Summary: Na+-transporting oxaloacetate decarboxylase beta subunit
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 "Oxaloacetate decarboxylase". More...
Oxaloacetate decarboxylase Edit Wikipedia article
Oxaloacetate decarboxylase is a carboxy-lyase involved in the conversion of oxaloacetate into pyruvate.
It is categorized under EC 4.1.1.3.
External links
- PMID 15647905
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.
Na+-transporting oxaloacetate decarboxylase beta subunit Provide feedback
Members of this family are integral membrane proteins. The decarboxylation reactions they catalyse are coupled to the vectorial transport of Na+ across the cytoplasmic membrane, thereby creating a sodium ion motive force that is used for ATP synthesis [2].
Literature references
-
Laussermair E, Schwarz E, Oesterhelt D, Reinke H, Beyreuther K, Dimroth P; , J Biol Chem 1989;264:14710-14715.: The sodium ion translocating oxaloacetate decarboxylase of Klebsiella pneumoniae. Sequence of the integral membrane-bound subunits beta and gamma. PUBMED:2549031 EPMC:2549031
-
Bott M, Pfister K, Burda P, Kalbermatter O, Woehlke G, Dimroth P; , Eur J Biochem 1997;250:590-599.: Methylmalonyl-CoA decarboxylase from Propionigenium modestum--cloning and sequencing of the structural genes and purification of the enzyme complex. PUBMED:9428714 EPMC:9428714
Internal database links
SCOOP: | SBF |
External database links
Transporter classification: | 3.B.1 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR005661
Members of this family are integral membrane proteins. The decarboxylation reactions they catalyse are coupled to the vectorial transport of Na + across the cytoplasmic membrane, thereby creating a sodium ion motive force that is used for ATP synthesis [ PUBMED:9428714 ].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | lyase activity (GO:0016829) |
Biological process | sodium ion transport (GO:0006814) |
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 CPA_AT (CL0064), which has the following description:
This Clan contains transporter proteins that belong to the CPA superfamily and AT superfamily according to TCDB [1].
The clan contains the following 15 members:
Asp-Al_Ex Cons_hypoth698 DUF3100 DUF819 Glt_symporter KdgT LrgB Lys_export Mem_trans Na_H_antiport_1 Na_H_Exchanger OAD_beta SBF SBF_like Sbt_1Alignments
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.
Seed (180) |
Full (2212) |
Representative proteomes | UniProt (16175) |
||||
---|---|---|---|---|---|---|---|
RP15 (457) |
RP35 (1352) |
RP55 (2279) |
RP75 (3665) |
||||
Jalview | |||||||
HTML | |||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
Format an alignment
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 (180) |
Full (2212) |
Representative proteomes | UniProt (16175) |
||||
---|---|---|---|---|---|---|---|
RP15 (457) |
RP35 (1352) |
RP55 (2279) |
RP75 (3665) |
||||
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: | COG1883 |
Previous IDs: | OadB_MmdB; |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Bateman A |
Number in seed: | 180 |
Number in full: | 2212 |
Average length of the domain: | 350 aa |
Average identity of full alignment: | 53 % |
Average coverage of the sequence by the domain: | 93.16 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
|
||||||||||||
Model details: |
|
||||||||||||
Model length: | 349 | ||||||||||||
Family (HMM) version: | 16 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
Sunburst controls
HideWeight segments by...
Change the size of the sunburst
Colour assignments
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
Selections
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...
Tree controls
HideThe 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.
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 OAD_beta domain has been found. There are 6 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.
Loading structure mapping...
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.
Protein | Predicted structure | External Information |
---|---|---|
A0A0H3GJ14 | View 3D Structure | Click here |
Q03031 | View 3D Structure | Click here |
Q8ZQS6 | View 3D Structure | Click here |
Q8ZRY4 | View 3D Structure | Click here |
Q9CL24 | View 3D Structure | Click here |
Q9KTU5 | View 3D Structure | Click here |
Q9RF98 | View 3D Structure | Click here |
Q9ZAA6 | View 3D Structure | Click here |