Summary: Bacterial extracellular solute-binding protein
Bacterial extracellular solute-binding protein Provide feedback
This family also includes the bacterial extracellular solute-binding protein family POTD/POTF.
Spurlino JC, Lu GY, Quiocho FA; , J Biol Chem 1991;266:5202-5219.: The 2.3-A resolution structure of the maltose- or maltodextrin-binding protein, a primary receptor of bacterial active transport and chemotaxis. PUBMED:2002054 EPMC:2002054
Bruns CM, Nowalk AJ, Arvai AS, McTigue MA, Vaughan KG, Mietzner TA, McRee DE; , Nat Struct Biol 1997;4:919-924.: Structure of Haemophilus influenzae Fe(+3)-binding protein reveals convergent evolution within a superfamily. PUBMED:9360608 EPMC:9360608
Vassylyev DG, Tomitori H, Kashiwagi K, Morikawa K, Igarashi K; , J Biol Chem 1998;273:17604-17609.: Crystal structure and mutational analysis of the Escherichia coli putrescine receptor. Structural basis for substrate specificity. PUBMED:9651355 EPMC:9651355
Internal database links
|Similarity to PfamA using HHSearch:||SBP_bac_6 SBP_bac_8 SBP_bac_11|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR006059
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 and a high affinity periplasmic solute-binding protein. In Gram-positive bacteria, which are surrounded by a single membrane and therefore have 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 through 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 into eight family clusters [PUBMED:8336670], which generally correlate with the nature of the solute bound. Family 1 includes the maltose/maltodextrin-binding proteins of Enterobacteriaceae (gene malE) [PUBMED:7853407] and Streptococcus pneumoniae malX; multiple oligosaccharide binding protein of Streptococcus mutans (gene msmE); Escherichia coli glycerol-3-phosphate-binding protein; Serratia marcescens iron-binding protein (gene sfuA) and the homologous proteins (gene fbp) from Haemophilus influenzae and Neisseria; and the E. coli thiamine-binding protein (gene tbpA).
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 23 members:DUF3834 HisG Lig_chan-Glu_bd Lipoprotein_8 Lipoprotein_9 LysR_substrate Mycoplasma_p37 NMT1 NMT1_2 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_7 SBP_bac_8 TctC Transferrin VitK2_biosynth
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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Curation and family details
|Seed source:||Pfam-B_269 (release 4.0)|
|Author:||Bateman A, Griffiths-Jones SR|
|Number in seed:||129|
|Number in full:||9759|
|Average length of the domain:||292.70 aa|
|Average identity of full alignment:||15 %|
|Average coverage of the sequence by the domain:||65.96 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||20|
|Download:||download the raw HMM for this family|
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There are 3 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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_1 domain has been found. There are 267 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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