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 2105  species 0  interactions 3902  sequences 5  architectures

Family: DcuC (PF03606)

Summary: C4-dicarboxylate anaerobic carrier

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 "Anaerobic C4-dicarboxylate membrane transporter protein". More...

Anaerobic C4-dicarboxylate membrane transporter protein Edit Wikipedia article

Anaerobic c4-dicarboxylate membrane transporter
Identifiers
Symbol DcuA_DcuB
Pfam PF03605
Pfam clan CL0182
InterPro IPR004668
TCDB 2.A.13
C4-dicarboxylate anaerobic carrier
Identifiers
Symbol DcuC
Pfam PF03606
Pfam clan CL0182
InterPro IPR018385
TCDB 9.B.50

In molecular biology, the anaerobic C4-dicarboxylate membrane transporter protein family (or C4-dicarboxylate Uptake (Dcu) family) is a family of proteins which includes the DcuA, DcuB and DcuC proteins. Many members of this family are predicted to have 12 GES predicted transmembrane regions, however the one member of this family whose membrane topology has been experimentally determined has 10 transmembrane regions, with both the N- and C-termini localized to the periplasm.[1]

The DcuA and DcuB proteins are involved in the transport of aspartate, malate, fumarate and succinate in many species and are thought to function as antiporters with any two of these substrates.[2][3][4] Since DcuA is encoded in an operon with the gene for aspartase, and DcuB is encoded in an operon with the gene for fumarase, their physiological functions may be to catalyse aspartate:fumarate and fumarate:malate exchange during the anaerobic utilization of aspartate and fumarate, respectively.[5] The Escherichia coli DcuA and DcuB proteins have very different expression patterns.[6] DcuA is constitutively expressed; DcuB is strongly induced anaerobically by FNR and C4-dicarboxylates, while it is repressed by nitrate and subject to CRP-mediated catabolite repression. DcuB is the major C4-dicarboxylate carrier for fumarate respiration with high fumarate-succinate exchange activity. It is synthesized only in the absence of oxygen and nitrate and in the presence of C4-dicarboxylates.[6][7][8][9] DcuA is expressed constitutively in aerobic and anaerobic growth and can substitute for DcuB.[5][6]

DcuC has 12 GES predicted transmembrane regions, is induced only under anaerobic conditions, and is not repressed by glucose. DcuC may therefore function as a succinate efflux system during anaerobic glucose fermentation. However, when overexpressed, it can replace either DcuA or DcuB in catalysing fumarate-succinate exchange and fumarate uptake.[10][11] DcuC shows the same transport modes as DcuA and DcuB (exchange, uptake, and presumably efflux of C4-dicarboxylates).[12]

References[edit]

  1. ^ Golby P, Kelly DJ, Guest JR, Andrews SC (September 1998). "Topological analysis of DcuA, an anaerobic C4-dicarboxylate transporter of Escherichia coli". J. Bacteriol. 180 (18): 4821–7. PMC 107505. PMID 9733683. 
  2. ^ Six S, Andrews SC, Roberts RE, Unden G, Guest JR (November 1993). "Construction and properties of Escherichia coli mutants defective in two genes encoding homologous membrane proteins with putative roles in anaerobic C4-dicarboxylic acid transport". Biochem. Soc. Trans. 21 (4): 342S. PMID 8131924. 
  3. ^ Nogrady N, Imre A, Rychlik I, Barrow PA, Nagy B (December 2003). "Genes responsible for anaerobic fumarate and arginine metabolism are involved in growth suppression in Salmonella enterica serovar Typhimurium in vitro, without influencing colonisation inhibition in the chicken in vivo". Vet. Microbiol. 97 (3-4): 191–9. doi:10.1016/j.vetmic.2003.08.011. PMID 14654290. 
  4. ^ Ullmann R, Gross R, Simon J, Unden G, Kroger A (October 2000). "Transport of C(4)-dicarboxylates in Wolinella succinogenes". J. Bacteriol. 182 (20): 5757–64. PMC 94697. PMID 11004174. 
  5. ^ a b Six S, Andrews SC, Unden G, Guest JR (November 1994). "Escherichia coli possesses two homologous anaerobic C4-dicarboxylate membrane transporters (DcuA and DcuB) distinct from the aerobic dicarboxylate transport system (Dct)". J. Bacteriol. 176 (21): 6470–8. PMC 197000. PMID 7961398. 
  6. ^ a b c Golby P, Kelly DJ, Guest JR, Andrews SC (December 1998). "Transcriptional regulation and organization of the dcuA and dcuB genes, encoding homologous anaerobic C4-dicarboxylate transporters in Escherichia coli". J. Bacteriol. 180 (24): 6586–96. PMC 107762. PMID 9852003. 
  7. ^ Engel P, Kramer R, Unden G (September 1992). "Anaerobic fumarate transport in Escherichia coli by an fnr-dependent dicarboxylate uptake system which is different from the aerobic dicarboxylate uptake system". J. Bacteriol. 174 (17): 5533–9. PMC 206496. PMID 1512189. 
  8. ^ Golby P, Davies S, Kelly DJ, Guest JR, Andrews SC (February 1999). "Identification and characterization of a two-component sensor-kinase and response-regulator system (DcuS-DcuR) controlling gene expression in response to C4-dicarboxylates in Escherichia coli". J. Bacteriol. 181 (4): 1238–48. PMC 93502. PMID 9973351. 
  9. ^ Zientz E, Bongaerts J, Unden G (October 1998). "Fumarate regulation of gene expression in Escherichia coli by the DcuSR (dcuSR genes) two-component regulatory system". J. Bacteriol. 180 (20): 5421–5. PMC 107591. PMID 9765574. 
  10. ^ Engel P, Kramer R, Unden G (June 1994). "Transport of C4-dicarboxylates by anaerobically grown Escherichia coli. Energetics and mechanism of exchange, uptake and efflux". Eur. J. Biochem. 222 (2): 605–14. doi:10.1111/j.1432-1033.1994.tb18903.x. PMID 8020497. 
  11. ^ Zientz E, Janausch IG, Six S, Unden G (June 1999). "Functioning of DcuC as the C4-dicarboxylate carrier during glucose fermentation by Escherichia coli". J. Bacteriol. 181 (12): 3716–20. PMC 93849. PMID 10368146. 
  12. ^ Zientz E, Six S, Unden G (December 1996). "Identification of a third secondary carrier (DcuC) for anaerobic C4-dicarboxylate transport in Escherichia coli: roles of the three Dcu carriers in uptake and exchange". J. Bacteriol. 178 (24): 7241–7. PMC 178639. PMID 8955408. 

This article incorporates text from the public domain Pfam and InterPro IPR004668

This article incorporates text from the public domain Pfam and InterPro IPR018385

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.

C4-dicarboxylate anaerobic carrier Provide feedback

No Pfam abstract.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR018385

Escherichia coli contains four different secondary carriers (DcuA, DcuB, DcuC, and DctA) for C4-dicarboxylates [PUBMED:10482502, PUBMED:1512189, PUBMED:7961398, PUBMED:8955408] DcuA is used for aerobic growth on C4-dicarboxylates [PUBMED:10482502, PUBMED:5541510], whereas the Dcu carriers (encoded by the dcuA, dcuB, and dcuC genes) are used under anaerobic conditions and form a distinct family of carriers [PUBMED:1512189, PUBMED:8020497, PUBMED:9889977, PUBMED:7961398, PUBMED:9230919, PUBMED:8955408]. Each of the Dcu carriers is able to catalyze the uptake, antiport, and possibly also efflux of C4-dicarboxylates. DcuB is the major C4-dicarboxylate carrier for fumarate respiration with high fumarate-succinate exchange activity. It is synthesized only in the absence of oxygen and nitrate and in the presence of C4-dicarboxylates [PUBMED:1512189, PUBMED:9973351, PUBMED:9852003, PUBMED:9765574]. DcuA is expressed constitutively in aerobic and anaerobic growth and can substitute for DcuB [PUBMED:9852003, PUBMED:7961398]. These proteins are members of the C4-dicarboxylate Uptake C (DcuC) family. DcuC has 12 GES predicted transmembrane regions, is induced only under anaerobic conditions, and is not repressed by glucose. DcuC may therefore function as a succinate efflux system during anaerobic glucose fermentation. However, when overexpressed, it can replace either DcuA or DcuB in catalyzing fumarate-succinate exchange and fumarate uptake [PUBMED:8020497, PUBMED:10368146]. DcuC shows the same transport modes as DcuA and DcuB (exchange, uptake, and presumably efflux of C4-dicarboxylates) [PUBMED:8955408].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

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

Loading domain graphics...

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...

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
(13)
Full
(3902)
Representative proteomes NCBI
(3372)
Meta
(265)
RP15
(106)
RP35
(193)
RP55
(281)
RP75
(339)
Jalview View  View  View  View  View  View  View  View 
HTML View  View  View  View  View  View     
PP/heatmap 1 View  View  View  View  View     
Pfam viewer View  View             

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

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

Format an alignment

  Seed
(13)
Full
(3902)
Representative proteomes NCBI
(3372)
Meta
(265)
RP15
(106)
RP35
(193)
RP55
(281)
RP75
(339)
Alignment:
Format:
Order:
Sequence:
Gaps:
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
(13)
Full
(3902)
Representative proteomes NCBI
(3372)
Meta
(265)
RP15
(106)
RP35
(193)
RP55
(281)
RP75
(339)
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 View help on the curation process

Seed source: TIGRFAMs
Previous IDs: none
Type: Family
Author: TIGRFAMs, Griffiths-Jones SR
Number in seed: 13
Number in full: 3902
Average length of the domain: 444.50 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 97.14 %

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 22.7 22.7
Trusted cut-off 22.7 22.7
Noise cut-off 22.6 22.6
Model length: 465
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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...

Loading sunburst data...

Tree controls

Hide

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

Loading...

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.