Summary: Bacterial extracellular solute-binding proteins, family 3
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Bacterial extracellular solute-binding proteins, family 3 Provide feedback
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Internal database links
|SCOOP:||VitK2_biosynth DNA_PPF DctP Spuma_A9PTase OpuAC Pox_I6 ERG2_Sigma1R BLYB SspK NMT1 Lig_chan-Glu_bd Med25_SD1 DUF3834 Phosphonate-bd DUF3991 NMT1_2 YhfZ_C IFS NMT1_3|
|Similarity to PfamA using HHSearch:||Lig_chan DctP NMT1 Lig_chan-Glu_bd DUF3834 Phosphonate-bd SBP_bac_11 YhfZ_C|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR001638
Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. The protein components of these traffic systems include one or two transmembrane protein components, one or two membrane-associated ATP-binding proteins (ABC transporters; see INTERPRO) and a high affinity periplasmic solute-binding protein. The latter are thought to bind the substrate in the vicinity of the inner membrane, and to transfer it to a complex of inner membrane proteins for concentration into the cytoplasm.
In Gram-positive bacteria which are surrounded by a single membrane and have therefore no periplasmic region, the equivalent proteins are bound to the membrane via an N-terminal lipid anchor. These homologue proteins do not play an integral role in the transport process per se, but probably serve as receptors to trigger or initiate translocation of the solute throught the membrane by binding to external sites of the integral membrane proteins of the efflux system.
In addition, at least some solute-binding proteins function in the initiation of sensory transduction pathways.
On the basis of sequence similarities, the vast majority of these solute-binding proteins can be grouped [PUBMED:8336670] into eight families or clusters, which generally correlate with the nature of the solute bound.
Family 3 groups together specific amino acids and opine-binding periplasmic proteins and a periplasmic homologue with catalytic activity.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||transporter activity (GO:0005215)|
|Biological process||transport (GO:0006810)|
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Periplasmic binding proteins (PBPs) consist of two large lobes that close around the bound ligand. This architecture is reiterated in transcriptional regulators, such as the lac repressors. In the process of evolution, genes encoding the PBPs have fused with genes for integral membrane proteins. Thus, diverse mammalian receptors contain extracellular ligand binding domains that are homologous to the PBPs; these include glutamate/glycine-gated ion channels such as the NMDA receptor, G protein-coupled receptors, including metabotropic glutamate, GABA-B, calcium sensing, and pheromone receptors, and atrial natriuretic peptide-guanylate cyclase receptors .
The clan contains the following 25 members:DctP DUF3834 HisG Lig_chan-Glu_bd Lipoprotein_8 Lipoprotein_9 LysR_substrate Mycoplasma_p37 NMT1 NMT1_2 NMT1_3 OpuAC PBP_like PBP_like_2 Phosphonate-bd SBP_bac_1 SBP_bac_11 SBP_bac_3 SBP_bac_5 SBP_bac_6 SBP_bac_8 TctC Transferrin VitK2_biosynth YhfZ_C
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Curation and family details
|Number in seed:||285|
|Number in full:||120026|
|Average length of the domain:||219.20 aa|
|Average identity of full alignment:||21 %|
|Average coverage of the sequence by the domain:||65.96 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||16|
|Download:||download the raw HMM for this family|
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the SBP_bac_3 domain has been found. There are 137 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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