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205  structures 6198  species 0  interactions 24493  sequences 75  architectures

Family: Peripla_BP_2 (PF01497)

Summary: Periplasmic binding protein

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Periplasmic binding protein Provide feedback

This family includes bacterial periplasmic binding proteins. Several of which are involved in iron transport.

Literature references

  1. 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

Internal database links

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).

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan Chelatase (CL0043), which has the following description:

Metallated tetrapyrroles are used as prosthetic groups in proteins involved in biologically important processes such as photosynthesis, oxygen transport, drug metabolism and nitric oxide synthesis. In living organisms, metallation is catalysed by a group of enzymes called chelatases. This clan contains ferrochelatase (heme) and cobalt chelatase [1].

The clan contains the following 7 members:

CbiK CbiX DUF3364 Ferrochelatase Oxidored_nitro Peripla_BP_2 ZnuA


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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...


This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_461 (release 4.0)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bashton M , Bateman A
Number in seed: 23
Number in full: 24493
Average length of the domain: 233.40 aa
Average identity of full alignment: 16 %
Average coverage of the sequence by the domain: 70.02 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.5 27.5
Trusted cut-off 27.5 27.5
Noise cut-off 27.4 27.4
Model length: 237
Family (HMM) version: 20
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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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 Peripla_BP_2 domain has been found. There are 205 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 sequence.

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