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1664  structures 5964  species 17  interactions 242652  sequences 837  architectures

Clan: PBP (CL0177)


Periplasmic binding protein clan Add an annotation

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 [2].

This clan contains 23 families and the total number of domains in the clan is 242652. The clan was built by A Bateman.

Literature references

  1. Tam R, Saier MH Jr; , Microbiol Rev 1993;57:320-346.: Structural, functional, and evolutionary relationships among extracellular solute-binding receptors of bacteria. PUBMED:8336670 EPMC:8336670
  2. Felder CB, Graul RC, Lee AY, Merkle HP, Sadee W; , AAPS PharmSci 1999;1:E2.: The Venus flytrap of periplasmic binding proteins: an ancient protein module present in multiple drug receptors. PUBMED:11741199 EPMC:11741199


This clan contains the following 23 member families:

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

Domain organisation

Below is a listing of the unique domain organisations or architectures from this clan. More...

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The table below shows the number of occurrences of each domain throughout the sequence database. More...

Pfam family Num. domains Alignment
LysR_substrate (PF03466) 85941 (35.4%) View
SBP_bac_3 (PF00497) 31454 (13.0%) View
SBP_bac_5 (PF00496) 27055 (11.1%) View
SBP_bac_8 (PF13416) 17239 (7.1%) View
SBP_bac_1 (PF01547) 9759 (4.0%) View
SBP_bac_11 (PF13531) 7719 (3.2%) View
PBP_like_2 (PF12849) 7526 (3.1%) View
NMT1 (PF09084) 7206 (3.0%) View
OpuAC (PF04069) 7137 (2.9%) View
TctC (PF03401) 6762 (2.8%) View
Lipoprotein_9 (PF03180) 6507 (2.7%) View
SBP_bac_7 (PF03480) 6254 (2.6%) View
Pfam family Num. domains Alignment
SBP_bac_6 (PF13343) 6234 (2.6%) View
NMT1_2 (PF13379) 4162 (1.7%) View
HisG (PF01634) 3683 (1.5%) View
Phosphonate-bd (PF12974) 3450 (1.4%) View
Transferrin (PF00405) 1389 (0.6%) View
Lig_chan-Glu_bd (PF10613) 1132 (0.5%) View
VitK2_biosynth (PF02621) 1044 (0.4%) View
PBP_like (PF12727) 867 (0.4%) View
Lipoprotein_8 (PF02030) 61 (0.0%) View
Mycoplasma_p37 (PF06646) 52 (0.0%) View
DUF3834 (PF12916) 19 (0.0%) View
Total: 23 Total: 242652 Clan alignment

Please note: Clan alignments can be very large and can cause problems for some browsers. Read the note above before viewing.

Family relationships

This diagram shows the relationships between members of this clan. More...

Species distribution

Tree controls


This tree shows the occurrence of the domains in this clan across different species. More...



There are 17 interactions for this clan. More...

Interacting families
LysR_substrate HTH_1
SBP_bac_3 SBP_bac_3
SBP_bac_7 SBP_bac_7
Lig_chan-Glu_bd Lig_chan-Glu_bd
HisG tRNA-synt_2b
VitK2_biosynth VitK2_biosynth
SBP_bac_1 BPD_transp_1
Transferrin Transferrin
TctC TctC
SBP_bac_5 SBP_bac_5


For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the MSD group, to allow us to map Pfam domains onto UniProt three-dimensional structures. The table below shows the mapping between the Pfam families in this clan, the corresponding UniProt entries, and the region of the three-dimensional structures that are available for that sequence.

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