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0  structures 969  species 0  interactions 1424  sequences 5  architectures

Family: OAD_beta (PF03977)

Summary: Na+-transporting oxaloacetate decarboxylase beta subunit

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This is the Wikipedia entry entitled "Oxaloacetate decarboxylase". More...

Oxaloacetate decarboxylase Edit Wikipedia article

oxaloacetate decarboxylase
Identifiers
EC number 4.1.1.3
CAS number 9024-98-0
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / EGO
Na+-transporting oxaloacetate decarboxylase beta subunit
Identifiers
Symbol OAD_beta
Pfam PF03977
Pfam clan CL0064
InterPro IPR005661
TCDB 3.B.1
Oxaloacetate decarboxylase, gamma chain
Identifiers
Symbol OAD_gamma
Pfam PF04277
InterPro IPR005899
TCDB 3.B.1

Oxaloacetate decarboxylase is a carboxy-lyase involved in the conversion of oxaloacetate into pyruvate.

It is categorized under EC 4.1.1.3.

In some bacteria this enzyme is a trimer, composed of alpha, beta and gamma subunits.[1][2] The beta and gamma subunits are integral membrane proteins.[2][3]

See also[edit]

References[edit]

  1. ^ Bott M, Pfister K, Burda P, Kalbermatter O, Woehlke G, Dimroth P (December 1997). "Methylmalonyl-CoA decarboxylase from Propionigenium modestum--cloning and sequencing of the structural genes and purification of the enzyme complex". Eur. J. Biochem. 250 (2): 590–9. doi:10.1111/j.1432-1033.1997.0590a.x. PMID 9428714. 
  2. ^ a b Laussermair E, Schwarz E, Oesterhelt D, Reinke H, Beyreuther K, Dimroth P (1989). "The sodium ion translocating oxaloacetate decarboxylase of Klebsiella pneumoniae. Sequence of the integral membrane-bound subunits beta and gamma.". J Biol Chem 264 (25): 14710–5. PMID 2549031. 
  3. ^ Schmid M, Wild MR, Dahinden P, Dimroth P (2002). "Subunit gamma of the oxaloacetate decarboxylase Na(+) pump: interaction with other subunits/domains of the complex and binding site for the Zn(2+) metal ion.". Biochemistry 41 (4): 1285–92. doi:10.1021/bi015764l. PMID 11802728. 

Further reading[edit]

  • Dahinden P, Auchli Y, Granjon T et al. (2005). "Oxaloacetate decarboxylase of Vibrio cholerae: purification, characterization, and expression of the genes in Escherichia coli". Arch. Microbiol. 183 (2): 121–9. doi:10.1007/s00203-004-0754-5. PMID 15647905. 

External links[edit]

This article incorporates text from the public domain Pfam and InterPro IPR005661

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

  1. 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

  2. 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


External database links

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

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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 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 13 members:

Asp-Al_Ex Cons_hypoth698 DUF340 DUF4137 DUF819 DUF897 Glt_symporter KdgT Mem_trans Na_H_antiport_1 Na_H_Exchanger OAD_beta SBF

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...

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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
(9)
Full
(1424)
Representative proteomes NCBI
(1037)
Meta
(261)
RP15
(113)
RP35
(184)
RP55
(234)
RP75
(273)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(9)
Full
(1424)
Representative proteomes NCBI
(1037)
Meta
(261)
RP15
(113)
RP35
(184)
RP55
(234)
RP75
(273)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(9)
Full
(1424)
Representative proteomes NCBI
(1037)
Meta
(261)
RP15
(113)
RP35
(184)
RP55
(234)
RP75
(273)
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.

Pfam alignments:

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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: COG1883
Previous IDs: OadB_MmdB;
Type: Family
Author: Bateman A
Number in seed: 9
Number in full: 1424
Average length of the domain: 354.20 aa
Average identity of full alignment: 54 %
Average coverage of the sequence by the domain: 94.72 %

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 30.0 30.0
Trusted cut-off 30.4 30.5
Noise cut-off 29.9 29.9
Model length: 360
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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