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Structural units important for activity of a novel-type phosphoserine phosphatase from Hydrogenobacter thermophilus TK-6 revealed by crystal structure analysis.

Chiba Y, Horita S, Ohtsuka J, Arai H, Nagata K, Igarashi Y, Tanokura M, Ishii M
J Biol Chem 288 11448-58 (2013)
Cited: 9 times
EuropePMC logo PMID: 23479726

Abstract

Novel-type serine-synthesizing enzymes, termed metal-independent phosphoserine phosphatases (iPSPs), were recently identified and characterized from Hydrogenobacter thermophilus, a chemolithoautotrophic bacterium belonging to the order Aquificales. iPSPs are cofactor-dependent phosphoglycerate mutase (dPGM)-like phosphatases that have significant amino acid sequence similarity to dPGMs but lack phosphoglycerate mutase activity. Genes coding dPGM-like phosphatases have been identified in a broad range of organisms; however, predicting the function of the corresponding proteins based on sequence information alone is difficult due to their diverse substrate preferences. Here, we determined the crystal structure of iPSP1 from H. thermophilus in the apo-form and in complex with its substrate L-phosphoserine to find structural units important for its phosphatase activity toward L-phosphoserine. Structural and biochemical characterization of iPSP1 revealed that the side chains of His(85) and C-terminal region characteristic of iPSP1 are responsible for the PSP activity. The importance of these structural units for PSP activity was confirmed by high PSP activity observed in two novel dPGM-like proteins from Cyanobacteria and Chloroflexus in which the two structural units were conserved. We anticipate that our present findings will facilitate understanding of the serine biosynthesis pathways of organisms that lack gene(s) encoding conventional PSPs, as the structural information revealed here will help to identify iPSP from sequence databases.

Articles - 4ij6 mentioned but not cited (2)

  1. Structural units important for activity of a novel-type phosphoserine phosphatase from Hydrogenobacter thermophilus TK-6 revealed by crystal structure analysis. Chiba Y, Horita S, Ohtsuka J, Arai H, Nagata K, Igarashi Y, Tanokura M, Ishii M. J Biol Chem 288 11448-11458 (2013)
  2. Mechanism of dephosphorylation of glucosyl-3-phosphoglycerate by a histidine phosphatase. Zheng Q, Jiang D, Zhang W, Zhang Q, Zhao Q, Jin J, Li X, Yang H, Bartlam M, Shaw N, Zhou W, Rao Z. J Biol Chem 289 21242-21251 (2014)


Articles citing this publication (7)

  1. Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis. Broddrick JT, Rubin BE, Welkie DG, Du N, Mih N, Diamond S, Lee JJ, Golden SS, Palsson BO. Proc Natl Acad Sci U S A 113 E8344-E8353 (2016)
  2. Genomics-Based Reconstruction and Predictive Profiling of Amino Acid Biosynthesis in the Human Gut Microbiome. Ashniev GA, Petrov SN, Iablokov SN, Rodionov DA. Microorganisms 10 740 (2022)
  3. A Novel Assay for Phosphoserine Phosphatase Exploiting Serine Acetyltransferase as the Coupling Enzyme. Marchesani F, Zangelmi E, Bruno S, Bettati S, Peracchi A, Campanini B. Life (Basel) 11 485 (2021)
  4. Phosphoserine Phosphatase Is Required for Serine and One-Carbon Unit Synthesis in Hydrogenobacter thermophilus. Kim K, Chiba Y, Kobayashi A, Arai H, Ishii M. J Bacteriol 199 e00409-17 (2017)
  5. Discovery of an intermolecular disulfide bond required for the thermostability of a heterodimeric protein from the thermophile Hydrogenobacter thermophilus. Kim KT, Chiba Y, Arai H, Ishii M. Biosci Biotechnol Biochem 80 232-240 (2016)
  6. Discovery and analysis of a novel type of the serine biosynthetic enzyme phosphoserine phosphatase in Thermus thermophilus. Chiba Y, Yoshida A, Shimamura S, Kameya M, Tomita T, Nishiyama M, Takai K. FEBS J 286 726-736 (2019)
  7. Functional characterization of two members of histidine phosphatase superfamily in Mycobacterium tuberculosis. Coker OO, Warit S, Rukseree K, Summpunn P, Prammananan T, Palittapongarnpim P. BMC Microbiol 13 292 (2013)


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