Summary
Periplasmic binding protein clan
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 27 families and the total number of domains in the clan is 532144. The clan was built by A Bateman.
Literature references
- 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
- 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
Members
This clan contains the following 27 member families:
CypI DctP DUF3834 HisG Lig_chan-Glu_bd Lipoprotein_8 Lipoprotein_9 LysR_substrate NMT1 NMT1_2 NMT1_3 OpuAC PBP_like PBP_like_2 PDT Phosphonate-bd Porphobil_deam SBP_bac_1 SBP_bac_11 SBP_bac_3 SBP_bac_5 SBP_bac_6 SBP_bac_8 TctC Transferrin VitK2_biosynth YhfZ_CDomain organisation
Below is a listing of the unique domain organisations or architectures from this clan. More...
Loading domain graphics...
Alignments
The table below shows the number of occurrences of each domain throughout the sequence database. More...
| Pfam family | Num. domains | Alignment |
|---|---|---|
| LysR_substrate (PF03466) | 146371 (27.5%) | View |
| SBP_bac_3 (PF00497) | 53227 (10.0%) | View |
| SBP_bac_5 (PF00496) | 50123 (9.4%) | View |
| SBP_bac_8 (PF13416) | 44265 (8.3%) | View |
| SBP_bac_1 (PF01547) | 35190 (6.6%) | View |
| TctC (PF03401) | 26616 (5.0%) | View |
| DctP (PF03480) | 22513 (4.2%) | View |
| NMT1 (PF09084) | 21110 (4.0%) | View |
| Lig_chan-Glu_bd (PF10613) | 15390 (2.9%) | View |
| PBP_like_2 (PF12849) | 14193 (2.7%) | View |
| SBP_bac_11 (PF13531) | 13763 (2.6%) | View |
| OpuAC (PF04069) | 12352 (2.3%) | View |
| SBP_bac_6 (PF13343) | 10577 (2.0%) | View |
| PDT (PF00800) | 9771 (1.8%) | View |
| continued | ||
| Pfam family | Num. domains | Alignment |
|---|---|---|
| Porphobil_deam (PF01379) | 9712 (1.8%) | View |
| HisG (PF01634) | 8518 (1.6%) | View |
| NMT1_2 (PF13379) | 7943 (1.5%) | View |
| Phosphonate-bd (PF12974) | 7198 (1.4%) | View |
| NMT1_3 (PF16868) | 7047 (1.3%) | View |
| Lipoprotein_9 (PF03180) | 6729 (1.3%) | View |
| Transferrin (PF00405) | 4158 (0.8%) | View |
| VitK2_biosynth (PF02621) | 2865 (0.5%) | View |
| PBP_like (PF12727) | 2107 (0.4%) | View |
| YhfZ_C (PF14503) | 237 (0.0%) | View |
| Lipoprotein_8 (PF02030) | 70 (0.0%) | View |
| CypI (PF06646) | 64 (0.0%) | View |
| DUF3834 (PF12916) | 35 (0.0%) | View |
| Total: 27 | Total: 532144 | 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
HideThis tree shows the occurrence of the domains in this clan across different species. More...
Loading...
Structures
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.
Loading structure mapping...
