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Literature summary for 2.4.1.217 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
Search for more literature for 2.4.1.217

Cloned(Commentary)

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

Crystallization (Commentary)

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

KM Value [mM]

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

Metals/Ions

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

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
GDP-glucose + 3-phospho-D-glycerate Rubrobacter xylanophilus
-
 GDP + 2-(alpha-D-glucosyl)-3-phosphoglycerate
-
 ?
GDP-mannose + 3-phospho-D-glycerate Thermus thermophilus
-
 GDP + 2-(alpha-D-mannosyl)-3-phosphoglycerate
-
 ?
GDP-mannose + 3-phospho-D-glycerate Rhodothermus marinus
-
 GDP + 2-(alpha-D-mannosyl)-3-phosphoglycerate
-
 ?
GDP-mannose + 3-phospho-D-glycerate Pyrococcus horikoshii
-
 GDP + 2-(alpha-D-mannosyl)-3-phosphoglycerate
-
 ?
GDP-mannose + 3-phospho-D-glycerate Rubrobacter xylanophilus
-
 GDP + 2-(alpha-D-mannosyl)-3-phosphoglycerate
-
 ?
GDP-mannose + 3-phospho-D-glycerate Palaeococcus ferrophilus
-
 GDP + 2-(alpha-D-mannosyl)-3-phosphoglycerate
-
 ?
GDP-mannose + 3-phospho-D-glycerate Thermus thermophilus HB27 / ATCC BAA-163 / DSM 7039
-
 GDP + 2-(alpha-D-mannosyl)-3-phosphoglycerate
-
 ?
GDP-mannose + 3-phospho-D-glycerate Pyrococcus horikoshii OT-3
-
 GDP + 2-(alpha-D-mannosyl)-3-phosphoglycerate
-
 ?
additional information Rhodothermus marinus all MPGSs have high affinity for GDP-mannose and 3-D-phosphoglycerate ?
-
 ?
additional information Pyrococcus horikoshii all MPGSs have high affinity for GDP-mannose and 3-D-phosphoglycerate ?
-
 ?
additional information Palaeococcus ferrophilus all MPGSs have high affinity for GDP-mannose and 3-D-phosphoglycerate ?
-
 ?
additional information Thermus thermophilus all MPGSs have high affinity for GDP-mannose and 3-D-phosphoglycerate. Substrate binding structure, overview ?
-
 ?
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 ?
-
 ?
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 ?
-
 ?
additional information Pyrococcus horikoshii OT-3 all MPGSs have high affinity for GDP-mannose and 3-D-phosphoglycerate ?
-
 ?

Organism

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

Reaction

Reaction Comment Organism Reaction ID
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
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)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
GDP-glucose + 3-phospho-D-glycerate
-
 Rubrobacter xylanophilus GDP + 2-(alpha-D-glucosyl)-3-phosphoglycerate
-
 ?
GDP-mannose + 3-phospho-D-glycerate
-
 Thermus thermophilus GDP + 2-(alpha-D-mannosyl)-3-phosphoglycerate
-
 ?
GDP-mannose + 3-phospho-D-glycerate
-
 Rhodothermus marinus GDP + 2-(alpha-D-mannosyl)-3-phosphoglycerate
-
 ?
GDP-mannose + 3-phospho-D-glycerate
-
 Pyrococcus horikoshii GDP + 2-(alpha-D-mannosyl)-3-phosphoglycerate
-
 ?
GDP-mannose + 3-phospho-D-glycerate
-
 Rubrobacter xylanophilus GDP + 2-(alpha-D-mannosyl)-3-phosphoglycerate
-
 ?
GDP-mannose + 3-phospho-D-glycerate
-
 Palaeococcus ferrophilus GDP + 2-(alpha-D-mannosyl)-3-phosphoglycerate
-
 ?
GDP-mannose + 3-phospho-D-glycerate
-
 Thermus thermophilus HB27 / ATCC BAA-163 / DSM 7039 GDP + 2-(alpha-D-mannosyl)-3-phosphoglycerate
-
 ?
GDP-mannose + 3-phospho-D-glycerate
-
 Pyrococcus horikoshii OT-3 GDP + 2-(alpha-D-mannosyl)-3-phosphoglycerate
-
 ?
additional information substrate binding structure, overview Pyrococcus horikoshii ?
-
 ?
additional information substrate binding structure, overview Rubrobacter xylanophilus ?
-
 ?
additional information substrate binding structure, overview Palaeococcus ferrophilus ?
-
 ?
additional information all MPGSs have high affinity for GDP-mannose and 3-D-phosphoglycerate Rhodothermus marinus ?
-
 ?
additional information all MPGSs have high affinity for GDP-mannose and 3-D-phosphoglycerate Pyrococcus horikoshii ?
-
 ?
additional information all MPGSs have high affinity for GDP-mannose and 3-D-phosphoglycerate Palaeococcus ferrophilus ?
-
 ?
additional information all MPGSs have high affinity for GDP-mannose and 3-D-phosphoglycerate. Substrate binding structure, overview Thermus thermophilus ?
-
 ?
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 ?
-
 ?
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 ?
-
 ?
additional information the enzyme is highly specific for 3-phospho-D-glycerate Thermus thermophilus ?
-
 ?
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 ?
-
 ?
additional information the enzyme is highly specific for 3-phospho-D-glycerate Thermus thermophilus HB27 / ATCC BAA-163 / DSM 7039 ?
-
 ?
additional information substrate binding structure, overview Pyrococcus horikoshii OT-3 ?
-
 ?
additional information all MPGSs have high affinity for GDP-mannose and 3-D-phosphoglycerate Pyrococcus horikoshii OT-3 ?
-
 ?

Subunits

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

Synonyms

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

Temperature Optimum [°C]

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

Temperature Stability [°C]

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

pH Optimum

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

General Information

General Information Comment Organism
evolution the enzyme is included in the glycosyltransferase family GT55 Thermus thermophilus
evolution the enzyme is included in the glycosyltransferase family GT55 Rhodothermus marinus
evolution the enzyme is included in the glycosyltransferase family GT55 Pyrococcus horikoshii
evolution the enzyme is included in the glycosyltransferase family GT55 Palaeococcus ferrophilus
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
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
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
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
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
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
additional information the catalytic pocket of MPGS is solvent-exposed at the NDP-sugar binding region, allowing ready access of the substrate Thermus thermophilus
additional information the catalytic pocket of MPGS is solvent-exposed at the NDP-sugar binding region, allowing ready access of the substrate Rhodothermus marinus
additional information the catalytic pocket of MPGS is solvent-exposed at the NDP-sugar binding region, allowing ready access of the substrate Pyrococcus horikoshii
additional information the catalytic pocket of MPGS is solvent-exposed at the NDP-sugar binding region, allowing ready access of the substrate Rubrobacter xylanophilus
additional information the catalytic pocket of MPGS is solvent-exposed at the NDP-sugar binding region, allowing ready access of the substrate Palaeococcus ferrophilus