Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
0  structures 3043  species 0  interactions 19281  sequences 11  architectures

Family: DctQ (PF04290)

Summary: Tripartite ATP-independent periplasmic transporters, DctQ component

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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

Tripartite ATP-independent periplasmic transporter Edit Wikipedia article

DctP component of Tripartite ATP-independent periplasmic transporter
Pfam clanCL0177
DctQ component of Tripartite ATP-independent periplasmic transporter
DctM-like transporters
Pfam clanCL0182

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.


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]


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]


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]


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 substrate 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]


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.


  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. doi:10.1128/jb.179.17.5482-5493.1997. 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. doi:10.1099/00221287-145-12-3431. 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. S2CID 30920843.
  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. S2CID 32085592.
  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" (PDF). J. Biol. Chem. 281 (31): 22212–22222. doi:10.1074/jbc.M603463200. PMID 16702222. S2CID 37483123.
  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

  • [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.

Tripartite ATP-independent periplasmic transporters, DctQ component Provide feedback

The function of the members of this family is unknown, but DctQ homologues are invariably found in the tripartite ATP-independent periplasmic transporters [1].

Literature references

  1. Rabus R, Jack DL, Kelly DJ, Saier MH Jr; , Microbiology 1999;145:3431-3445.: TRAP transporters: an ancient family of extracytoplasmic solute-receptor-dependent secondary active transporters. PUBMED:10627041 EPMC:10627041

  2. Kelly DJ, Thomas GH; , FEMS Microbiol Rev 2001;25:405-424.: The tripartite ATP-independent periplasmic (TRAP) transporters of bacteria and archaea. PUBMED:11524131 EPMC:11524131

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007387

This family consists of DctQ homologues found in TRAP transporters [ PUBMED:10627041 ].

The tripartite ATP-independent periplasmic (TRAP) transporters are substrate-binding protein (SBP)-dependent secondary transporters ubiquitous in prokaryotes, but absent from eukaryotes. They are comprised of an SBP of the DctP or TAXI families and two integral membrane proteins of unequal sizes that form the DctQ and DctM protein families (the small and large membrane components respectively). The TRAP transporter for sialic acid consists of the SBP siaP, and siaQM (termed siaT in some cases), encoding the fused integral membrane protein [ PUBMED:20584082 ].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

Loading domain graphics...


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 and the UniProtKB sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

Representative proteomes UniProt
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

Representative proteomes UniProt

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

Representative proteomes UniProt
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...


This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

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 View help on the curation process

Seed source: COG3090
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Mifsud W
Number in seed: 74
Number in full: 19281
Average length of the domain: 135.10 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 67.59 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 28.3 28.3
Trusted cut-off 28.3 28.3
Noise cut-off 28.2 28.2
Model length: 133
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

Sunburst controls


Weight segments by...

Change the size of the sunburst


Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

Loading sunburst data...

Tree controls


The tree shows the occurrence of this domain across different species. More...


Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

trRosetta Structure

The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.

The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;