Summary: Taurine catabolism dioxygenase TauD, TfdA family
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This is the Wikipedia entry entitled "TauD protein domain". More...
TauD protein domain Edit Wikipedia article
TauD | |||||||||
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![]() ensemble refinement of the protein crystal structure of gene product from arabidopsis thaliana at3g21360 | |||||||||
Identifiers | |||||||||
Symbol | TauD | ||||||||
Pfam | PF02668 | ||||||||
Pfam clan | CL0029 | ||||||||
InterPro | IPR003819 | ||||||||
SCOP2 | 1gy9 / SCOPe / SUPFAM | ||||||||
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In molecular biology, TauDrefers to a protein that in many enteric bacteria is used to breakdown taurine (2-aminoethanesulphonic acid) as a source of sulphur.
Function
This family consists of TauD/TfdA taurine catabolism dioxygenases. The Escherichia coli tauD gene is required for the utilization of taurine (2-aminoethanesulphonic acid) as a sulphur source and is expressed only under conditions of sulphate starvation. TauD is an alpha-ketoglutarate-dependent dioxygenase catalyzing the oxygenolytic release of sulphite from taurine.[1] The 2,4-dichlorophenoxyacetic acid/alpha-ketoglutarate dioxygenase from Burkholderia sp. (strain RASC) also belongs to this family.[2] TfdA from Ralstonia eutropha (Alcaligenes eutrophus) is a 2,4-D monooxygenase.[3]
Structure
References
- ^ Eichhorn E, van der Ploeg JR, Kertesz MA, Leisinger T (1997). "Characterization of alpha-ketoglutarate-dependent taurine dioxygenase from Escherichia coli". J. Biol. Chem. 272 (37): 23031–6. PMID 9287300.
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ignored (help)CS1 maint: multiple names: authors list (link) - ^ Suwa Y, Wright AD, Fukimori F, Nummy KA, Hausinger RP, Holben WE, Forney LJ (1996). "Characterization of a chromosomally encoded 2,4-dichlorophenoxyacetic acid/alpha-ketoglutarate dioxygenase from Burkholderia sp. strain RASC". Appl. Environ. Microbiol. 62 (7): 2464–9. PMC 168028. PMID 8779585.
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ignored (help)CS1 maint: multiple names: authors list (link) - ^ Streber WR, Timmis KN, Zenk MH (1987). "Analysis, cloning, and high-level expression of 2,4-dichlorophenoxyacetate monooxygenase gene tfdA of Alcaligenes eutrophus JMP134". J. Bacteriol. 169 (7): 2950–5. PMC 212332. PMID 3036764.
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ignored (help)CS1 maint: multiple names: authors list (link)
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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.
Taurine catabolism dioxygenase TauD, TfdA family Provide feedback
This family consists of taurine catabolism dioxygenases of the TauD, TfdA family. TauD from E. coli P37610 is a alpha-ketoglutarate-dependent taurine dioxygenase [1]. This enzyme catalyses the oxygenolytic release of sulfite from taurine [1]. TfdA from Burkholderia sp. Q45423 is a 2,4-dichlorophenoxyacetic acid/alpha-ketoglutarate dioxygenase [2]. TfdA from Alcaligenes eutrophus JMP134 P10088 is a 2,4-dichlorophenoxyacetate monooxygenase [3]. Also included are gamma-Butyrobetaine hydroxylase enzymes EC:1.14.11.1 [4].
Literature references
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Eichhorn E, van der Ploeg JR, Kertesz MA, Leisinger T; , J Biol Chem 1997;272:23031-23036.: Characterization of alpha-ketoglutarate-dependent taurine dioxygenase from Escherichia coli. PUBMED:9287300 EPMC:9287300
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Suwa Y, Wright AD, Fukimori F, Nummy KA, Hausinger RP, Holben WE, Forney LJ; , Appl Environ Microbiol 1996;62:2464-2469.: Characterization of a chromosomally encoded 2,4-dichlorophenoxyacetic acid/alpha-ketoglutarate dioxygenase from Burkholderia sp. strain RASC. PUBMED:8779585 EPMC:8779585
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Streber WR, Timmis KN, Zenk MH; , J Bacteriol 1987;169:2950-2955.: Analysis, cloning, and high-level expression of 2,4-dichlorophenoxyacetate monooxygenase gene tfdA of Alcaligenes eutrophus JMP134. PUBMED:3036764 EPMC:3036764
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Ruetschi U, Nordin I, Odelhog B, Jornvall H, Lindstedt S; , Eur J Biochem 1993;213:1075-1080.: gamma-Butyrobetaine hydroxylase. Structural characterization of the Pseudomonas enzyme. PUBMED:8504802 EPMC:8504802
Internal database links
SCOOP: | CsiD |
Similarity to PfamA using HHSearch: | CsiD |
External database links
SCOP: | 1gy9 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR003819
This domain is found in TauD/TfdA taurine catabolism dioxygenases. The Escherichia coli tauD gene is required for the utilisation of taurine (2-aminoethanesulphonic acid) as a sulphur source and is expressed only under conditions of sulphate starvation. TauD is an alpha-ketoglutarate-dependent dioxygenase catalysing the oxygenolytic release of sulphite from taurine [ PUBMED:9287300 ]. The 2,4-dichlorophenoxyacetic acid/alpha-ketoglutarate dioxygenase from Burkholderia sp. (strain RASC) also belongs to this family [ PUBMED:8779585 ]. TfdA from Ralstonia eutropha (Alcaligenes eutrophus) is a 2,4-D monooxygenase [ PUBMED:3036764 ].
This domain is also found in gamma-butyrobetaine hydroxylase (GBBH), the enzyme responsible for the biosynthesis of L-carnitine, a key molecule of fatty acid metabolism. The GBBH monomer consists of this catalytic double-stranded beta-helix (DBSH) domain, which is found in all 2-ketoglutarate (2KG) oxygenases, and a smaller N-terminal domain [ PUBMED:20599753 ].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | oxidoreductase activity (GO:0016491) |
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 Cupin (CL0029), which has the following description:
This clan represents the conserved barrel domain of the 'cupin' superfamily [1] ('cupa' is the Latin term for a small barrel). The cupin fold is found in a wide variety of enzymes, but notably contains the non-enzymatic seed storage proteins also.
The clan contains the following 69 members:
2OG-Fe_Oxy_2 2OG-FeII_Oxy 2OG-FeII_Oxy_2 2OG-FeII_Oxy_3 2OG-FeII_Oxy_4 2OG-FeII_Oxy_5 2OG-FeII_Oxy_6 3-HAO AIM24 AraC_binding AraC_binding_2 AraC_N ARD Asp_Arg_Hydrox AUDH_Cupin Auxin_BP CDO_I CENP-C_C cNMP_binding CsiD Cupin_1 Cupin_2 Cupin_3 Cupin_5 Cupin_6 Cupin_7 Cupin_8 DIOX_N DMSP_lyase dTDP_sugar_isom DUF1479 DUF1971 DUF386 DUF4437 DUF4867 DUF5070 DUF6016 Ectoine_synth ERG2_Sigma1R EutQ FdtA FTO_NTD GPI HgmA_C HgmA_N HutD JmjC JmjC_2 JmjN KduI Lyx_isomer MannoseP_isomer Ofd1_CTDD Oxygenase-NA PCO_ADO PhyH Pirin Pirin_C Pirin_C_2 PMI_typeI_C PMI_typeI_cat Popeye Pox_C4_C10 Ppnp TauD Tet_JBP Ureidogly_lyase VIT VIT_2Alignments
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...
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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 (119) |
Full (18506) |
Representative proteomes | UniProt (63734) |
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RP15 (2383) |
RP35 (7627) |
RP55 (15502) |
RP75 (27002) |
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Jalview | |||||||
HTML | |||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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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 (119) |
Full (18506) |
Representative proteomes | UniProt (63734) |
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RP15 (2383) |
RP35 (7627) |
RP55 (15502) |
RP75 (27002) |
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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.
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: | COG2175 |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Bashton M |
Number in seed: | 119 |
Number in full: | 18506 |
Average length of the domain: | 264.7 aa |
Average identity of full alignment: | 18 % |
Average coverage of the sequence by the domain: | 70.34 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 268 | ||||||||||||
Family (HMM) version: | 19 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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 TauD domain has been found. There are 248 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 sequence.
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AlphaFold Structure Predictions
The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.