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2876  structures 5332  species 74  interactions 233285  sequences 1362  architectures

Clan: PBP (CL0177)

Summary

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 27 families and the total number of domains in the clan is 233285. 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

Members

This clan contains the following 27 member families:

DctP DUF3834 HisG Lig_chan-Glu_bd Lipoprotein_8 Lipoprotein_9 LysR_substrate Mycoplasma_p37 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_C

Domain organisation

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

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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) 67877 (29.1%) View
SBP_bac_3 (PF00497) 24877 (10.7%) View
SBP_bac_5 (PF00496) 22753 (9.8%) View
SBP_bac_8 (PF13416) 19953 (8.6%) View
SBP_bac_1 (PF01547) 11631 (5.0%) View
TctC (PF03401) 10114 (4.3%) View
DctP (PF03480) 9324 (4.0%) View
NMT1 (PF09084) 8911 (3.8%) View
PBP_like_2 (PF12849) 6952 (3.0%) View
SBP_bac_11 (PF13531) 6228 (2.7%) View
OpuAC (PF04069) 5488 (2.4%) View
SBP_bac_6 (PF13343) 5192 (2.2%) View
PDT (PF00800) 4507 (1.9%) View
Porphobil_deam (PF01379) 4196 (1.8%) View
continued
Pfam family Num. domains Alignment
HisG (PF01634) 3962 (1.7%) View
NMT1_2 (PF13379) 3727 (1.6%) View
Lipoprotein_9 (PF03180) 3703 (1.6%) View
Lig_chan-Glu_bd (PF10613) 3701 (1.6%) View
Phosphonate-bd (PF12974) 3373 (1.4%) View
NMT1_3 (PF16868) 2970 (1.3%) View
Transferrin (PF00405) 1266 (0.5%) View
VitK2_biosynth (PF02621) 1237 (0.5%) View
PBP_like (PF12727) 1136 (0.5%) View
YhfZ_C (PF14503) 107 (0.0%) View
Lipoprotein_8 (PF02030) 43 (0.0%) View
Mycoplasma_p37 (PF06646) 32 (0.0%) View
DUF3834 (PF12916) 25 (0.0%) View
Total: 27 Total: 233285 Clan alignment
 

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Family relationships

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

Species distribution

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

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Interactions

There are 74 interactions for this clan. More...

Interacting families
A B
ACT PDT
ANF_receptor Lig_chan-Glu_bd
BPD_transp_1 SBP_bac_1
Calc_CGRP_IAPP SBP_bac_1
DctP DctP
HisG HisG
HisG_C
HTH_1 LysR_substrate
Lectin_legB Transferrin
Lig_chan Lig_chan-Glu_bd
SBP_bac_3
Lig_chan-Glu_bd Lig_chan
Lig_chan-Glu_bd
Lipoprotein_9 Lipoprotein_9
LysR_substrate HTH_1
LysR_substrate
MHC_II_alpha Transferrin
MHC_II_beta Transferrin
Mycoplasma_p37 Mycoplasma_p37
NMT1 NMT1
NMT1_2 NMT1_2
OpuAC OpuAC
PAZ SBP_bac_1
PBP_like_2 PBP_like_2
PDT ACT
PDT
Peptidase_S8 Transferrin
Phosphonate-bd Phosphonate-bd
Plug Transferrin
Porin_1 Transferrin
Porphobil_deam Porphobil_deam
Porphobil_deamC
Porphobil_deamC Porphobil_deam
Renin_r SBP_bac_1
Ribosomal_L7Ae SBP_bac_1
SBP_bac_1 ArgoL1
Beta-lactamase2
BPD_transp_1
C2-set_2
Calc_CGRP_IAPP
CARD
CHCH
DUF1325
E6
Homeobox
I-set
Kinesin
MalF_P2
Renin_r
Ribosomal_L7Ae
RVT_3
SBP_bac_1
SMN
Synuclein
Tryp_alpha_amyl
SBP_bac_11 SBP_bac_11
SBP_bac_3 Lig_chan
SBP_bac_3
SBP_bac_5 SBP_bac_5
SBP_bac_6 SBP_bac_6
SBP_bac_8 CARD
PYRIN
SBP_bac_8
TbpB_B_D Transferrin
TctC TctC
TFR_dimer Transferrin
TonB_dep_Rec Transferrin
Transferrin Porin_1
TbpB_B_D
Transferrin
tRNA-synt_His HisG
VitK2_biosynth VitK2_biosynth
WD40 SBP_bac_1
YhfZ_C YhfZ_C

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.

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