehydratase from human liver (hSDH) has been solved at 2.5 Å-resolution by molecular replacement. The structure is a homodimer and reveals a fold typical for ␤-family PLP-dependent enzymes. Each monomer serves as an active unit and is subdivided into two distinct domains: a small domain and a PLP-binding domain that covalently anchors the cofactor. Both domains show the typical open ␣/␤ architecture of PLP enzymes. Comparison with the rSDH-(PLP-OMS) holo-enzyme reveals a large structural difference in active sites caused by the artifical O-methylserine. Furthermore, the activity of hSDH-PLP was assayed and it proved to show catalytic activity. That suggests that the structure of hSDH-PLP is the first structure of the active natural holo-SDH.Keywords: serine dehydratase; pyridoxal phosphate-dependent (PLP) enzyme; human liver; deamination; crystal structure L-serine dehydratase (SDH) (EC 4.2.1.17) catalyzes the deamination of L-serine to yield ammonia and pyruvate (Fig. 1). The enzyme from a number of sources also acts on L-threonine to yield 2-oxobutanoate (Ogawa et al. 2000). SDH is a pyridoxal 5Ј-phosphate (PLP) dependent enzyme and has been assigned to the ␤ family of PLP enzymes (Mehta and Christen 2000). L-threonine dehydratase (TDH) (EC 4.2.1.19) (Nakagawa 1971) also catalyzes the degradation of L-threonine and L-serine by the same mechanism and, therefore, is thought to be similar to SDH.SDH is widely distributed in nature, but its physicochemical properties are considerably different from species to species. For example, rat liver serine dehydratase (rSDH) is a dimer (Xue et al. 1999;Ogawa et al. 2002), whereas yeast and Escherichia coli biosynthetic threonine dehydratase (eTDH), the first enzyme in the isoleucine synthesis pathway, is a tetramer and is feedback-inhibited by isoleucine and heterotropically activated by valine. E. coli biodegradative threonine dehydratase (d-eTDH) induced anaerobically in tryptone-yeast extract medium is a tetramer and is allosterically activated by AMP (Madison and Thompson 1976). However, E. coli D-SDH is a monomer (Marceau et al. 1988b). On the other hand, the sequence alignment of SDHs shows only moderate sequence homology.In spite of the great variety in primary and quaternary structures of SDHs, two conserved sequence motifs have been identified. One is Ser-Xaa-Lys-Ile-Arg-Gly, which is well conserved among SDHs from human (Ogawa et al. 1989a), rat (Ogawa et al. 1989b, tomato (Samach et al.Reprint requests to: Zihe Rao, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China; e-mail: raozh@ibp.ac.cn; fax: +86-10-6486-7566.Abbreviations: SDH, serine dehydratase; TDH, threonine dehydratase; PLP, pyridoxal 5Ј-phosphate; hSDH human serine dehydratase; rSDH, rat serine dehydratase; ...

show abstract

L-Serine ammonia-lyase

2010

Class 4–6 Lyases, Isomerases, Ligases

View full text Add to dashboard Cite

Crystallization and preliminary crystallographic analysis of human serine dehydratase

Cited by 6 publications

References 28 publications

Glutamine 89 is a key residue in the allosteric modulation of human serine racemase activity by ATP

Glutamine 89 is a key residue in the allosteric modulation of human serine racemase activity by ATP

Crystal structure of the pyridoxal‐5′‐phosphate‐dependent serine dehydratase from human liver

L-Serine ammonia-lyase

Contact Info

Product

Resources

About