Summary: DctM-like transporters

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Wikipedia: Tripartite ATP-independent periplasmic transporter
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Tripartite ATP-independent periplasmic transporter Edit Wikipedia article

DctP component of Tripartite ATP-independent periplasmic transporter

Identifiers

Symbol

DctP

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe; PDBj
PDBsum	structure summary

DctQ component of Tripartite ATP-independent periplasmic transporter

Identifiers

Symbol

DctQ

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe; PDBj
PDBsum	structure summary

DctM-like transporters

Identifiers

Symbol

DctM

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe; PDBj
PDBsum	structure summary

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

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

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. 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". 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

[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.

DctM-like transporters 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

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

External database links

PANDIT:	PF06808
Pseudofam:	PF06808
SYSTERS:	DctM

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 17 members:

ABG_transport ArsB CitMHS DctM DcuA_DcuB DcuC DUF1504 DUF1646 DUF401 GntP_permease Lactate_perm MatC_N Na_H_antiport_2 Na_H_antiporter Na_sulph_symp NhaB SCFA_trans

Alignments

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.

Alignment types

We make a range of alignments for each Pfam-A family:

seed: the curated alignment from which the HMM for the family is built
full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
NCBI: alignment generated by searching the NCBI sequence database using the family HMM
meta: alignment generated by searching the metagenomics sequence database using the family HMM

Viewing

You can see the alignments as HTML or in three different sequence viewers:

jalview: a Java applet developed at the University of Dundee. You will need Java installed before running jalview
HTML: an HTML page showing the whole alignment.Please note: full Pfam alignments can be very large. These HTML views are extremely large and often cause problems for browsers. Please use either jalview or the Pfam viewer if you have trouble viewing the HTML version
PP/Heatmap: an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.
Pfam viewer: an HTML-based viewer that uses DAS to retrieve alignment fragments on request

Reformatting

You can download (or view in your browser) a text representation of a Pfam alignment in various formats:

Selex
Stockholm
FASTA
MSF

You can also change the order in which sequences are listed in the alignment, change how insertions are represented, alter the characters that are used to represent gaps in sequences and, finally, choose whether to download the alignment or to view it in your browser directly.

Downloading

You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.

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.

	Seed (18)	Full (7152)	Representative proteomes				NCBI (7864)	Meta (11933)
	Seed (18)	Full (7152)	RP15 (616)	RP35 (1374)	RP55 (1743)	RP75 (2023)	NCBI (7864)	Meta (11933)
Jalview	View	View	View	View	View	View	View	View
HTML	View		View	View	View	View
PP/heatmap	₁		View	View	View	View
Pfam viewer	View	View

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

Key: available, not generated, — not available.

Format an alignment

	Seed (18)	Full (7152)	Representative proteomes				NCBI (7864)	Meta (11933)
	Seed (18)	Full (7152)	RP15 (616)	RP35 (1374)	RP55 (1743)	RP75 (2023)	NCBI (7864)	Meta (11933)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

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.

	Seed (18)	Full (7152)	Representative proteomes				NCBI (7864)	Meta (11933)
	Seed (18)	Full (7152)	RP15 (616)	RP35 (1374)	RP55 (1743)	RP75 (2023)	NCBI (7864)	Meta (11933)
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.

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...

Trees

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

Seed source:

Pfam-B_4075 (release 10.0)

Previous IDs:

none

Type:

Family

Author:

Vella Briffa B, Bateman A

Number in seed:

18

Number in full:

7152

Average length of the domain:

404.70 aa

Average identity of full alignment:

26 %

Average coverage of the sequence by the domain:

85.53 %

HMM information

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	21.8	21.8
Trusted cut-off	21.8	21.8
Noise cut-off	21.7	21.7

Model length:

416

Family (HMM) version:

7

Download:

download the raw HMM for this family

Species distribution

Sunburst
Tree

Sunburst controls

Show

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...

This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.

How the sunburst is generated

The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.

In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:

superkingdom
kingdom
phylum
class
order
family
genus
species

Colouring and labels

Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.

As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.

Anomalies in the taxonomy tree

There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.

Missing taxonomic levels

Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.

Unmapped species names

The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.

So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".

Sub-species

Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.

Too many species/sequences

For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.

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Tree controls

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

Species trees

We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.

Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.

If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.

Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.

We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

You can use the tree controls to manipulate how the interactive tree is displayed:

show/hide the summary boxes
highlight species that are represented in the seed alignment
expand/collapse the tree or expand it to a given depth
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Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: DctM (PF06808)

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Summary: DctM-like transporters

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Tripartite ATP-independent periplasmic transporter Edit Wikipedia article

Contents

History

Substrates

Composition

Mechanism

Structure

Substrate binding protein (SBP)

Membrane subunits

References

External links

DctM-like transporters Provide feedback

Literature references

External database links

InterPro entry IPR010656

Domain organisation

Pfam Clan

Alignments

Alignment types

Viewing

Reformatting

Downloading

View options

Format an alignment

Download options

External links

HMM logo

Trees

Curation and family details

Curation

HMM information

Species distribution

Sunburst controls

Weight segments by...

Change the size of the sunburst

Colour assignments

Selections

Currently selected:

How the sunburst is generated

Colouring and labels

Anomalies in the taxonomy tree

Missing taxonomic levels

Unmapped species names

Sub-species

Too many species/sequences

Tree controls

Annotation

Download tree

Selected sequences

Species trees

Interactive tree