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54  structures 1778  species 1  interaction 6254  sequences 19  architectures

Family: SBP_bac_7 (PF03480)

Summary: Bacterial extracellular solute-binding protein, family 7

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This is the Wikipedia entry entitled "Tripartite ATP-independent periplasmic transporter". More...

Tripartite ATP-independent periplasmic transporter Edit Wikipedia article

SBP_bac_7
Identifiers
Symbol SBP_bac_7
Pfam PF03480
Pfam clan CL0177
InterPro IPR018389
TCDB 2.A.56

Tripartite ATP-independent periplasmic transporters (TRAP transporters) are a large family of solute transporters found in bacteria and archaea, but not in eukaryotes, that appear to be specific for the uptake of organic acids. They are unique in that they utilize a substrate binding protein (SBP) in combination with a secondary transporter.

History[edit]

A schematic illustrating the key features of a TRAP transporter in comparison to an ABC transporter and a classical secondary transporter.

TRAP transporters were discovered in the laboratory of Prof. David J. Kelly at the University of Sheffield, UK. His group were working on the mechanism used by the photosynthetic bacterium Rhodobacter capsulatus to take up certain dicarboxylic acids. They characterised a binding protein component (DctP) of a transporter that recognized these compounds, which they assumed would form part of a typical ABC transporter, but when they sequenced the genes surrounding dctP they found two other genes encoding integral membrane proteins, dctQ and dctM, but no genes encoding components of an ABC transporter.[1] They further showed that uptake of the same dicarboxylates was independent of ATP and that uptake required an electrochemical ion gradient, making this a unique binding protein-dependent secondary transporter.[1]

Since these early studies, it has become clear that TRAP transporters are present in many bacteria and archaea,[2] with many bacterial having multiple TRAP transporters, some having over 20 different systems.[3]

Substrates[edit]

To date, most substrates for TRAP transporters contain a common feature which is that they are organic acids.[4] This includes C4-dicarboxylates such as succinate, malate and fumarate,[1] keto-acids such as pyruvate and alpha-ketobutyrate[5][6] and the sugar acid, N-acetyl neuraminic acid (or sialic acid).[7] Other substrates include the compatible solute ectoine and hydroxyectoine and pyroglutamate.[4]

Composition[edit]

All known TRAP transporters contain 3 protein domains. These are the solute binding protein (the SBP), the small membrane protein domain and the large membrane protein domain. Following the nomenclature for the first characterized TRAP transporter, DctPQM, these subunits are usually named P, Q and M respectively.[4] Around 10% of TRAP transporters have natural genetic fusions between the two membrane protein components, and in the one well studied example of this in the sialic acid specific TRAP transporter from Haemophilus influenzae the fused gene has been named siaQM. The large M subunit is predicted to have 12 transmembrane helices and the small Q subunit to have 4 transmembrane helices and the fused QM proteins are predicted to have 17 transmembrane helices.[4]

Mechanism[edit]

By using an SBP, TRAP transporters share some similarity to ABC transporters in that the substrate for the transporter is initially recognized outside of the cytoplasmic membrane. In Gram-negative bacteria, the SBP is usually free in the periplasm and expressed at relatively high levels compared to the membrane domains.[1] In Gram positive bacteria and archaea, the SBP is tethered to the cytoplasmic membrane. In both types of systems the SBP binds to substrate, usually with low micromolar affinity,[4] which causes a significant conformation change in the protein, akin to a Venus flytrap closing. The trapped subtrate is then delivered to the membrane domains of the transporter, where the electrochemical ion gradient is somehow exploited to open the SBP, extract the substrate and catalyse its movement across the membrane. For the SiaPQM TRAP transporter which has been studied in a fully reconstituted in vitro form, uptake uses a Na+ gradient and not proton gradient to drive uptake.[8] The SiaPQM systems also exhibits unique properties for a secondary transporter in that it cannot catalyse bidirectional transport as the SBP imposes that movement is only in the direction of uptake into the cell.[8]

Structure[edit]

Substrate binding protein (SBP)[edit]

Following the first structure of a TRAP SBP in 2005,[9] there are now over 10 different structures available.[10][11][12] They all have very similar overall structures, with two globular domains linked by a hinge. The substrate binding site is formed by both the domains which enclose the substrate. A highly conserved arginine residue in the TRAP SBPs forms a salt bridge with a carboxylate group on the substrate, which is important for substrate recognition.[10]

Membrane subunits[edit]

There are currently no structures for the membrane domains of any TRAP transporter. It is not even known which subunit(s) made a direct interaction with the SBP subunit during the transport cycle.

References[edit]

  1. ^ a b c d Forward J.A., Behrendt M.C., Wyborn N.R., Cross R., Kelly D.J. (1997). "TRAP transporters: a new family of periplasmic solute transport systems encoded by the dctPQM genes of Rhodobacter capsulatus and by homologs in diverse gram-negative bacteria". J. Bacteriol. 179 (17): 5482–5493. PMC 179420. PMID 9287004. 
  2. ^ Rabus R., Jack D.L., Kelly D.J., Saier M.H. Jr. (1999). "TRAP transporters: an ancient family of extracytoplasmic solute-receptor-dependent secondary active transporters". Microbiology 145 (12): 3431–3445. PMID 10627041. 
  3. ^ Mulligan C., Kelly D.J., Thomas G.H. (2007). "Tripartite ATP-independent periplasmic transporters: application of a relational database for genome-wide analysis of transporter gene frequency and organization". J. Mol. Microbiol. Biotechnol. 12 (3–4): 218–226. doi:10.1159/000099643. PMID 17587870. 
  4. ^ a b c d e Mulligan C., Fischer M., Thomas G. (2010). "Tripartite ATP-independent periplasmic (TRAP) transporters in bacteria and archaea". FEMS Microbiol. Rev. 35 (1): 68–86. doi:10.1111/j.1574-6976.2010.00236.x. PMID 20584082. 
  5. ^ Thomas GH, Southworth T, León-Kempis MR, Leech A, Kelly DJ (2006). "Novel ligands for the extracellular solute receptors of two bacterial TRAP transporters". Microbiology 152 (2): 187–198. doi:10.1099/mic.0.28334-0. PMID 16385129. 
  6. ^ Pernil R, Herrero A, Flores E. (2010). "A TRAP transporter for pyruvate and other monocarboxylate 2-oxoacids in the cyanobacterium Anabaena sp. strain PCC 7120". J. Bacteriol. 192 (22): 6089–6092. doi:10.1128/JB.00982-10. PMC 2976462. PMID 20851902. 
  7. ^ Severi E, Randle G, Kivlin P, Whitfield K, Young R, Moxon R, Kelly D, Hood D, Thomas GH. (2005). "Sialic acid transport in Haemophilus influenzae is essential for lipopolysaccharide sialylation and serum resistance and is dependent on a novel tripartite ATP-independent periplasmic transporter". Mol. Microbiol. 58 (4): 1173–1185. doi:10.1111/j.1365-2958.2005.04901.x. PMID 16262798. 
  8. ^ a b Mulligan C., Geertsma E.R., Severi E., Kelly D.J., Poolman B., Thomas G.H. (2009). "The substrate-binding protein imposes directionality on an electrochemical sodium gradient-driven TRAP transporter". Proc. Natl. Acad. Sci. USA. 106 (6): 1778–1783. doi:10.1073/pnas.0809979106. PMC 2644114. PMID 19179287. 
  9. ^ Müller A., Severi E., Mulligan C., Watts A.G., Kelly D.J., Wilson K.S., Wilkinson A.J., Thomas G.H. (2006). "Conservation of structure and mechanism in primary and secondary transporters exemplified by SiaP, a sialic acid binding virulence factor from Haemophilus influenzae". J. Biol. Chem. 281 (31): 22212–22222. doi:10.1074/jbc.M603463200. PMID 16702222. 
  10. ^ a b Johnston J.W., Coussens N.P., Allen S., Houtman J.C., Turner K.H., Zaleski A., Ramaswamy S., Gibson B.W., Apicella M.A. (2008). "Characterization of the N-acetyl-5-neuraminic acid-binding site of the extracytoplasmic solute receptor (SiaP) of nontypeable Haemophilus influenzae strain 2019". J. Biol. Chem. 283 (2): 855–865. doi:10.1074/jbc.M706603200. PMID 17947229. 
  11. ^ Gonin S., Arnoux P., Pierru B., Lavergne J., Alonso B., Sabaty M., Pignol D. (2007). "Crystal structures of an Extracytoplasmic Solute Receptor from a TRAP transporter in its open and closed forms reveal a helix-swapped dimer requiring a cation for alpha-keto acid binding". BMC Struct. Biol. 7: 11. doi:10.1186/1472-6807-7-11. PMC 1839085. PMID 17362499. 
  12. ^ Fischer M, Zhang QY, Hubbard RE, Thomas GH (2010). "Caught in a TRAP: substrate-binding proteins in secondary transport". Trends Microbiol. 18 (10): 471–478. doi:10.1016/j.tim.2010.06.009. PMID 20656493. 

External links[edit]

  • [1] The lab page of Prof. David Kelly, University of Sheffield, UK
  • [2] The lab page of Dr. Gavin Thomas, University of York, UK.

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Bacterial extracellular solute-binding protein, family 7 Provide feedback

This family of proteins is involved in binding extracellular solutes for transport across the bacterial cytoplasmic membrane. This family includes P37735 a C4-dicarboxylate-binding protein [1] and the sialic acid-binding protein SiaP. The structure of the SiaP receptor has revealed an overall topology similar to ATP binding cassette ESR (extracytoplasmic solute receptors) proteins [2]. Upon binding of sialic acid, SiaP undergoes domain closure about a hinge region and kinking of an alpha-helix hinge component [2].

Literature references

  1. Shaw JG, Hamblin MJ, Kelly DJ; , Mol Microbiol 1991;5:3055-3062.: Purification, characterization and nucleotide sequence of the periplasmic C4-dicarboxylate-binding protein (DctP) from Rhodobacter capsulatus. PUBMED:1809844 EPMC:1809844

  2. Muller A, Severi E, Mulligan C, Watts AG, Kelly DJ, Wilson KS, Wilkinson AJ, Thomas GH; , J Biol Chem. 2006;281:22212-22222.: Conservation of structure and mechanism in primary and secondary transporters exemplified by SiaP, a sialic acid binding virulence factor from Haemophilus influenzae. PUBMED:16702222 EPMC:16702222

  3. Severi E, Randle G, Kivlin P, Whitfield K, Young R, Moxon R, Kelly D, Hood D, Thomas GH; , Mol Microbiol. 2005;58:1173-1185.: Sialic acid transport in Haemophilus influenzae is essential for lipopolysaccharide sialylation and serum resistance and is dependent on a novel tripartite ATP-independent periplasmic transporter. PUBMED:16262798 EPMC:16262798

  4. Fischer M, Zhang QY, Hubbard RE, Thomas GH;, Trends Microbiol. 2010;18:471-478.: Caught in a TRAP: substrate-binding proteins in secondary transport. PUBMED:20656493 EPMC:20656493


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR018389

This family of proteins are involved in binding extracellular solutes for transport across the bacterial cytoplasmic membrane. This family includes a C4-dicarboxylate-binding protein DctP [PUBMED:16262798, PUBMED:1809844] and the sialic acid-binding protein SiaP. The structure of the SiaP receptor has revealed an overall topology similar to ATP binding cassette ESR (extracytoplasmic solute receptors) proteins [PUBMED:16702222]. Upon binding of sialic acid, SiaP undergoes domain closure about a hinge region and kinking of an alpha-helix hinge component [PUBMED:16702222].

Gene Ontology

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Domain organisation

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Pfam Clan

This family is a member of clan PBP (CL0177), which has the following description:

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].

The clan contains the following 23 members:

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

Alignments

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  Seed
(35)
Full
(6254)
Representative proteomes NCBI
(5551)
Meta
(7504)
RP15
(536)
RP35
(1184)
RP55
(1514)
RP75
(1762)
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  Seed
(35)
Full
(6254)
Representative proteomes NCBI
(5551)
Meta
(7504)
RP15
(536)
RP35
(1184)
RP55
(1514)
RP75
(1762)
Alignment:
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  Seed
(35)
Full
(6254)
Representative proteomes NCBI
(5551)
Meta
(7504)
RP15
(536)
RP35
(1184)
RP55
(1514)
RP75
(1762)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

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

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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Trees

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Curation and family details

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Curation View help on the curation process

Seed source: Pfam-B_808 (release 7.0)
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 35
Number in full: 6254
Average length of the domain: 278.70 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 82.64 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.5 20.5
Trusted cut-off 20.6 20.5
Noise cut-off 20.4 20.4
Model length: 286
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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Interactions

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SBP_bac_7

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 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 SBP_bac_7 domain has been found. There are 54 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 seqence.

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