Summary: Tripartite ATP-independent periplasmic transporter, DctM component
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Tripartite ATP-independent periplasmic transporter Edit Wikipedia article
| DctP component of Tripartite ATP-independent periplasmic transporter | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Identifiers | |||||||||
| Symbol | DctP | ||||||||
| Pfam | PF03480 | ||||||||
| Pfam clan | CL0177 | ||||||||
| InterPro | IPR018389 | ||||||||
| TCDB | 2.A.56 | ||||||||
| |||||||||
| DctQ component of Tripartite ATP-independent periplasmic transporter | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Identifiers | |||||||||
| Symbol | DctQ | ||||||||
| Pfam | PF04290 | ||||||||
| InterPro | IPR007387 | ||||||||
| TCDB | 2.A.56 | ||||||||
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| DctM-like transporters | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Identifiers | |||||||||
| Symbol | DctM | ||||||||
| Pfam | PF06808 | ||||||||
| Pfam clan | CL0182 | ||||||||
| InterPro | IPR010656 | ||||||||
| 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 or related molecules containing a carboxylate or sulfonate group. They are unique in that they utilize a substrate binding protein (SBP) in combination with a secondary transporter.
Contents
History
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
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
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
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
Substrate binding protein (SBP)
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
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
- ^ 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.
- ^ 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. doi:10.1099/00221287-145-12-3431. PMID 10627041.
- ^ 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.
- ^ 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.
- ^ 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.
- ^ 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.
- ^ 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.
- ^ 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.
- ^ 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" (PDF). J. Biol. Chem. 281 (31): 22212–22222. doi:10.1074/jbc.M603463200. PMID 16702222.
- ^ 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.
- ^ 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.
- ^ 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
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.
Tripartite ATP-independent periplasmic transporter, DctM component Provide feedback
This family contains a diverse range of predicted transporter proteins. Including the DctM subunit of the bacterial and archaeal TRAP C4-dicarboxylate transport (Dct) system permease. In general, C4-dicarboxylate transport systems allow C4-dicarboxylates like succinate, fumarate, and malate to be taken up. TRAP C4-dicarboxylate carriers are secondary carriers that use an electrochemical H+ gradient as the driving force for transport. DctM is an integral membrane protein that is one of the constituents of TRAP carriers [1]. Note that many family members are hypothetical proteins.
Literature references
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Janausch IG, Zientz E, Tran QH, Kroger A, Unden G; , Biochim Biophys Acta 2002;1553:39-56.: C4-dicarboxylate carriers and sensors in bacteria. PUBMED:11803016 EPMC:11803016
Internal database links
| SCOOP: | ArsB CitMHS DcuC GntP_permease Lactate_perm MatC_N Na_H_antiport_2 Na_H_antiporter Na_sulph_symp TrkA_C |
| Similarity to PfamA using HHSearch: | GntP_permease CitMHS DcuC |
External database links
| Transporter classification: | 2.A.56 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR010656
This domain represents a conserved region located towards the N terminus of the DctM subunit of the bacterial and archaeal TRAP C4-dicarboxylate transport (Dct) system permease. In general, C4-dicarboxylate transport systems allow C4-dicarboxylates like succinate, fumarate, and malate to be taken up. TRAP C4-dicarboxylate carriers are secondary carriers that use an electrochemical H+ gradient as the driving force for transport. DctM is an integral membrane protein that is one of the constituents of TRAP carriers [PUBMED:11803016, PUBMED:11524131]. Note that many family members are hypothetical proteins.
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
This family is a member of clan IT (CL0182), which has the following description:
This superfamily of secondary carriers specific for cationic and anionic compounds, has been termed the ion transporter (IT) superfamily [1].
The clan contains the following 19 members:
ABG_transport ArsB CitMHS CitMHS_2 DctM DcuA_DcuB DcuC DUF1646 DUF401 EXS GntP_permease Lactate_perm MatC_N Na_H_antiport_2 Na_H_antiport_3 Na_H_antiporter Na_sulph_symp NhaB SCFA_transAlignments
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
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| Seed (17) |
Full (22267) |
Representative proteomes | UniProt (82079) |
NCBI (124919) |
Meta (11836) |
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| RP15 (2388) |
RP35 (10824) |
RP55 (22979) |
RP75 (36380) |
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| PP/heatmap | 1 | ||||||||
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| Seed (17) |
Full (22267) |
Representative proteomes | UniProt (82079) |
NCBI (124919) |
Meta (11836) |
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|---|---|---|---|---|---|---|---|---|---|
| RP15 (2388) |
RP35 (10824) |
RP55 (22979) |
RP75 (36380) |
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| Raw Stockholm | |||||||||
| Gzipped | |||||||||
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
Curation
| Seed source: | Pfam-B_4075 (release 10.0) |
| Previous IDs: | none |
| Type: | Family |
| Sequence Ontology: | SO:0100021 |
| Author: |
Vella Briffa B  , Bateman A
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| Number in seed: | 17 |
| Number in full: | 22267 |
| Average length of the domain: | 404.70 aa |
| Average identity of full alignment: | 25 % |
| Average coverage of the sequence by the domain: | 86.02 % |
HMM information
| HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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| Model details: |
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| Model length: | 416 | ||||||||||||
| Family (HMM) version: | 13 | ||||||||||||
| Download: | download the raw HMM for this family |
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