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Literature summary extracted from

  • Borges, N.; Jorge, C.D.; Goncalves, L.G.; Goncalves, S.; Matias, P.M.; Santos, H.
    Mannosylglycerate: structural analysis of biosynthesis and evolutionary history (2014), Extremophiles, 18, 835-852.
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
2.4.1.217 phylogenetic analysis Thermus thermophilus
2.4.1.217 phylogenetic analysis Rhodothermus marinus
2.4.1.217 phylogenetic analysis Pyrococcus horikoshii
2.4.1.217 phylogenetic analysis Rubrobacter xylanophilus
2.4.1.217 phylogenetic analysis Palaeococcus ferrophilus

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
2.4.1.217 enzyme in apo-form and in complex with GMP and GDP-mannose Rubrobacter xylanophilus

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
2.4.1.217 0.13
-
 3-phospho-D-glycerate pH 7.0, 80-90°C Thermus thermophilus
2.4.1.217 0.14
-
 3-phospho-D-glycerate pH 6.4-7.4, 90°C Pyrococcus horikoshii
2.4.1.217 0.17
-
 GDP-mannose pH 6.4-7.4, 90°C Pyrococcus horikoshii
2.4.1.217 0.26
-
 GDP-mannose pH 7.0-8.0, 70-75°C Rubrobacter xylanophilus
2.4.1.217 0.33
-
 GDP-mannose pH 7.0, 80-90°C Thermus thermophilus
2.4.1.217 0.34
-
 3-phospho-D-glycerate pH 7.0-8.0, 70-75°C Rubrobacter xylanophilus
2.4.1.217 0.5
-
 GDP-mannose pH 7.5, 80°C Rhodothermus marinus
2.4.1.217 0.63
-
 3-phospho-D-glycerate pH 7.5, 80°C Rhodothermus marinus
2.4.1.217 1.21
-
 GDP-glucose pH 7.0-8.0, 70-75°C Rubrobacter xylanophilus

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
2.4.1.217 Mg2+ binding structure overview Thermus thermophilus
2.4.1.217 Mg2+ binding structure overview Rhodothermus marinus
2.4.1.217 Mg2+ binding structure overview Pyrococcus horikoshii
2.4.1.217 Mg2+ binding structure overview Rubrobacter xylanophilus
2.4.1.217 Mg2+ binding structure overview Palaeococcus ferrophilus
2.4.1.217 Mn2+ binding structure overview Thermus thermophilus
2.4.1.217 Mn2+ binding structure overview Rhodothermus marinus
2.4.1.217 Mn2+ binding structure overview Pyrococcus horikoshii
2.4.1.217 Mn2+ binding structure overview Rubrobacter xylanophilus
2.4.1.217 Mn2+ binding structure overview Palaeococcus ferrophilus
2.4.1.217 Zn2+ binding structure overview Thermus thermophilus
2.4.1.217 Zn2+ binding structure overview Rhodothermus marinus
2.4.1.217 Zn2+ binding structure overview Pyrococcus horikoshii
2.4.1.217 Zn2+ binding structure overview Rubrobacter xylanophilus
2.4.1.217 Zn2+ binding structure overview Palaeococcus ferrophilus

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2.4.1.217 GDP-glucose + 3-phospho-D-glycerate Rubrobacter xylanophilus
-
 GDP + 2-(alpha-D-glucosyl)-3-phosphoglycerate
-
 ?
2.4.1.217 GDP-mannose + 3-phospho-D-glycerate Thermus thermophilus
-
 GDP + 2-(alpha-D-mannosyl)-3-phosphoglycerate
-
 ?
2.4.1.217 GDP-mannose + 3-phospho-D-glycerate Rhodothermus marinus
-
 GDP + 2-(alpha-D-mannosyl)-3-phosphoglycerate
-
 ?
2.4.1.217 GDP-mannose + 3-phospho-D-glycerate Pyrococcus horikoshii
-
 GDP + 2-(alpha-D-mannosyl)-3-phosphoglycerate
-
 ?
2.4.1.217 GDP-mannose + 3-phospho-D-glycerate Rubrobacter xylanophilus
-
 GDP + 2-(alpha-D-mannosyl)-3-phosphoglycerate
-
 ?
2.4.1.217 GDP-mannose + 3-phospho-D-glycerate Palaeococcus ferrophilus
-
 GDP + 2-(alpha-D-mannosyl)-3-phosphoglycerate
-
 ?
2.4.1.217 GDP-mannose + 3-phospho-D-glycerate Thermus thermophilus HB27 / ATCC BAA-163 / DSM 7039
-
 GDP + 2-(alpha-D-mannosyl)-3-phosphoglycerate
-
 ?
2.4.1.217 GDP-mannose + 3-phospho-D-glycerate Pyrococcus horikoshii OT-3
-
 GDP + 2-(alpha-D-mannosyl)-3-phosphoglycerate
-
 ?
2.4.1.217 additional information Rhodothermus marinus all MPGSs have high affinity for GDP-mannose and 3-D-phosphoglycerate ?
-
 ?
2.4.1.217 additional information Pyrococcus horikoshii all MPGSs have high affinity for GDP-mannose and 3-D-phosphoglycerate ?
-
 ?
2.4.1.217 additional information Palaeococcus ferrophilus all MPGSs have high affinity for GDP-mannose and 3-D-phosphoglycerate ?
-
 ?
2.4.1.217 additional information Thermus thermophilus all MPGSs have high affinity for GDP-mannose and 3-D-phosphoglycerate. Substrate binding structure, overview ?
-
 ?
2.4.1.217 additional information Rubrobacter xylanophilus all MPGSs have high affinity for GDP-mannose and 3-D-phosphoglycerate. The enzyme from Rubrobacter xylanophilus is promiscuous and produces the phosphorylated form of glucosylglycerate (GPG) from GDP-glucose plus 3-D-phosphoglycerate with high efficiency. In spite of the less favorable parameters for the synthesis of mannosylglycerate, this is the only free glyceryl glycoside found in Rubrobacter xylanophilus cells ?
-
 ?
2.4.1.217 additional information Thermus thermophilus HB27 / ATCC BAA-163 / DSM 7039 all MPGSs have high affinity for GDP-mannose and 3-D-phosphoglycerate. Substrate binding structure, overview ?
-
 ?
2.4.1.217 additional information Pyrococcus horikoshii OT-3 all MPGSs have high affinity for GDP-mannose and 3-D-phosphoglycerate ?
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
2.4.1.217 Palaeococcus ferrophilus
-
-
-
2.4.1.217 Pyrococcus horikoshii
-
-
-
2.4.1.217 Pyrococcus horikoshii OT-3
-
-
-
2.4.1.217 Rhodothermus marinus
-
-
-
2.4.1.217 Rubrobacter xylanophilus
-
-
-
2.4.1.217 Thermus thermophilus
-
-
-
2.4.1.217 Thermus thermophilus HB27 / ATCC BAA-163 / DSM 7039
-
-
-

Reaction

EC Number Reaction Comment Organism Reaction ID
2.4.1.217 GDP-mannose + 3-phospho-D-glycerate = GDP + 2-(alpha-D-mannosyl)-3-phosphoglycerate front-face SNi-like reaction mechanism, detailed overview. The binding of GDP-mannose:Mn2+ to the enzyme from Rhodothermus marinus induces significant conformational changes in the flexible loop. In particular, Tyr220 plays a pivotal role both in D-glycerate binding and in catalysis: it is reoriented towards the pocket interior and either interacts with the a phosphate of GDP-mannose Rhodothermus marinus
a
2.4.1.217 GDP-mannose + 3-phospho-D-glycerate = GDP + 2-(alpha-D-mannosyl)-3-phosphoglycerate front-face SNi-like reaction mechanism, overview Thermus thermophilus
a

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.4.1.217 GDP-glucose + 3-phospho-D-glycerate
-
 Rubrobacter xylanophilus GDP + 2-(alpha-D-glucosyl)-3-phosphoglycerate
-
 ?
2.4.1.217 GDP-mannose + 3-phospho-D-glycerate
-
 Thermus thermophilus GDP + 2-(alpha-D-mannosyl)-3-phosphoglycerate
-
 ?
2.4.1.217 GDP-mannose + 3-phospho-D-glycerate
-
 Rhodothermus marinus GDP + 2-(alpha-D-mannosyl)-3-phosphoglycerate
-
 ?
2.4.1.217 GDP-mannose + 3-phospho-D-glycerate
-
 Pyrococcus horikoshii GDP + 2-(alpha-D-mannosyl)-3-phosphoglycerate
-
 ?
2.4.1.217 GDP-mannose + 3-phospho-D-glycerate
-
 Rubrobacter xylanophilus GDP + 2-(alpha-D-mannosyl)-3-phosphoglycerate
-
 ?
2.4.1.217 GDP-mannose + 3-phospho-D-glycerate
-
 Palaeococcus ferrophilus GDP + 2-(alpha-D-mannosyl)-3-phosphoglycerate
-
 ?
2.4.1.217 GDP-mannose + 3-phospho-D-glycerate
-
 Thermus thermophilus HB27 / ATCC BAA-163 / DSM 7039 GDP + 2-(alpha-D-mannosyl)-3-phosphoglycerate
-
 ?
2.4.1.217 GDP-mannose + 3-phospho-D-glycerate
-
 Pyrococcus horikoshii OT-3 GDP + 2-(alpha-D-mannosyl)-3-phosphoglycerate
-
 ?
2.4.1.217 additional information substrate binding structure, overview Pyrococcus horikoshii ?
-
 ?
2.4.1.217 additional information substrate binding structure, overview Rubrobacter xylanophilus ?
-
 ?
2.4.1.217 additional information substrate binding structure, overview Palaeococcus ferrophilus ?
-
 ?
2.4.1.217 additional information all MPGSs have high affinity for GDP-mannose and 3-D-phosphoglycerate Rhodothermus marinus ?
-
 ?
2.4.1.217 additional information all MPGSs have high affinity for GDP-mannose and 3-D-phosphoglycerate Pyrococcus horikoshii ?
-
 ?
2.4.1.217 additional information all MPGSs have high affinity for GDP-mannose and 3-D-phosphoglycerate Palaeococcus ferrophilus ?
-
 ?
2.4.1.217 additional information all MPGSs have high affinity for GDP-mannose and 3-D-phosphoglycerate. Substrate binding structure, overview Thermus thermophilus ?
-
 ?
2.4.1.217 additional information all MPGSs have high affinity for GDP-mannose and 3-D-phosphoglycerate. The enzyme from Rubrobacter xylanophilus is promiscuous and produces the phosphorylated form of glucosylglycerate (GPG) from GDP-glucose plus 3-D-phosphoglycerate with high efficiency. In spite of the less favorable parameters for the synthesis of mannosylglycerate, this is the only free glyceryl glycoside found in Rubrobacter xylanophilus cells Rubrobacter xylanophilus ?
-
 ?
2.4.1.217 additional information besides its physiological substrate D-glycerate, RmaMGS is also able to use D-lactate and glycolate as sugar acceptors, thus displaying some acceptor plasticity. Substrate binding structure, overview Rhodothermus marinus ?
-
 ?
2.4.1.217 additional information the enzyme is highly specific for 3-phospho-D-glycerate Thermus thermophilus ?
-
 ?
2.4.1.217 additional information all MPGSs have high affinity for GDP-mannose and 3-D-phosphoglycerate. Substrate binding structure, overview Thermus thermophilus HB27 / ATCC BAA-163 / DSM 7039 ?
-
 ?
2.4.1.217 additional information the enzyme is highly specific for 3-phospho-D-glycerate Thermus thermophilus HB27 / ATCC BAA-163 / DSM 7039 ?
-
 ?
2.4.1.217 additional information substrate binding structure, overview Pyrococcus horikoshii OT-3 ?
-
 ?
2.4.1.217 additional information all MPGSs have high affinity for GDP-mannose and 3-D-phosphoglycerate Pyrococcus horikoshii OT-3 ?
-
 ?

Subunits

EC Number Subunits Comment Organism
2.4.1.217 More monomer structure from crystal structure modeling, overview Thermus thermophilus
2.4.1.217 More monomer structure from crystal structure modeling, overview Rhodothermus marinus
2.4.1.217 More monomer structure from crystal structure modeling, overview Pyrococcus horikoshii
2.4.1.217 More monomer structure from crystal structure modeling, overview Rubrobacter xylanophilus
2.4.1.217 More monomer structure from crystal structure modeling, overview Palaeococcus ferrophilus

Synonyms

EC Number Synonyms Comment Organism
2.4.1.217 MPGS
-
 Thermus thermophilus
2.4.1.217 MPGS
-
 Rhodothermus marinus
2.4.1.217 MPGS
-
 Pyrococcus horikoshii
2.4.1.217 MPGS
-
 Palaeococcus ferrophilus
2.4.1.217 MPGS/GPGS
-
 Rubrobacter xylanophilus

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
2.4.1.217 70 75
-
 Rubrobacter xylanophilus
2.4.1.217 80 90
-
 Thermus thermophilus
2.4.1.217 80 90
-
 Rhodothermus marinus
2.4.1.217 90
-
-
 Palaeococcus ferrophilus
2.4.1.217 90 100
-
 Pyrococcus horikoshii

Temperature Stability [°C]

EC Number Temperature Stability Minimum [°C] Temperature Stability Maximum [°C] Comment Organism
2.4.1.217 60
-
 half-life is 23-28 min dependent on the substrate Rubrobacter xylanophilus
2.4.1.217 80
-
 half-life is 40 min Rhodothermus marinus
2.4.1.217 80
-
 half-life is 189 min Thermus thermophilus
2.4.1.217 83
-
 half-life is 18 min Palaeococcus ferrophilus
2.4.1.217 90
-
 half-life is 22 min Thermus thermophilus
2.4.1.217 98
-
 half-life is 16 min Pyrococcus horikoshii
2.4.1.217 100
-
 half-life is 10 min Thermus thermophilus

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
2.4.1.217 6.4 7.4
-
 Pyrococcus horikoshii
2.4.1.217 7 8
-
 Rubrobacter xylanophilus
2.4.1.217 7
-
-
 Thermus thermophilus
2.4.1.217 7
-
-
 Palaeococcus ferrophilus
2.4.1.217 7.5
-
-
 Rhodothermus marinus

General Information

EC Number General Information Comment Organism
2.4.1.217 evolution the enzyme is included in the glycosyltransferase family GT55 Thermus thermophilus
2.4.1.217 evolution the enzyme is included in the glycosyltransferase family GT55 Rhodothermus marinus
2.4.1.217 evolution the enzyme is included in the glycosyltransferase family GT55 Pyrococcus horikoshii
2.4.1.217 evolution the enzyme is included in the glycosyltransferase family GT55 Palaeococcus ferrophilus
2.4.1.217 evolution the promiscuous MPGS/GPGS from Rubrobacter xylanophilus (RxyMPGS) is included within the retaining GT81 family, members of the GT55 and GT81 families preserved a common structural core, defined by the alpha/beta/alpha region containing 7 beta-strands in the order 3-2-1-4-6-5-7, with beta6 antiparallel to the rest, that could be included into the MGS-like family Rubrobacter xylanophilus
2.4.1.217 metabolism mannosylglycerate metabolism overview: pathways for the synthesis and hydrolysis of mannosylglycerate (MG). In the single-step pathway mannosylglycerate synthase (MGS) catalyzes the direct condensation of GDP-mannose with D-glycerate to produce MG. In the two-step pathway, mannosyl-3-phosphoglycerate synthase (MPGS) catalyzes the conversion of GDP-mannose and D-3-phosphoglycerate into mannosyl-3-phosphoglycerate (MPG) which is dephosphorylated into MG by mannosyl-3-phosphoglycerate phosphatase (MPGP) Thermus thermophilus
2.4.1.217 metabolism mannosylglycerate metabolism overview: pathways for the synthesis and hydrolysis of mannosylglycerate (MG). In the single-step pathway mannosylglycerate synthase (MGS) catalyzes the direct condensation of GDP-mannose with D-glycerate to produce MG. In the two-step pathway, mannosyl-3-phosphoglycerate synthase (MPGS) catalyzes the conversion of GDP-mannose and D-3-phosphoglycerate into mannosyl-3-phosphoglycerate (MPG) which is dephosphorylated into MG by mannosyl-3-phosphoglycerate phosphatase (MPGP) Rhodothermus marinus
2.4.1.217 metabolism mannosylglycerate metabolism overview: pathways for the synthesis and hydrolysis of mannosylglycerate (MG). In the single-step pathway mannosylglycerate synthase (MGS) catalyzes the direct condensation of GDP-mannose with D-glycerate to produce MG. In the two-step pathway, mannosyl-3-phosphoglycerate synthase (MPGS) catalyzes the conversion of GDP-mannose and D-3-phosphoglycerate into mannosyl-3-phosphoglycerate (MPG) which is dephosphorylated into MG by mannosyl-3-phosphoglycerate phosphatase (MPGP) Pyrococcus horikoshii
2.4.1.217 metabolism mannosylglycerate metabolism overview: pathways for the synthesis and hydrolysis of mannosylglycerate (MG). In the single-step pathway mannosylglycerate synthase (MGS) catalyzes the direct condensation of GDP-mannose with D-glycerate to produce MG. In the two-step pathway, mannosyl-3-phosphoglycerate synthase (MPGS) catalyzes the conversion of GDP-mannose and D-3-phosphoglycerate into mannosyl-3-phosphoglycerate (MPG) which is dephosphorylated into MG by mannosyl-3-phosphoglycerate phosphatase (MPGP) Palaeococcus ferrophilus
2.4.1.217 metabolism mannosylglycerate metabolism overview: pathways for the synthesis and hydrolysis of mannosylglycerate (MG). In the single-step pathway mannosylglycerate synthase (MGS)catalyzes the direct condensation of GDP-mannose with D-glycerate to produce MG. In the two-step pathway, mannosyl-3-phosphoglycerate synthase (MPGS) catalyzes the conversion of GDP-mannose and D-3-phosphoglycerate into mannosyl-3-phosphoglycerate (MPG) which is dephosphorylated into MG by mannosyl-3-phosphoglycerate phosphatase (MPGP) Rubrobacter xylanophilus
2.4.1.217 additional information the catalytic pocket of MPGS is solvent-exposed at the NDP-sugar binding region, allowing ready access of the substrate Thermus thermophilus
2.4.1.217 additional information the catalytic pocket of MPGS is solvent-exposed at the NDP-sugar binding region, allowing ready access of the substrate Rhodothermus marinus
2.4.1.217 additional information the catalytic pocket of MPGS is solvent-exposed at the NDP-sugar binding region, allowing ready access of the substrate Pyrococcus horikoshii
2.4.1.217 additional information the catalytic pocket of MPGS is solvent-exposed at the NDP-sugar binding region, allowing ready access of the substrate Rubrobacter xylanophilus
2.4.1.217 additional information the catalytic pocket of MPGS is solvent-exposed at the NDP-sugar binding region, allowing ready access of the substrate Palaeococcus ferrophilus