Summary: Carboxyl transferase domain
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This is the Wikipedia entry entitled "Carboxyl transferase domain". More...
Carboxyl transferase domain Edit Wikipedia article
Carboxyl_trans | |||||||||
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![]() crystal structure of the carboxyltransferase subunit of the bacterial ion pump glutaconyl-coenzyme a decarboxylase | |||||||||
Identifiers | |||||||||
Symbol | Carboxyl_trans | ||||||||
Pfam | PF01039 | ||||||||
Pfam clan | CL0127 | ||||||||
InterPro | IPR000022 | ||||||||
SCOPe | 1od2 / SUPFAM | ||||||||
TCDB | 3.B.1 | ||||||||
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In molecular biology, proteins containing the carboxyl transferase domain include biotin-dependent carboxylases.[1][2] This domain carries out the following reaction: transcarboxylation from biotin to an acceptor molecule. There are two recognised types of carboxyl transferase. One of them uses acyl-CoA and the other uses 2-oxo acid as the acceptor molecule of carbon dioxide. All of the members in this family use acyl-CoA as the acceptor molecule.
References
- ^ Toh H, Kondo H, Tanabe T (August 1993). "Molecular evolution of biotin-dependent carboxylases". Eur. J. Biochem. 215 (3): 687–96. doi:10.1111/j.1432-1033.1993.tb18080.x. PMID 8102604.
- ^ Thornton CG, Kumar GK, Haase FC, Phillips NF, Woo SB, Park VM, Magner WJ, Shenoy BC, Wood HG, Samols D (September 1993). "Primary structure of the monomer of the 12S subunit of transcarboxylase as deduced from DNA and characterization of the product expressed in Escherichia coli". J. Bacteriol. 175 (17): 5301–8. PMC 206582. PMID 8366018.
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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.
Carboxyl transferase domain Provide feedback
All of the members in this family are biotin dependent carboxylases. The carboxyl transferase domain carries out the following reaction; transcarboxylation from biotin to an acceptor molecule. There are two recognised types of carboxyl transferase. One of them uses acyl-CoA and the other uses 2-oxoacid as the acceptor molecule of carbon dioxide. All of the members in this family utilise acyl-CoA as the acceptor molecule.
Literature references
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Thornton CG, Kumar GK, Haase FC, Phillips NF, Woo SB, Park VM, Magner WJ, Shenoy BC, Wood HG, Samols D; , J Bacteriol 1993;175:5301-5308.: Primary structure of the monomer of the 12S subunit of transcarboxylase as deduced from DNA and characterization of the product expressed in Escherichia coli. PUBMED:8366018 EPMC:8366018
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Toh H, Kondo H, Tanabe T; , Eur J Biochem 1993;215:687-696.: Molecular evolution of biotin-dependent carboxylases. PUBMED:8102604 EPMC:8102604
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Zhang H, Yang Z, Shen Y, Tong L; , Science 2003;299:2064-2067.: Crystal structure of the carboxyltransferase domain of acetyl-coenzyme A carboxylase. PUBMED:12663926 EPMC:12663926
Internal database links
SCOOP: | ACCA ECH_1 MdcE |
External database links
SCOP: | 1od2 |
Transporter classification: | 3.B.1 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR034733
All of the members in this family are biotin dependent carboxylases [PUBMED:8102604, PUBMED:8366018]. The carboxyl transferase domain carries out the following reaction; transcarboxylation from biotin to an acceptor molecule. There are two recognised types of carboxyl transferase. One of them uses acyl-CoA and the other uses 2-oxoacid as the acceptor molecule of carbon dioxide. All of the members in this family utilise acyl-CoA as the acceptor molecule.
In bacteria, the acetyl coenzyme A carboxylase (ACC) is a complex consisting of two subunits: alpha and beta. This domain also recognizes the bacterial ACC beta-subunit.
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 ClpP_crotonase (CL0127), which has the following description:
This family includes several peptidases of peptidase clan SK as well as crotonase like proteins.
The clan contains the following 10 members:
ACCA Carboxyl_trans CLP_protease ECH_1 ECH_2 MdcE Peptidase_S41 Peptidase_S49 Peptidase_S49_N SDH_sahAlignments
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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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 (28) |
Full (22697) |
Representative proteomes | UniProt (99547) |
NCBI (148523) |
Meta (7285) |
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RP15 (2772) |
RP35 (9971) |
RP55 (21739) |
RP75 (37370) |
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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 (28) |
Full (22697) |
Representative proteomes | UniProt (99547) |
NCBI (148523) |
Meta (7285) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (2772) |
RP35 (9971) |
RP55 (21739) |
RP75 (37370) |
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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: | Pfam-B_299 (release 3.0) |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Finn RD |
Number in seed: | 28 |
Number in full: | 22697 |
Average length of the domain: | 401.30 aa |
Average identity of full alignment: | 27 % |
Average coverage of the sequence by the domain: | 64.45 % |
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: | 494 | ||||||||||||
Family (HMM) version: | 23 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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...
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Interactions
There are 6 interactions for this family. More...
Carboxyl_trans Biotin_lipoyl Biotin_lipoyl ACCA ACCA Biotin_carb_CStructures
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 Carboxyl_trans domain has been found. There are 237 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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