PBPbBacterial periplasmic substrate-binding proteins |
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| SMART accession number: | SM00062 |
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| Description: | bacterial proteins, eukaryotic ones are in PBPe |
| Interpro abstract (IPR001638): | Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. The protein components of these traffic systems include one or two transmembrane protein components, one or two membrane-associated ATP-binding proteins (ABC transporters; see IPR003439) and a high affinity periplasmic solute-binding protein. The latter are thought to bind the substrate in the vicinity of the inner membrane, and to transfer it to a complex of inner membrane proteins for concentration into the cytoplasm. In Gram-positive bacteria which are surrounded by a single membrane and have therefore no periplasmic region, the equivalent proteins are bound to the membrane via an N-terminal lipid anchor. These homologue proteins do not play an integral role in the transport process per se, but probably serve as receptors to trigger or initiate translocation of the solute throught the membrane by binding to external sites of the integral membrane proteins of the efflux system. In addition, at least some solute-binding proteins function in the initiation of sensory transduction pathways. On the basis of sequence similarities, the vast majority of these solute-binding proteins can be grouped [(PUBMED:8336670)] into eight families or clusters, which generally correlate with the nature of the solute bound. Family 3 groups together specific amino acids and opine-binding periplasmic proteins and a periplasmic homologue with catalytic activity. |
| GO process: | transport (GO:0006810) |
| GO component: | outer membrane-bounded periplasmic space (GO:0030288) |
| GO function: | transporter activity (GO:0005215) |
| Family alignment: |
There are 9677 PBPb domains in 9238 proteins in SMART's nrdb database.
Click on the following links for more information.
- Evolution (species in which this domain is found)
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- Metabolism (metabolic pathways involving proteins which contain this domain)
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Click the image to view the interactive version of the map in iPath% proteins involved KEGG pathway ID Description 85.59 map02010 ABC transporters - General 6.15 map02020 Two-component system - General 3.87 map02040 Flagellar assembly 3.16 
map00400Phenylalanine, tyrosine and tryptophan biosynthesis 0.18 map00260Glycine, serine and threonine metabolism 0.18 map00770Pantothenate and CoA biosynthesis 0.18 map00930Caprolactam degradation 0.18 map00760Nicotinate and nicotinamide metabolism 0.18 map00300Lysine biosynthesis 0.18 map00240Pyrimidine metabolism 0.18 map00530Aminosugars metabolism This information is based on mapping of SMART genomic protein database to KEGG orthologous groups. Percentage points are related to the number of proteins with PBPb domain which could be assigned to a KEGG orthologous group, and not all proteins containing PBPb domain. Please note that proteins can be included in multiple pathways, ie. the numbers above will not always add up to 100%.
- Structure (3D structures containing this domain)
3D Structures of PBPb domains in PDB
PDB code Main view Title 1ftj 
Crystal structure of the glur2 ligand binding core (s1s2j) in complex with glutamate at 1.9 resolution 1ftk 
Crystal structure of the glur2 ligand binding core (s1s2i) in complex with kainate at 1.6 a resolution 1ftl 
Crystal structure of the glur2 ligand binding core (s1s2j) in complex with the antagonist dnqx at 1.8 a resolution 1ftm 
Crystal structure of the glur2 ligand binding core (s1s2j) in complex with ampa at 1.7 resolution 1fto 
Crystal structure of the glur2 ligand binding core (s1s2j) in the apo state at 2.0 a resolution 1fw0 
Crystal structure of the glur2 ligand binding core (s1s2j) in complex with kainate at 2.0 a resolution 1ggg 
Glutamine binding protein open ligand-free structure 1gr2 
Structure of a glutamate receptor ligand binding core (glur2) complexed with kainate 1hpb 
The bacterial periplasmic histidine-binding protein: structure(slash)function analysis of the ligand-binding site and comparison with related proteins 1hsl 
Refined 1.89 angstroms structure of the histidine-binding protein complexed with histidine and its relationship with many other active transport(slash)chemosensory receptors 1ii5 
Crystal structure of the glur0 ligand binding core complex with l-glutamate 1iit 
Glur0 ligand binding core complex with l-serine 1iiw 
Glur0 ligand binding core: closed-cleft ligand-free structure 1laf 
Structural bases for multiple ligand specificity of the periplasmic lysine-, arginine-, ornithine-binding protein 1lag 
Structural bases for multiple ligand specificity of the periplasmic lysine-, arginine-, ornithine-binding protein 1lah 
Structural bases for multiple ligand specificity of the periplasmic lysine-, arginine-, ornithine-binding protein 1lb8 
Crystal structure of the non-desensitizing glur2 ligand binding core mutant (s1s2j-l483y) in complex with ampa at 2.3 resolution 1lb9 
Crystal structure of the non-desensitizing glur2 ligand binding core mutant (s1s2j-l483y) in complex with antagonist dnqx at 2.3 a resolution 1lbb 
Crystal structure of the glur2 ligand binding domain mutant (s1s2j-n754d) in complex with kainate at 2.1 a resolution 1lbc 
Crystal structure of glur2 ligand binding core (s1s2j- n775s) in complex with cyclothiazide (ctz) as well as glutamate at 1.8 a resolution 1lst 
Three-dimensional structures of the periplasmic lysine-, arginine-, ornithine-binding protein with and without a ligand 1m5b 
X-ray structure of the glur2 ligand binding core (s1s2j) in complex with 2-me-tet-ampa at 1.85 a resolution. 1m5c 
X-ray structure of the glur2 ligand binding core (s1s2j) in complex with br-hibo at 1.65 a resolution 1m5d 
X-ray structure of the glur2 ligand binding core (s1s2j- y702f) in complex with br-hibo at 1.73 a resolution 1m5e 
X-ray structure of the glur2 ligand binding core (s1s2j) in complex with acpa at 1.46 a resolution 1m5f 
X-ray structure of the glur2 ligand binding core (s1s2j- y702f) in complex with acpa at 1.95 a resolution 1mm6 
Crystal structure of the glur2 ligand binding core (s1s2j) in complex with quisqualate in a non zinc crystal form at 2.15 angstroms resolution 1mm7 
Crystal structure of the glur2 ligand binding core (s1s2j) in complex with quisqualate in a zinc crystal form at 1.65 angstroms resolution 1mqd 
X-ray structure of the glur2 ligand-binding core (s1s2j) in complex with (s)-des-me-ampa at 1.46 a resolution. crystallization in the presence of lithium sulfate. 1mqg 
Crystal structure of the glur2 ligand binding core (s1s2j) in complex with iodo-willardiine at 2.15 angstroms resolution 1mqh 
Crystal structure of the glur2 ligand binding core (s1s2j) in complex with bromo-willardiine at 1.8 angstroms resolution 1mqi 
Crystal structure of the glur2 ligand binding core (s1s2j) in complex with fluoro-willardiine at 1.35 angstroms resolution 1mqj 
Crystal structure of the glur2 ligand binding core (s1s2j) in complex with willardiine at 1.65 angstroms resolution 1ms7 
X-ray structure of the glur2 ligand-binding core (s1s2j) in complex with (s)-des-me-ampa at 1.97 a resolution, crystallization in the presence of zinc acetate 1mxu 
Crystal structure of the glur2 ligand binding core (s1s2j) in complex with bromo-willardiine (control for the crystal titration experiments) 1mxv 
Crystal titration experiments (ampa co-crystals soaked in mm brw) 1mxw 
Crystal titration experiments (ampa co-crystals soaked in 1 mm brw) 1mxx 
Crystal titration experiments (ampa co-crystals soaked in um brw) 1mxy 
Crystal titration experiments (ampa co-crystals soaked in um brw) 1mxz 
Crystal titration experiments (ampa co-crystals soaked in 1 um brw) 1my0 
Crystal titration experiments (ampa co-crystals soaked in nm brw) 1my1 
Crystal titration experiments (ampa co-crystals soaked in nm brw) 1my2 
Crystal titration experiment (ampa complex control) 1my3 
Crystal structure of glutamate receptor ligand-binding core in complex with bromo-willardiine in the zn crystal form 1my4 
Crystal structure of glutamate receptor ligand-binding core in complex with iodo-willardiine in the zn crystal form 1n0t 
X-ray structure of the glur2 ligand-binding core (s1s2j) in complex with the antagonist (s)-atpo at 2.1 a resolution. 1nnk 
X-ray structure of the glur2 ligand-binding core (s1s2j) in complex with (s)-atpa at 1.85 a resolution. crystallization with zinc ions. 1nnp 
X-ray structure of the glur2 ligand-binding core (s1s2j) in complex with (s)-atpa at 1.9 a resolution. crystallization without zinc ions. 1p1n 
Glur2 ligand binding core (s1s2j) mutant l650t in complex with kainate 1p1o 
Crystal structure of the glur2 ligand-binding core (s1s2j) mutant l650t in complex with quisqualate 1p1q 
Crystal structure of the glur2 ligand binding core (s1s2j) l650t mutant in complex with ampa 1p1u 
Crystal structure of the glur2 ligand-binding core (s1s2j) l650t mutant in complex with ampa (ammonium sulfate crystal form) 1p1w 
Crystal structure of the glur2 ligand-binding core (s1s2j) with the l483y and l650t mutations and in complex with ampa 1pb7 
Crystal structure of the nr1 ligand binding core in complex with glycine at 1.35 angstroms resolution 1pb8 
Crystal structure of the nr1 ligand binding core in complex with d-serine at 1.45 angstroms resolution 1pb9 
Crystal structure of the nr1 ligand binding core in complex with d-cycloserine at 1.60 angstroms resolution 1pbq 
Crystal structure of the nr1 ligand binding core in complex with 5,7-dichlorokynurenic acid (dcka) at 1.90 angstroms resolution 1s50 
X-ray structure of the glur6 ligand binding core (s1s2a) in complex with glutamate at 1.65 a resolution 1s7y 
Crystal structure of the glur6 ligand binding core in complex with glutamate at 1.75 a resolution orthorhombic form 1s9t 
Crystal structure of the glur6 ligand binding core in complex with quisqualate at 1.8a resolution 1sd3 
Crystal structure of the glur6 ligand binding core in complex with 2s,4r-4-methylglutamate at 1.8 angstrom resolution 1syh 
X-ray structure of the glur2 ligand-binding core (s1s2j) in complex with (s)-cpw399 at 1.85 a resolution. 1syi 
X-ray structure of the y702f mutant of the glur2 ligand- binding core (s1s2j) in complex with (s)-cpw399 at 2.1 a resolution. 1tt1 
Crystal structure of the glur6 ligand binding core in complex with kainate 1.93 a resolution 1txf 
Crystal structure of the glur5 ligand binding core in complex with glutamate at 2.1 angstrom resolution 1vso 
Crystal structure of the ligand-binding core of iglur5 in complex with the antagonist (s)-atpo at 1.85 a resolution 1wdn 
Glutamine-binding protein 1wvj 
Exploring the glur2 ligand-binding core in complex with the bicyclic ampa analogue (s)-4-ahcp 1xhy 
X-ray structure of the y702f mutant of the glur2 ligand- binding core (s1s2j) in complex with kainate at 1.85 a resolution 1xt8 
Crystal structure of cysteine-binding protein from campylobacter jejuni at 2.0 a resolution 1y1m 
Crystal structure of the nr1 ligand binding core in complex with cycloleucine 1y1z 
Crystal structure of the nr1 ligand binding core in complex with acbc 1y20 
Crystal structure of the nr1 ligand-binding core in complex with acpc 1ycj 
Crystal structure of the kainate receptor glur5 ligand- binding core in complex with (s)-glutamate 2a5s 
Crystal structure of the nr2a ligand binding core in complex with glutamate 2a5t 
Crystal structure of the nr1/nr2a ligand-binding cores complex 2aix 
X-ray structure of the glur2 ligand-binding core (s1s2j) in complex with (s)-thio-atpa at 2.2 a resolution. 2al4 
Crystal structure of the glur2 ligand binding core (s1s2j) in complex with quisqualate and cx614. 2al5 
Crystal structure of the glur2 ligand binding core (s1s2j) in complex with fluoro-willardiine and aniracetam 2anj 
Crystal structure of the glur2 ligand binding core (s1s2j- y450w) mutant in complex with the partial agonist kainic acid at 2.1 a resolution 2cmo 
The structure of a mixed glur2 ligand-binding core dimer in complex with (s)-glutamate and the antagonist (s)-ns1209 2f34 
Crystal structure of the glur5 ligand binding core dimer with ubp310 at 1.74 angstroms resolution 2f35 
Crystal structure of the glur5 ligand binding core with ubp302 at 1.87 angstroms resolution 2f36 
Crystal structure of the glur5 ligand binding core dimer with glutamate at 2.1 angstroms resolution 2gfe 
Crystal structure of the glur2 a476e s673d ligand binding core mutant at 1.54 angstroms resolution 2i0b 
Crystal structure of the glur6 ligand binding core elkq mutant dimer at 1.96 angstroms resolution 2i0c 
Crystal structure of the glur6 ligand binding core dimer crosslinked by disulfide bonds between y490c and l752c at 2.25 angstroms resolution 2i3v 
Measurement of conformational changes accompanying desensitization in an ionotropic glutamate receptor: structure of g725c mutant 2i3w 
Measurement of conformational changes accompanying desensitization in an ionotropic glutamate receptor: structure of s729c mutant 2ia4 
Crystal structure of novel amino acid binding protein from shigella flexneri 2iee 
Crystal structure of yckb_bacsu from bacillus subtilis. northeast structural genomics consortium target sr574. 2lao 
Three-dimensional structures of the periplasmic lysine-, arginine-, ornithine-binding protein with and without a ligand 2o1m 
Crystal structure of the probable amino-acid abc transporter extracellular-binding protein ytmk from bacillus subtilis. northeast structural genomics consortium target sr572 2ojt 
Structure and mechanism of kainate receptor modulation by anions 2p2a 
X-ray structure of the glur2 ligand binding core (s1s2j) in complex with 2-bn-tet-ampa at 2.26a resolution 2pbw 
Crystal structure of the ligand-binding core of iglur5 in complex with the partial agonist domoic acid at 2.5 a resolution 2pvu 
Crystal structures of the arginine-, lysine-, histidine- binding protein artj from the thermophilic bacterium geobacillus stearothermophilus 2pyy 
Crystal structure of the glur0 ligand-binding core from nostoc punctiforme in complex with (l)-glutamate 2q2a 
Crystal structures of the arginine-, lysine-, histidine- binding protein artj from the thermophilic bacterium geobacillus stearothermophilus 2q2c 
Crystal structures of the arginine-, lysine-, histidine- binding protein artj from the thermophilic bacterium geobacillus stearothermophilus 2q88 
Crystal structure of ehub in complex with ectoine 2q89 
Crystal structure of ehub in complex with hydroxyectoine 2qs1 
Crystal structure of the glur5 ligand binding core dimer in complex with ubp315 at 1.80 angstroms resolution 2qs2 
Crystal structure of the glur5 ligand binding core dimer in complex with ubp318 at 1.80 angstroms resolution 2qs3 
Crystal structure of the glur5 ligand binding core dimer in complex with ubp316 at 1.76 angstroms resolution 2qs4 
Crystal structure of the glur5 ligand binding core dimer in complex with ly466195 at 1.58 angstroms resolution 2rc7 
Crystal structure of the nr3a ligand binding core complex with glycine at 1.58 angstrom resolution 2rc8 
Crystal structure of the nr3a ligand binding core complex with d-serine at 1.45 angstrom resolution 2rc9 
Crystal structure of the nr3a ligand binding core complex with acpc at 1.96 angstrom resolution 2rca 
Crystal structure of the nr3b ligand binding core complex with glycine at 1.58 angstrom resolution 2rcb 
Crystal structure of the nr3b ligand binding core complex with d-serine at 1.62 angstrom resolution 2uxa 
Crystal structure of the glur2-flip ligand binding domain, r/g unedited. 2v25 
Structure of the campylobacter jejuni antigen peb1a, an aspartate and glutamate receptor with bound aspartate 2v3t 
Structure of the ligand-binding core of the ionotropic glutamate receptor-like glurdelta2 in the apo form 2v3u 
Structure of the ligand-binding core of the ionotropic glutamate receptor-like glurdelta2 in complex with d- serine 2vha 
Debp 2wky 
Crystal structure of the ligand-binding core of glur5 in complex with the agonist 4-ahcp 2zns 
Crystal structure of the ligand-binding core of the human ionotropic glutamate receptor, glur5, in complex with glutamate 2znt 
Crystal structure of the ligand-binding core of the human ionotropic glutamate receptor, glur5, in complex with a novel selective agonist, dysiherbaine 2znu 
Crystal structure of the ligand-binding core of the human ionotropic glutamate receptor, glur5, in complex with a novel selective agonist, neodysiherbaine a 3b6q 
Crystal structure of the glur2 ligand binding core (s1s2j) mutant t686a in complex with glutamate at 2.0 resolution 3b6t 
Crystal structure of the glur2 ligand binding core (s1s2j) t686a mutant in complex with quisqualate at 2.1 resolution 3b6w 
Crystal structure of the glur2 ligand binding core (s1s2j) t686s mutant in complex with glutamate at 1.7 resolution 3b7d 
Crystal structure of the glur2 ligand binding core (hs1s2j) in complex with cnqx at 2.5 a resolution 3bbr 
Crystal structure of the iglur2 ligand binding core (s1s2j- n775s) in complex with a dimeric positive modulator as well as glutamate at 2.25 a resolution 3bft 
Structure of the ligand-binding core of glur2 in complex with the agonist (s)-tdpa at 2.25 a resolution 3bfu 
Structure of the ligand-binding core of glur2 in complex with the agonist (r)-tdpa at 1.95 a resolution 3bki 
Crystal structure of the glur2 ligand binding core (s1s2j) in complex with fqx at 1.87 angstroms 3c31 
Crystal structure of glur5 ligand-binding core in complex with lithium at 1.49 angstrom resolution 3c32 
Crystal structure of glur5 ligand-binding core in complex with sodium at 1.72 angstrom resolution 3c33 
Crystal structure of glur5 ligand-binding core in complex with potassium at 1.78 angstrom resolution 3c34 
Crystal structure of glur5 ligand-binding core in complex with rubidium at 1.82 angstrom resolution 3c35 
Crystal structure of glur5 ligand-binding core in complex with cesium at 1.97 angstrom resolution 3c36 
Crystal structure of glur5 ligand-binding core in complex with ammonium ions at 1.68 angstrom resolution 3del 
The structure of ct381, the arginine binding protein from the periplasm chlamydia trachomatis 3dln 
Crystal structure of the binding domain of the ampa subunit glur3 bound to glutamate 3dp4 
Crystal structure of the binding domain of the ampa subunit glur3 bound to ampa 3dp6 
Crystal structure of the binding domain of the ampa subunit glur2 bound to glutamate 3e4r 
Crystal structure of the alkanesulfonate binding protein (ssua) from the phytopathogenic bacteria xanthomonas axonopodis pv. citri bound to hepes 3en3 
Crystal structure of the glur4 ligand-binding domain in complex with kainate 3epe 
Crystal structure of the glur4 ligand-binding domain in complex with glutamate 3fas 
X-ray structure of iglur4 flip ligand-binding core (s1s2) in complex with (s)-glutamate at 1.40a resolution 3fat 
X-ray structure of iglur4 flip ligand-binding core (s1s2) in complex with (s)-ampa at 1.90a resolution 3g3f 
Crystal structure of the glur6 ligand binding domain dimer with glutamate and nacl at 1.38 angstrom resolution 3g3g 
Crystal structure of the glur6 ligand binding domain dimer k665r mutant with glutamate and nacl at 1.3 angstrom resolution 3g3h 
Crystal structure of the glur6 ligand binding domain dimer k665r i749l q753k mutant with glutamate and nacl at 1.5 angstrom resolution 3g3i 
Crystal structure of the glur6 ligand binding domain dimer i442h k494e i749l q753k mutant with glutamate and nacl at 1.37 angstrom resolution 3g3j 
Crystal structure of the glur6 ligand binding domain dimer i442h k494e k665r i749l q753k mutant with glutamate and nacl at 1.32 angstrom resolution 3g3k 
Crystal structure of the glur6 ligand binding domain dimer i442h k494e k665r i749l q753k e757q mutant with glutamate and nacl at 1.24 angstrom resolution 3gba 
X-ray structure of iglur5 ligand-binding core (s1s2) in complex with dysiherbaine at 1.35a resolution 3gbb 
X-ray strucutre of iglur5 ligand-binding core (s1s2) in complex with msviii-19 at 2.10a resolution 3h03 
Crystal structure of the binding domain of the ampa subunit glur2 bound to ubp277 3h06 
Crystal structure of the binding domain of the ampa subunit glur2 bound to the willardiine antagonist, ubp282 3h6t 
Crystal structure of the iglur2 ligand-binding core (s1s2j- n754s) in complex with glutamate and cyclothiazide at 2.25 a resolution 3h6u 
Crystal structure of the iglur2 ligand-binding core (s1s2j- n754s) in complex with glutamate and ns1493 at 1.85 a resolution 3h6v 
Crystal structure of the iglur2 ligand-binding core (s1s2j- n754s) in complex with glutamate and ns5206 at 2.10 a resolution 3h6w 
Crystal structure of the iglur2 ligand-binding core (s1s2j- n754s) in complex with glutamate and ns5217 at 1.50 a resolution 3h7m 
Crystal structure of a histidine kinase sensor domain with similarity to periplasmic binding proteins 3hv1 
Crystal structure of a polar amino acid abc uptake transporter substrate binding protein from streptococcus thermophilus 3i6v 
Crystal structure of a periplasmic his/glu/gln/arg/opine family-binding protein from silicibacter pomeroyi in complex with lysine 3ijo 
Crystal structure of the ampa subunit glur2 bound to the allosteric modulator, althiazide 3ijx 
Crystal structure of the ampa subunit glur2 bound to the allosteric modulator, hydrochlorothiazide 3ik6 
Crystal structure of the ampa subunit glur2 bound to the allosteric modulator, chlorothiazide 3il1 
Crystal structure of the ampa subunit glur2 bound to the allosteric modulator, idra-21 3ilt 
Crystal structure of the ampa subunit glur2 bound to the allosteric modulator, trichlormethiazide 3ilu 
Crystal structure of the ampa subunit glur2 bound to the allosteric modulator, hydroflumethiazide 3k4u 
Crystal structure of putative binding component of abc transporter from wolinella succinogenes dsm 1740 complexed with lysine 3kbr 
The crystal structure of cyclohexadienyl dehydratase precursor from pseudomonas aeruginosa pa01 - Links (links to other resources describing this domain)
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PFAM SBP_bac_3 INTERPRO IPR001638 PROSITE SBP_BACTERIAL_3