cupin domain-containing protein, part of a functionally diverse superfamily with the active site generally located at the center of a conserved domain forming a beta-barrel fold
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ...
9-404
5.72e-140
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP (deoxythymidine diphosphates)-4-dehydrorhamnose 3,5-epimerase)-like cupins. RmlC is a dTDP-sugar isomerase involved in the synthesis of L-rhamnose, a saccharide required for the virulence of some pathogenic bacteria. Cupins are a functionally diverse superfamily originally discovered based on the highly conserved motif found in germin and germin-like proteins. This conserved motif forms a beta-barrel fold found in all of the cupins, giving rise to the name cupin ('cupa' is the Latin term for small barrel). The active site of members of this superfamily is generally located at the center of a conserved barrel and usually includes a metal ion. The different functional classes in this superfamily include single domain bacterial isomerases and epimerases involved in the modification of cell wall carbohydrates, two domain bicupins such as the desiccation-tolerant seed storage globulins, and multidomain nuclear transcription factors involved in legume root nodulation.
The actual alignment was detected with superfamily member PLN02288:
Pssm-ID: 477354 [Multi-domain] Cd Length: 394 Bit Score: 405.59 E-value: 5.72e-140
type I phosphomannose isomerase in eukaryotes and bacteria, N-terminal cupin domain; This ...
9-314
2.88e-131
type I phosphomannose isomerase in eukaryotes and bacteria, N-terminal cupin domain; This subfamily contains type I phosphomannose isomerase (PMI; E.C. 5.3.1.8; also known as mannose-6-phosphate isomerase) found in eukaryotes and some bacteria such as Salmonella enterica. PMI catalyzes the reversible isomerization of fructose-6-phosphate (F6P) and mannose-6-phosphate (M6P), the first committed step in the synthesis of mannosylated glycoproteins. The active site, located within the N-terminal jelly roll-like beta-barrel cupin fold, contains a single essential zinc atom and forms a deep, open cavity large enough to contain M6P or F6P. PMI type I also has a C-terminal beta-barrel fold which has diverged considerably from the N-terminal domain and is not included here. This subfamily contains an alpha helical domain that is found in eukaryotic and some prokaryotic PMIs but is not present in their archaeal counterparts. F6P is a substrate for glycolysis and gluconeogenesis, while M6P is a substrate for production of activated mannose donor guanosine 5'-diphosphate D-mannose, an important precursor of mannosylated biomolecules such as glycoproteins, bacterial exopolysaccharides and fungal cell wall components. PMI is also essential for survival, virulence and possibly pathogenicity of some bacteria and protozoan parasites, as well as for cell wall integrity of certain yeasts. Thus, PMI is a potential target against fungal infections causing serious illness or death.
Pssm-ID: 380414 [Multi-domain] Cd Length: 247 Bit Score: 377.66 E-value: 2.88e-131
Phosphomannose isomerase type I, catalytic domain; This entry represents the catalytic domain ...
6-154
1.96e-76
Phosphomannose isomerase type I, catalytic domain; This entry represents the catalytic domain of Phosphomannose isomerase type I enzymes (EC 5.3.1.8) which contains a zinc-binding site. It is composed of beta-strands connected by long loops in a jelly roll conformation.
Pssm-ID: 466660 [Multi-domain] Cd Length: 143 Bit Score: 234.00 E-value: 1.96e-76
mannose-6-phosphate isomerase, class I; The names phosphomannose isomerase and ...
12-403
3.98e-42
mannose-6-phosphate isomerase, class I; The names phosphomannose isomerase and mannose-6-phosphate isomerase are synonomous. This family contains two rather deeply branched groups. One group contains an experimentally determined phosphomannose isomerase of Streptococcus mutans as well as three uncharacterized paralogous proteins of Bacillus subtilis, all at more than 50 % identity to each other, plus a more distant homolog from Archaeoglobus fulgidus. The other group contains members from E. coli, budding yeast, Borrelia burgdorferi, etc. [Energy metabolism, Sugars]
Pssm-ID: 272966 [Multi-domain] Cd Length: 302 Bit Score: 150.28 E-value: 3.98e-42
type I phosphomannose isomerase in eukaryotes and bacteria, N-terminal cupin domain; This ...
9-314
2.88e-131
type I phosphomannose isomerase in eukaryotes and bacteria, N-terminal cupin domain; This subfamily contains type I phosphomannose isomerase (PMI; E.C. 5.3.1.8; also known as mannose-6-phosphate isomerase) found in eukaryotes and some bacteria such as Salmonella enterica. PMI catalyzes the reversible isomerization of fructose-6-phosphate (F6P) and mannose-6-phosphate (M6P), the first committed step in the synthesis of mannosylated glycoproteins. The active site, located within the N-terminal jelly roll-like beta-barrel cupin fold, contains a single essential zinc atom and forms a deep, open cavity large enough to contain M6P or F6P. PMI type I also has a C-terminal beta-barrel fold which has diverged considerably from the N-terminal domain and is not included here. This subfamily contains an alpha helical domain that is found in eukaryotic and some prokaryotic PMIs but is not present in their archaeal counterparts. F6P is a substrate for glycolysis and gluconeogenesis, while M6P is a substrate for production of activated mannose donor guanosine 5'-diphosphate D-mannose, an important precursor of mannosylated biomolecules such as glycoproteins, bacterial exopolysaccharides and fungal cell wall components. PMI is also essential for survival, virulence and possibly pathogenicity of some bacteria and protozoan parasites, as well as for cell wall integrity of certain yeasts. Thus, PMI is a potential target against fungal infections causing serious illness or death.
Pssm-ID: 380414 [Multi-domain] Cd Length: 247 Bit Score: 377.66 E-value: 2.88e-131
Phosphomannose isomerase type I, catalytic domain; This entry represents the catalytic domain ...
6-154
1.96e-76
Phosphomannose isomerase type I, catalytic domain; This entry represents the catalytic domain of Phosphomannose isomerase type I enzymes (EC 5.3.1.8) which contains a zinc-binding site. It is composed of beta-strands connected by long loops in a jelly roll conformation.
Pssm-ID: 466660 [Multi-domain] Cd Length: 143 Bit Score: 234.00 E-value: 1.96e-76
mannose-6-phosphate isomerase, class I; The names phosphomannose isomerase and ...
12-403
3.98e-42
mannose-6-phosphate isomerase, class I; The names phosphomannose isomerase and mannose-6-phosphate isomerase are synonomous. This family contains two rather deeply branched groups. One group contains an experimentally determined phosphomannose isomerase of Streptococcus mutans as well as three uncharacterized paralogous proteins of Bacillus subtilis, all at more than 50 % identity to each other, plus a more distant homolog from Archaeoglobus fulgidus. The other group contains members from E. coli, budding yeast, Borrelia burgdorferi, etc. [Energy metabolism, Sugars]
Pssm-ID: 272966 [Multi-domain] Cd Length: 302 Bit Score: 150.28 E-value: 3.98e-42
Phosphomannose isomerase type I, helical insertion domain; This entry represents the ...
170-257
1.20e-24
Phosphomannose isomerase type I, helical insertion domain; This entry represents the alpha-helical insertion domain of Phosphomannose isomerase type I enzymes (EC 5.3.1.8), in which the helices are packed closely, connected by short turns and loops. This domain packs closely against the catalytic domain, interrupting it.
Pssm-ID: 466661 [Multi-domain] Cd Length: 88 Bit Score: 96.76 E-value: 1.20e-24
Phosphomannose isomerase type I C-terminal; This is the C-terminal domain of Phosphomannose ...
337-381
1.96e-08
Phosphomannose isomerase type I C-terminal; This is the C-terminal domain of Phosphomannose isomerase type I enzymes (EC 5.3.1.8), which contains antiparallel beta-strands in an extended jelly roll topology with short loops connecting the strands.
Pssm-ID: 460127 [Multi-domain] Cd Length: 48 Bit Score: 50.06 E-value: 1.96e-08
Phosphomannose isomerase in bacteria and archaea, N-terminal cupin domain; This subfamily ...
95-165
1.61e-03
Phosphomannose isomerase in bacteria and archaea, N-terminal cupin domain; This subfamily contains type I phosphomannose isomerase (PMI; E.C. 5.3.1.8; also known as mannose-6-phosphate isomerase) found in many bacteria (e.g. Bacillus subtilis) and archaea. PMI catalyzes the reversible isomerization of fructose-6-phosphate (F6P) and mannose-6-phosphate (M6P), the first committed step in the synthesis of mannosylated glycoproteins. The active site, located within the N-terminal jelly roll-like beta-barrel cupin fold, contains a single essential zinc atom and forms a deep, open cavity large enough to contain M6P or F6P. PMI type I also has a C-terminal beta-barrel fold which has diverged considerably from the N-terminal domain and is not included here. This subfamily does not contain an alpha helical domain that exists in eukaryotic and some prokaryotic PMIs. F6P is a substrate for glycolysis and gluconeogenesis, while M6P is a substrate for production of activated mannose donor guanosine 5'-diphosphate D-mannose, an important precursor of mannosylated biomolecules such as glycoproteins, bacterial exopolysaccharides and fungal cell wall components. PMI is also essential for survival, virulence and possibly pathogenicity of some bacteria and protozoan parasites, as well as for cell wall integrity of certain yeasts. Thus, PMI is a potential target against fungal infections causing serious illness or death.
Pssm-ID: 380413 Cd Length: 173 Bit Score: 39.05 E-value: 1.61e-03
Database: CDSEARCH/cdd Low complexity filter: no Composition Based Adjustment: yes E-value threshold: 0.01
References:
Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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