menaquinone biosynthetic enzyme MqnA/MqnD family protein similar to Campylobacter jejuni MqnA which catalyzes the dehydration of chorismate into 3-[(1-carboxyvinyl)oxy]benzoate, a step in the biosynthesis of menaquinone
Chorismate dehydratase (menaquinone biosynthesis, futalosine pathway) [Coenzyme transport and ...
1-269
2.73e-116
Chorismate dehydratase (menaquinone biosynthesis, futalosine pathway) [Coenzyme transport and metabolism]; Chorismate dehydratase (menaquinone biosynthesis, futalosine pathway) is part of the Pathway/BioSystem: Menaquinone biosynthesis
:
Pssm-ID: 441036 Cd Length: 268 Bit Score: 334.50 E-value: 2.73e-116
Chorismate dehydratase (menaquinone biosynthesis, futalosine pathway) [Coenzyme transport and ...
1-269
2.73e-116
Chorismate dehydratase (menaquinone biosynthesis, futalosine pathway) [Coenzyme transport and metabolism]; Chorismate dehydratase (menaquinone biosynthesis, futalosine pathway) is part of the Pathway/BioSystem: Menaquinone biosynthesis
Pssm-ID: 441036 Cd Length: 268 Bit Score: 334.50 E-value: 2.73e-116
The conserved hypothetical protein SCO4506 exhibits the type 2 periplasmic-binidng protein ...
2-255
1.13e-109
The conserved hypothetical protein SCO4506 exhibits the type 2 periplasmic-binidng protein fold; This group includes the SCO4506 protein from Streptomyces coelicolor and related hypothetical proteins. SCO4506 is an ortholog of Ttha1568 (MqnD) from Thermus thermophilies HB8. MqnD is an enzyme within an alternative menaquinone biosynthetic pathway that catalyzes the conversion of cyclic de-hypoxanthine futalosine to 1,4-dihydroxy-6-naphthoate. Menaquinone (MK; vitamin K) is an essential lipid-soluble carrier that shuttles electrons between membrane-bound protein complexes in the electron transport chain. SCO4506 has significant structural homology with the members of type 2 periplasmic-binding fold protein superfamily. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.
Pssm-ID: 270352 Cd Length: 256 Bit Score: 317.57 E-value: 1.13e-109
Menaquinone biosynthesis; This family includes two enzymes which are involved in menaquinone ...
2-255
2.11e-82
Menaquinone biosynthesis; This family includes two enzymes which are involved in menaquinone biosynthesis. One which catalyzes the conversion of cyclic de-hypoxanthine futalosine to 1,4-dihydroxy-6-naphthoate, and one which may be involved in the conversion of chorismate to futalosine. These enzymes comprise two domains with alpha/beta structures, a large domain and a small domain. A pocket between the two domains may form the active site, a conserved histidine located within this pocket could be the catalytic base.
Pssm-ID: 426881 Cd Length: 252 Bit Score: 247.85 E-value: 2.11e-82
Chorismate dehydratase (menaquinone biosynthesis, futalosine pathway) [Coenzyme transport and ...
1-269
2.73e-116
Chorismate dehydratase (menaquinone biosynthesis, futalosine pathway) [Coenzyme transport and metabolism]; Chorismate dehydratase (menaquinone biosynthesis, futalosine pathway) is part of the Pathway/BioSystem: Menaquinone biosynthesis
Pssm-ID: 441036 Cd Length: 268 Bit Score: 334.50 E-value: 2.73e-116
The conserved hypothetical protein SCO4506 exhibits the type 2 periplasmic-binidng protein ...
2-255
1.13e-109
The conserved hypothetical protein SCO4506 exhibits the type 2 periplasmic-binidng protein fold; This group includes the SCO4506 protein from Streptomyces coelicolor and related hypothetical proteins. SCO4506 is an ortholog of Ttha1568 (MqnD) from Thermus thermophilies HB8. MqnD is an enzyme within an alternative menaquinone biosynthetic pathway that catalyzes the conversion of cyclic de-hypoxanthine futalosine to 1,4-dihydroxy-6-naphthoate. Menaquinone (MK; vitamin K) is an essential lipid-soluble carrier that shuttles electrons between membrane-bound protein complexes in the electron transport chain. SCO4506 has significant structural homology with the members of type 2 periplasmic-binding fold protein superfamily. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.
Pssm-ID: 270352 Cd Length: 256 Bit Score: 317.57 E-value: 1.13e-109
Menaquinone biosynthesis; This family includes two enzymes which are involved in menaquinone ...
2-255
2.11e-82
Menaquinone biosynthesis; This family includes two enzymes which are involved in menaquinone biosynthesis. One which catalyzes the conversion of cyclic de-hypoxanthine futalosine to 1,4-dihydroxy-6-naphthoate, and one which may be involved in the conversion of chorismate to futalosine. These enzymes comprise two domains with alpha/beta structures, a large domain and a small domain. A pocket between the two domains may form the active site, a conserved histidine located within this pocket could be the catalytic base.
Pssm-ID: 426881 Cd Length: 252 Bit Score: 247.85 E-value: 2.11e-82
Menaquinone biosynthetic enzyme and related hypothetical proteins; the type 2 ...
2-257
1.72e-76
Menaquinone biosynthetic enzyme and related hypothetical proteins; the type 2 periplasmic-binding protein fold; This family represents MqnD, an enzyme within the alternative menaquinone biosynthetic pathway, and related conserved hypothetical proteins. Menaquinone (MK; vitamin K) is an essential lipid-soluble carrier that shuttles electrons between membrane-bound protein complexes in the electron transport chain. The members include Ttha1568, MqnD from Thermus thermophiles HB8, and the conserved hypothetical proteins SCO4506 from Streptomyces coelicolor, Af1704 from Archaeoglobus DSM 4304, Dr0370 from Deinococcus radiodurans, and Ca3427 from candida albicans. They all have significant structural homology with the members of type 2 periplasmic-binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.
Pssm-ID: 270252 [Multi-domain] Cd Length: 261 Bit Score: 233.47 E-value: 1.72e-76
1,4-dihydroxy-6-naphtoate synthase (menaquinone biosynthesis, futalosine pathway) [Coenzyme transport and metabolism]; 1,4-dihydroxy-6-naphtoate synthase (menaquinone biosynthesis, futalosine pathway) is part of the Pathway/BioSystem: Menaquinone biosynthesis
Pssm-ID: 441710 Cd Length: 276 Bit Score: 55.92 E-value: 3.89e-09
The conserved hypothetical protein Af1704 exhibits the type 2 periplasmic-binding protein fold; ...
33-255
2.92e-07
The conserved hypothetical protein Af1704 exhibits the type 2 periplasmic-binding protein fold; This group includes the Af1704 protein from from Archaeoglobus fulgidus DSM 4304, which is an ortholog of Ttha1568 (MqnD) from Thermus thermophilies HB8. MqnD is an enzyme within an alternative menaquinone biosynthetic pathway that catalyzes the conversion of cyclic de-hypoxanthine futalosine to 1,4-dihydroxy-6-naphthoate. Menaquinone (MK; vitamin K) is an essential lipid-soluble carrier that shuttles electrons between membrane-bound protein complexes in the electron transport chain. Af1704 has significant structural homology with the members of type 2 periplasmic-binding fold protein superfamily. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.
Pssm-ID: 270354 Cd Length: 259 Bit Score: 50.30 E-value: 2.92e-07
Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ...
1-184
4.89e-06
Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent the ligand-binding domains found in solute binding proteins that serve as initial receptors in the transport, signal transduction and channel gating. The PBP2 proteins share the same architecture as periplasmic binding proteins type 1 (PBP1), but have a different topology. They are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The origin of PBP module can be traced across the distant phyla, including eukaryotes, archebacteria, and prokaryotes. The majority of PBP2 proteins are involved in the uptake of a variety of soluble substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the family includes ionotropic glutamate receptors and unorthodox sensor proteins involved in signal transduction. The substrate binding domain of the LysR transcriptional regulators and the oligopeptide-like transport systems also contain the type 2 periplasmic binding fold and thus they are significantly homologous to that of the PBP2; however, these two families are grouped into a separate hierarchy of the PBP2 superfamily due to the large number of protein sequences.
Pssm-ID: 270214 [Multi-domain] Cd Length: 196 Bit Score: 46.03 E-value: 4.89e-06
ABC transporter, phosphonate, periplasmic substrate-binding protein; This is a family of ...
37-227
3.35e-05
ABC transporter, phosphonate, periplasmic substrate-binding protein; This is a family of periplasmic proteins which are part of the transport system for alkylphosphonate uptake.
Pssm-ID: 432911 [Multi-domain] Cd Length: 243 Bit Score: 44.18 E-value: 3.35e-05
Putative substrate binding domain of sulfonate binding protein-like, the type 2 periplasmic ...
26-228
5.82e-04
Putative substrate binding domain of sulfonate binding protein-like, the type 2 periplasmic binding protein fold; This subfamily includes the periplasmic component of putative ABC-type sulfonate transport system similar to SsuA. These domains are found in eubacterial SsuA proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates, while other closest homologs are involved in thiamine (vitamin B1) biosynthetic pathway and desulfurization (DszB). After binding the ligand, SsuA interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The SsuA proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.
Pssm-ID: 270277 Cd Length: 258 Bit Score: 40.48 E-value: 5.82e-04
A menaquinone biosynthetic enzyme exhibits the type 2 periplasmic-binding protein fold; This ...
33-211
1.18e-03
A menaquinone biosynthetic enzyme exhibits the type 2 periplasmic-binding protein fold; This group includes Ttha1568 (MqnD) from Thermus thermophilies HB8, an enzyme within an alternative menaquinone biosynthetic pathway that catalyzes the conversion of cyclic de-hypoxanthine futalosine to 1,4-dihydroxy-6-naphthoate. Menaquinone (MK; vitamin K) is an essential lipid-soluble carrier that shuttles electrons between membrane-bound protein complexes in the electron transport chain. Ttha1568 has significant structural homology with the members of type 2 periplasmic-binding fold protein superfamily. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.
Pssm-ID: 270353 Cd Length: 260 Bit Score: 39.42 E-value: 1.18e-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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