1,4-dihydroxy-6-naphthoate synthase catalyzes the conversion of cyclic dehypoxanthine futalosine (cyclic DHFL) into 1,4-dihydroxy-6-naphthoate, a step in the biosynthesis of menaquinone (MK, vitamin K2)
A menaquinone biosynthetic enzyme exhibits the type 2 periplasmic-binding protein fold; This ...
11-269
2.60e-161
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: 448.50 E-value: 2.60e-161
A menaquinone biosynthetic enzyme exhibits the type 2 periplasmic-binding protein fold; This ...
11-269
2.60e-161
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: 448.50 E-value: 2.60e-161
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: 443.43 E-value: 5.46e-159
Menaquinone biosynthesis; This family includes two enzymes which are involved in menaquinone ...
12-269
3.02e-96
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: 283.29 E-value: 3.02e-96
A menaquinone biosynthetic enzyme exhibits the type 2 periplasmic-binding protein fold; This ...
11-269
2.60e-161
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: 448.50 E-value: 2.60e-161
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: 443.43 E-value: 5.46e-159
The conserved hypothetical protein Af1704 exhibits the type 2 periplasmic-binding protein fold; ...
12-269
8.70e-100
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: 292.59 E-value: 8.70e-100
Menaquinone biosynthesis; This family includes two enzymes which are involved in menaquinone ...
12-269
3.02e-96
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: 283.29 E-value: 3.02e-96
Menaquinone biosynthetic enzyme and related hypothetical proteins; the type 2 ...
12-269
1.21e-75
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: 231.54 E-value: 1.21e-75
Chorismate dehydratase (menaquinone biosynthesis, futalosine pathway) [Coenzyme transport and ...
25-283
1.01e-09
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: 57.92 E-value: 1.01e-09
The conserved hypothetical protein SCO4506 exhibits the type 2 periplasmic-binidng protein ...
25-224
1.11e-04
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: 42.54 E-value: 1.11e-04
Putative substrate binding domain of sulfonate binding protein-like, the type 2 periplasmic ...
82-240
2.34e-03
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: 38.56 E-value: 2.34e-03
The type 2 periplasmic ligand-binding protein domain of the sensor-kinase BvgS and histidine ...
92-154
5.02e-03
The type 2 periplasmic ligand-binding protein domain of the sensor-kinase BvgS and histidine kinase receptors, and related proteins; This family comprises the periplasmic sensor domain of the two-component sensor-kinase systems, such as the sensor protein BvgS of Bordetella pertussis and histidine kinase receptors (HisK), and uncharacterized related proteins. Typically, the two-component system consists of a membrane spanning sensor-kinase and a cytoplasmic response regulator. It serves as a stimulus-response coupling mechanism to enable microorganisms to sense and respond to changes in environmental conditions. The N-terminal sensing domain of the sensor kinase detects extracellular signals, such as small molecule ligands and ions, which then modulate the catalytic activity of the cytoplasmic kinase domain through a phosphorylation cascade. The periplasmic sensor domain belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises 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. 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 receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.
Pssm-ID: 270228 [Multi-domain] Cd Length: 220 Bit Score: 37.51 E-value: 5.02e-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.
of the residues that compose this conserved feature have been mapped to the query sequence.
Click on the triangle to view details about the feature, including a multiple sequence alignment
of your query sequence and the protein sequences used to curate the domain model,
where hash marks (#) above the aligned sequences show the location of the conserved feature residues.
The thumbnail image, if present, provides an approximate view of the feature's location in 3 dimensions.
Click on the triangle for interactive 3D structure viewing options.
Functional characterization of the conserved domain architecture found on the query.
Click here to see more details.
This image shows a graphical summary of conserved domains identified on the query sequence.
The Show Concise/Full Display button at the top of the page can be used to select the desired level of detail: only top scoring hits
(labeled illustration) or all hits
(labeled illustration).
Domains are color coded according to superfamilies
to which they have been assigned. Hits with scores that pass a domain-specific threshold
(specific hits) are drawn in bright colors.
Others (non-specific hits) and
superfamily placeholders are drawn in pastel colors.
if a domain or superfamily has been annotated with functional sites (conserved features),
they are mapped to the query sequence and indicated through sets of triangles
with the same color and shade of the domain or superfamily that provides the annotation. Mouse over the colored bars or triangles to see descriptions of the domains and features.
click on the bars or triangles to view your query sequence embedded in a multiple sequence alignment of the proteins used to develop the corresponding domain model.
The table lists conserved domains identified on the query sequence. Click on the plus sign (+) on the left to display full descriptions, alignments, and scores.
Click on the domain model's accession number to view the multiple sequence alignment of the proteins used to develop the corresponding domain model.
To view your query sequence embedded in that multiple sequence alignment, click on the colored bars in the Graphical Summary portion of the search results page,
or click on the triangles, if present, that represent functional sites (conserved features)
mapped to the query sequence.
Concise Display shows only the best scoring domain model, in each hit category listed below except non-specific hits, for each region on the query sequence.
(labeled illustration) Standard Display shows only the best scoring domain model from each source, in each hit category listed below for each region on the query sequence.
(labeled illustration) Full Display shows all domain models, in each hit category below, that meet or exceed the RPS-BLAST threshold for statistical significance.
(labeled illustration) Four types of hits can be shown, as available,
for each region on the query sequence:
specific hits meet or exceed a domain-specific e-value threshold
(illustrated example)
and represent a very high confidence that the query sequence belongs to the same protein family as the sequences use to create the domain model
non-specific hits
meet or exceed the RPS-BLAST threshold for statistical significance (default E-value cutoff of 0.01, or an E-value selected by user via the
advanced search options)
the domain superfamily to which the specific and non-specific hits belong
multi-domain models that were computationally detected and are likely to contain multiple single domains
Retrieve proteins that contain one or more of the domains present in the query sequence, using the Conserved Domain Architecture Retrieval Tool
(CDART).
Modify your query to search against a different database and/or use advanced search options
