type 2 periplasmic-binding protein (PBP2) is typically comprised of two globular subdomains connected by a flexible hinge; it binds its ligand in the cleft between these domains in a manner resembling a Venus flytrap; similar to the ligand-binding domains found in solute binding proteins that serve as initial receptors in the transport, signal transduction and channel gating
Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ...
31-258
5.07e-109
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.
The actual alignment was detected with superfamily member cd13599:
Pssm-ID: 473866 Cd Length: 228 Bit Score: 314.72 E-value: 5.07e-109
The membrane-associated lipoprotein Gna1946 from Neisseria meningitidis; the type 2 ...
31-258
5.07e-109
The membrane-associated lipoprotein Gna1946 from Neisseria meningitidis; the type 2 periplasmic binding protein fold; Gna1946 shares significant structural and sequence homology with the periplasmic substrate-binding domain of ATP-binding cassette (ABC) transporter involved in uptake of methionine (MetQ). The members of the MetQ-like family include the 32-kilodalton lipoprotein (Tp32) from Treponema pallidum, the membrane-associated lipoprotein-9 GmpC from Staphylococcus aureus, and Toll-like receptor 2-activating lipoprotein IlpA from Vibrio vulnificus. They all function as a receptor for methionine. This substrate-binding domain belongs to the 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. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea.
Pssm-ID: 270317 Cd Length: 228 Bit Score: 314.72 E-value: 5.07e-109
NlpA lipoprotein; This entry represents bacterial lipoproteins that belong to the NlpA family. ...
32-271
4.37e-98
NlpA lipoprotein; This entry represents bacterial lipoproteins that belong to the NlpA family. It contains several antigenic members, that may be involved in bacterial virulence. This entry includes the D-methionine binding lipoprotein MetQ, which is the substrate-binding component of a D-methionine permease, a binding protein-dependent, ATP-driven transport system. Other members of this family, such as NlpA, have been identified as putative substrate-binding components of ABC transporters. NlpA, is an inner-membrane-anchored lipoprotein that has been shown to have a minor role in methionine import.
Pssm-ID: 427184 Cd Length: 236 Bit Score: 287.24 E-value: 4.37e-98
lipoprotein, YaeC family; This family of putative lipoproteins contains a consensus site for ...
9-250
6.57e-39
lipoprotein, YaeC family; This family of putative lipoproteins contains a consensus site for lipoprotein signal sequence cleavage. Included in this family is the E. coli hypothetical protein yaeC. About half of the proteins between the noise and trusted cutoffs contain the consensus lipoprotein signature and may belong to this family. [Cell envelope, Other]
Pssm-ID: 129460 Cd Length: 258 Bit Score: 136.57 E-value: 6.57e-39
The membrane-associated lipoprotein Gna1946 from Neisseria meningitidis; the type 2 ...
31-258
5.07e-109
The membrane-associated lipoprotein Gna1946 from Neisseria meningitidis; the type 2 periplasmic binding protein fold; Gna1946 shares significant structural and sequence homology with the periplasmic substrate-binding domain of ATP-binding cassette (ABC) transporter involved in uptake of methionine (MetQ). The members of the MetQ-like family include the 32-kilodalton lipoprotein (Tp32) from Treponema pallidum, the membrane-associated lipoprotein-9 GmpC from Staphylococcus aureus, and Toll-like receptor 2-activating lipoprotein IlpA from Vibrio vulnificus. They all function as a receptor for methionine. This substrate-binding domain belongs to the 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. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea.
Pssm-ID: 270317 Cd Length: 228 Bit Score: 314.72 E-value: 5.07e-109
NlpA lipoprotein; This entry represents bacterial lipoproteins that belong to the NlpA family. ...
32-271
4.37e-98
NlpA lipoprotein; This entry represents bacterial lipoproteins that belong to the NlpA family. It contains several antigenic members, that may be involved in bacterial virulence. This entry includes the D-methionine binding lipoprotein MetQ, which is the substrate-binding component of a D-methionine permease, a binding protein-dependent, ATP-driven transport system. Other members of this family, such as NlpA, have been identified as putative substrate-binding components of ABC transporters. NlpA, is an inner-membrane-anchored lipoprotein that has been shown to have a minor role in methionine import.
Pssm-ID: 427184 Cd Length: 236 Bit Score: 287.24 E-value: 4.37e-98
The substrate-binding domain of the 32-kilodalton lipoprotein (Tp32) from Treponema pallidum ...
31-258
1.31e-71
The substrate-binding domain of the 32-kilodalton lipoprotein (Tp32) from Treponema pallidum binds L-methionine; the type 2 periplasmic-binding protein fold; This group includes the lipoprotein Tp32, a periplasmic component of a methionine uptake transporter system, and its closely related homologs. The Tp32 has both structural and sequential homology to the MetQ family of substrate-binding protein, and thus it belongs to the 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. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea.
Pssm-ID: 270315 Cd Length: 236 Bit Score: 219.84 E-value: 1.31e-71
The periplasmic-binding component of ABC-type methionine uptake transporter system and its ...
31-257
4.57e-71
The periplasmic-binding component of ABC-type methionine uptake transporter system and its related lipoproteins; the type 2 periplasmic-binding protein fold; This family represents the periplasmic substrate-binding domain of ATP-binding cassette (ABC) transporter involved in uptake of methionine (MetQ) and its related homologs. Members of the MetQ-like family include the 32-kilodalton lipoprotein (Tp32) from Treponema pallidum, the membrane-associated lipoprotein-9 GmpC from Staphylococcus aureus, and Toll-like receptor 2-activating lipoprotein IlpA from Vibrio vulnificus. They all function as a receptor for methionine. This substrate-binding domain belongs to the 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. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea.
Pssm-ID: 270244 Cd Length: 228 Bit Score: 218.34 E-value: 4.57e-71
Toll-like receptor 2-activating lipoprotein IlpA from Vibrio vulnificus and similar ...
35-257
1.81e-56
Toll-like receptor 2-activating lipoprotein IlpA from Vibrio vulnificus and similar lipoproteins; the type 2 periplasmic binding protein fold; This group includes the IlpA protein which has both structural and sequential homology to the MetQ family of substrate-binding protein, and thus belongs to the 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. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea.
Pssm-ID: 270316 Cd Length: 227 Bit Score: 181.01 E-value: 1.81e-56
Putative periplasmic-binding component of ABC-type methionine uptake transporter system-like; ...
31-257
3.46e-52
Putative periplasmic-binding component of ABC-type methionine uptake transporter system-like; the type 2 periplasmic binding protein fold; This subgroup shares significant sequence homology with the periplasmic substrate-binding domain of ATP-binding cassette (ABC) transporter involved in uptake of methionine (MetQ). The members of the MetQ-like family include the 32-kilodalton lipoprotein (Tp32) from Treponema pallidum, the membrane-associated lipoprotein-9 GmpC from Staphylococcus aureus, and Toll-like receptor 2-activating lipoprotein IlpA from Vibrio vulnificus. They all function as a receptor for methionine. This substrate-binding domain belongs to the 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. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea.
Pssm-ID: 270318 Cd Length: 228 Bit Score: 169.82 E-value: 3.46e-52
The periplasmic substrate-binding domain of the membrane-associated lipoprotein-9 GmpC; ...
45-256
9.03e-50
The periplasmic substrate-binding domain of the membrane-associated lipoprotein-9 GmpC; contains the type 2 periplasmic-binding protein fold; This group includes the membrane-associated lipoprotein-9 from Staphylococcus aureus that binds the dipeptide glycylmethionine (GlyMet). The lipoprotein-9 has both structural and sequential homology to the MetQ family of substrate-binding protein. The GlyMet binding protein belongs to the 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. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea.
Pssm-ID: 270314 Cd Length: 230 Bit Score: 163.69 E-value: 9.03e-50
lipoprotein, YaeC family; This family of putative lipoproteins contains a consensus site for ...
9-250
6.57e-39
lipoprotein, YaeC family; This family of putative lipoproteins contains a consensus site for lipoprotein signal sequence cleavage. Included in this family is the E. coli hypothetical protein yaeC. About half of the proteins between the noise and trusted cutoffs contain the consensus lipoprotein signature and may belong to this family. [Cell envelope, Other]
Pssm-ID: 129460 Cd Length: 258 Bit Score: 136.57 E-value: 6.57e-39
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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