Summary: Periplasmic binding protein
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This family includes bacterial periplasmic binding proteins. Several of which are involved in iron transport.
Staudenmaier H, Van Hove B, Yaraghi Z, Braun V; , J Bacteriol 1989;171:2626-2633.: Nucleotide sequences of the fecBCDE genes and locations of the proteins suggest a periplasmic-binding-protein-dependent transport mechanism for iron(III) dicitrate in Escherichia coli. PUBMED:2651410 EPMC:2651410
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR002491
ATP binding cassette (ABC) transporters are a ubiquitous family of importer and exporter proteins that consist of two alpha-helical transmembrane (TM) domains, which form a translocation pathway, and two cytoplasmic ABC domains, which power the transport reaction through binding and hydrolysis of ATP. In addition most bacterial importers employs a periplasmic substrate-binding protein (PBP) that delivers the ligand to the extracellular gate of the TM domains. These proteins bind their substrates selectively and with high affinity, which is thought to ensure the specificity of the transport reaction. Binding proteins in Gram-negative bacteria are present within the periplasm, whereas those in Gram-positive bacteria are tethered to the cell membrane via the acylation of a cysteine residue that is an integral component of a lipoprotein signal sequence. The cobalamin (vitamin B12) and the iron transport systems share many common attributes and probably evolved from the same origin [PUBMED:12475936, PUBMED:14514690, PUBMED:2651410].
The structure of the periplasmic-binding domain is composed of two subdomains, each consisting of a central beta-sheet and surrounding alpha-helices, linked by a rigid alpha-helix. The substrate binding site is located in a cleft between the two alpha/beta subdomains [PUBMED:12468528].
Some protein known to contain an iron siderophore/cobalamin periplasmic- binding domain are listed below:
- Escherichia coli vitamin B12 transport protein btuF. It is the periplasmic binding protein for the vitamin B12 transporter btuCD.
- Escherichia coli ferrichrome-binding periplasmic protein (fhuD). It binds iron(III)-hydroxamates.
- Staphylococcus aureus ferric hydroxamate receptor 2 (fhuD2).
- Escherichia coli ferrienterobactin-binding periplasmic protein fepB. It binds ferrienterobactin; part of the binding-protein-dependent transport system for uptake of ferrienterobactin.
- Vibrio cholerae periplasmic binding protein (viuP).
- Escherichia coli iron(III) dicitrate-binding periplasmic protein (fecB). It binds citrate-dependent iron(III); part of the binding-protein-dependent transport system for uptake of citrate-dependent iron(III).
- Erwinia chrysanthemi achromobactin-binding periplasmic protein (cbrA). It binds citrate-or chloride-dependent iron(III); part of the binding-protein-dependent transport system cbrABCD for uptake of the siderophore achromobactin.
- Yersinia pestis hemin-binding periplasmic protein (hmuT).
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||binding (GO:0005488)|
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This superfamily is characterised by a long alpha helical insertion in the interdomain linker in the Chelatase-like fold. Representative families include the periplasmic ferric siderophore binding proteins, the TroA-like nitrogenase iron-molybdenum proteins and the putative iron(III) transporter family, TM0189-like, or periplasmic-binding family.
The clan contains the following 2 members:Oxidored_nitro Peripla_BP_2
We make a range of alignments for each Pfam-A family:
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Curation and family details
|Seed source:||Pfam-B_461 (release 4.0)|
|Author:||Bashton M, Bateman A|
|Number in seed:||27|
|Number in full:||4975|
|Average length of the domain:||234.70 aa|
|Average identity of full alignment:||16 %|
|Average coverage of the sequence by the domain:||69.67 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 11927849 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||15|
|Download:||download the raw HMM for this family|
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There are 2 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 Peripla_BP_2 domain has been found. There are 94 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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