Crystal Structure of Phosphoserine Phosphatase from Methanococcus jannaschii, a Hyperthermophile, at 1.8 Å Resolution

Wang, Weiru; Kim, Rosalind; Jancarik, J.; Yokota, Hisao; Kim, Sung‐Hou

doi:10.1016/s0969-2126(00)00558-x

Cited by 135 publications

(216 citation statements)

References 36 publications

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“…Figure 2 shows the superposition of the backbones of these three HAD family phosphotransferases. The average B-factor of the -PGM cap domain is higher (B factor ) 41.9) than that of the core domain (B factor ) 26.58), consistent with the known mobility of the cap domain in several HAD structures (4,10,11).…”

Section: Resultssupporting

confidence: 77%

“…It consists of an antiparallel, four-helix bundle (R1-R4). Together the core and the cap domain give rise to a kidney-bean shaped monomer, similar to that seen in the structures of phosphonoacetaldehyde hydrolase (10) and phosphoserine phosphatase (11). Like these two phosphotransferases, -PGM is a member of the haloacid dehaloge- nase (HAD) enzyme superfamily as verified by the fact that it shares the common R/ core domain with other HAD family members.…”

Section: Resultsmentioning

confidence: 58%

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Caught in the Act: The Structure of Phosphorylated β-Phosphoglucomutase from Lactococcus lactis^,

et al. 2002

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Phosphoglucomutases catalyze the interconversion of D-glucose 1-phosphate and D-glucose 6-phosphate, a reaction central to energy metabolism in all cells and to the synthesis of cell wall polysaccharides in bacterial cells. Two classes of phosphoglucomutases (R-PGM and -PGM) are distinguished on the basis of their specificity for R-and -glucose-1-phosphate. -PGM is a member of the haloacid dehalogenase (HAD) superfamily, which includes the sarcoplasmic Ca 2+ -ATPase, phosphomannomutase, and phosphoserine phosphatase. -PGM is unusual among family members in that the common phosphoenzyme intermediate exists as a stable ground-state complex in this enzyme. Herein we report, for the first time, the three-dimensional structure of a -PGM and the first view of the true phosphoenzyme intermediate in the HAD superfamily. The crystal structure of the Mg(II) complex of phosphorylated -phosphoglucomutase ( -PGM) from Lactococcus lactis has been determined to 2.3 Å resolution by multiwavelength anomalous diffraction (MAD) phasing on selenomethionine, and refined to an R cryst ) 0.24 and R free ) 0.28. The active site of -PGM is located between the core and the cap domain and is freely solvent accessible. The residues within a 6 Å radius of the phosphorylated Asp8 include Asp10, Thr16, Ser114, Lys145, Glu169, and Asp170. The cofactor Mg 2+ is liganded with octahedral coordination geometry by the carboxylate side chains of Asp8, Glu169, Asp170, and the backbone carbonyl oxygen of Asp10 along with one oxygen from the Asp8-phosphoryl group and one water ligand. The phosphate group of the phosphoaspartyl residue, Asp8, interacts with the side chains of Ser114 and Lys145. The absence of a base residue near the aspartyl phosphate group accounts for the persistence of the phosphorylated enzyme under physiological conditions. Substrate docking shows that glucose-6-P can bind to the active site of phosphorylated -PGM in such a way as to position the C(1)OH near the phosphoryl group of the phosphorylated Asp8 and the C(6) phosphoryl group near the carboxylate group of Asp10. This result suggests a novel two-base mechanism for phosphoryl group transfer in a phosphorylated sugar.In this paper, we report the three-dimensional structure of the -phosphoglucomutase from Lactococcus lactis. Both R-and -phosphoglucomutases catalyze the interconversion of D-glucose-1-phosphate (G1P) and glucose-6-phosphate (G6P). This reaction is central to energy metabolism in all cells and is essential to the synthesis of cell wall polysaccharides in bacterial cells (1, 2). The R-phosphoglucomutase (R-PGM) acts on the R-C(1) anomer of G1P, while the -phosphoglucomutase ( -PGM) catalyzes the reaction of the -C(1) anomer. Both mutases employ Mg 2+ and -or R-glucose 1,6-diphosphate (G1,6-diP) as cofactors (1, 2). In addition, both mutases are monomeric proteins. The R-PGM (65 kDa) is, however, approximately twice the size of the -PGM (25 kDa) (3). The X-ray structure of R-PGM from rat reveals a 4-domain R-/ -protein. All four domains contribute residue...

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Section: Resultssupporting

confidence: 77%

Section: Resultsmentioning

confidence: 58%

Caught in the Act: The Structure of Phosphorylated β-Phosphoglucomutase from Lactococcus lactis^,

et al. 2002

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“…Motif II contains a Ser or Thr, generally in a hydrophobic context. The Ser or Thr side chain hydrogen bonds with a phosphoryl oxygen in the substrate, helping to orientate it in the correct position for nucleophilic attack by the first Asp in motif I (Wang et al, 2001). Motif III, (G/S)(D/S)X 3 (D/N), includes a conserved Lys that stabilizes the phosphorylated state of the phospho-Asp intermediate.…”

Section: Introductionmentioning

confidence: 99%

“…Motif III, (G/S)(D/S)X 3 (D/N), includes a conserved Lys that stabilizes the phosphorylated state of the phospho-Asp intermediate. In many HAD proteins, other residues in motif III interact with a divalent metal ion, usually Mg 2þ , as do some of the residues in motif I (Morais et al, 2000;Wang et al, 2001). The structures of several members of the HAD superfamily have been determined, including proteins of the bacterial twocomponent system, a HAD, a sarcoplasmic reticulum calcium pump, a phosphoserine phosphatase, a tRNA repair enzyme, a b-phosphoglucomutase, and a deoxyribonucleotidase (Ridder et al, 1997;Welch et al, 1998;Toyoshima et al, 2000;Wang et al, 2001;Galburt et al, 2002;Lahiri et al, 2002;RinaldoMatthis et al, 2002).…”

Section: Introductionmentioning

confidence: 99%

The Structure of a Cyanobacterial Sucrose-Phosphatase Reveals the Sugar Tongs That Release Free Sucrose in the Cell

et al. 2005

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Sucrose-phosphatase (SPP) catalyzes the final step in the pathway of sucrose biosynthesis in both plants and cyanobacteria, and the SPPs from these two groups of organisms are closely related. We have crystallized the enzyme from the cyanobacterium Synechocystis sp PCC 6803 and determined its crystal structure alone and in complex with various ligands. The protein consists of a core domain containing the catalytic site and a smaller cap domain that contains a glucose binding site. Two flexible hinge loops link the two domains, forming a structure that resembles a pair of sugar tongs. The glucose binding site plays a major role in determining the enzyme's remarkable substrate specificity and is also important for its inhibition by sucrose and glucose. It is proposed that the catalytic reaction is initiated by nucleophilic attack on the substrate by Asp9 and involves formation of a covalent phospho-Asp9-enzyme intermediate. From modeling based on the SPP structure, we predict that the noncatalytic SPP-like domain of the Synechocystis sucrose-phosphate synthase could bind sucrose-6 F -phosphate and propose that this domain might be involved in metabolite channeling between the last two enzymes in the pathway of sucrose synthesis.

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“…The crystal structure of the AphA enzyme has been recently solved [3], revealing that, despite the lack of sequence homology, AphA exhibits a haloacid dehalogenase fold similar to that of other phosphatases such as the phosphoserine phosphatase (PSP) of Methanococcus jannaschii (PDB: 1F5S) [3,4], and the human mitochondrial 5V-(3V)-deoxyribonucleotidase (dNT-2) (PDB: 1MH9) [3,5].…”

Section: Introductionmentioning

confidence: 99%

Biochemical characterization of the class B acid phosphatase (AphA) of Escherichia coli MG1655

Passariello

Forleo

Micheli

et al. 2006

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

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The AphA enzyme of Escherichia coli, a molecular class B periplasmic phosphatase that belongs to the DDDD superfamily of phosphohydrolases, was purified and subjected to biochemical characterization. Kinetic analysis with several substrates revealed that the enzyme essentially behaves as a broad-spectrum nucleotidase highly active on 3V-and 5V-mononucleotides and monodeoxynucleotides, but not active on cyclic nucleotides, or nucleotides di-and triphosphate. Mononucleotides are degraded to nucleosides, and AphA apparently does not exhibit any nucleotide phosphomutase activity. However, it can transphosphorylate nucleosides in the presence of phosphate donors. Kinetic properties of AphA are consistent with structural data, and suggest a role for the hydrophobic pocket present in the active site crevice, made by residues Phe 56, Leu71, Trp77 and Tyr193, in conferring preferential substrate specificity by accommodating compounds with aromatic rings. AphA was inhibited by several chelating agents, including EDTA, EGTA, 1,10-phenanthroline and dipicolinic acid, with EDTA being apparently the most powerful inhibitor. D

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Crystal Structure of Phosphoserine Phosphatase from Methanococcus jannaschii, a Hyperthermophile, at 1.8 Å Resolution

Cited by 135 publications

References 36 publications

Caught in the Act: The Structure of Phosphorylated β-Phosphoglucomutase from Lactococcus lactis^,

Caught in the Act: The Structure of Phosphorylated β-Phosphoglucomutase from Lactococcus lactis^,

The Structure of a Cyanobacterial Sucrose-Phosphatase Reveals the Sugar Tongs That Release Free Sucrose in the Cell

Biochemical characterization of the class B acid phosphatase (AphA) of Escherichia coli MG1655

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Crystal Structure of Phosphoserine Phosphatase from Methanococcus jannaschii, a Hyperthermophile, at 1.8 Å Resolution

Cited by 135 publications

References 36 publications

Caught in the Act: The Structure of Phosphorylated β-Phosphoglucomutase from Lactococcus lactis,

Caught in the Act: The Structure of Phosphorylated β-Phosphoglucomutase from Lactococcus lactis,

The Structure of a Cyanobacterial Sucrose-Phosphatase Reveals the Sugar Tongs That Release Free Sucrose in the Cell

Biochemical characterization of the class B acid phosphatase (AphA) of Escherichia coli MG1655

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Caught in the Act: The Structure of Phosphorylated β-Phosphoglucomutase from Lactococcus lactis^,

Caught in the Act: The Structure of Phosphorylated β-Phosphoglucomutase from Lactococcus lactis^,