Summary: Phosphoenolpyruvate carboxylase
Phosphoenolpyruvate carboxylase Provide feedback
This family of phosphoenolpyruvate carboxylases is based on seqeunces not picked up by the model for PEPcase, PF00311. Most of the family members are from Archaea.
Patel HM, Kraszewski JL, Mukhopadhyay B;, J Bacteriol. 2004;186:5129-5137.: The phosphoenolpyruvate carboxylase from Methanothermobacter thermautotrophicus has a novel structure. PUBMED:15262949 EPMC:15262949
Internal database links
|Similarity to PfamA using HHSearch:||PEPcase|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR007566
Phosphoenolpyruvate carboxylase (PEPCase), an enzyme found in all multicellular plants, catalyses the formation of oxaloacetate from phosphoenolpyruvate (PEP) and a hydrocarbonate ion [PUBMED:1450389]. This reaction is harnessed by C4 plants to capture and concentrate carbon dioxide into the photosynthetic bundle sheath cells. It also plays a key role in the nitrogen fixation pathway in legume root nodules: here it functions in concert with glutamine, glutamate and asparagine synthetases and aspartate amido transferase, to synthesise aspartate and asparagine, the major nitrogen transport compounds in various amine-transporting plant species [PUBMED:1421147].
PEPCase also plays an antipleurotic role in bacteria and plant cells, supplying oxaloacetate to the TCA cycle, which requires continuous input of C4 molecules in order to replenish the intermediates removed for amino acid biosynthesis [PUBMED:2779518]. The C terminus of the enzyme contains the active site that includes a conserved lysine residue, involved in substrate binding, and other conserved residues important for the catalytic mechanism [PUBMED:1508152].
Based on sequence similarity, PEPCase enzymes can be grouped into two distinct families, one found primarily in bacteria and plants, and another found primarily in archaea.
This entry represents the archaeal-type family.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||phosphoenolpyruvate carboxylase activity (GO:0008964)|
|Biological process||tricarboxylic acid cycle (GO:0006099)|
|carbon fixation (GO:0015977)|
- the number of sequences which exhibit this architecture
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This superfamily consists of a number of TIM barrel domains found in enzymes such as pyruvate kinase, malate synthase and citrate lyase.
The clan contains the following 11 members:C-C_Bond_Lyase HpcH_HpaI ICL Malate_synthase Pantoate_transf PEP-utilizers_C PEP_hydrolase PEP_mutase PEPcase PEPcase_2 PK
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
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Curation and family details
|Number in seed:||17|
|Number in full:||177|
|Average length of the domain:||458.10 aa|
|Average identity of full alignment:||37 %|
|Average coverage of the sequence by the domain:||98.78 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||2|
|Download:||download the raw HMM for this family|
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There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 PEPcase_2 domain has been found. There are 8 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 seqence.
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