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5  structures 3076  species 1  interaction 4128  sequences 6  architectures

Family: PEPcase (PF00311)

Summary: Phosphoenolpyruvate carboxylase

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This is the Wikipedia entry entitled "Phosphoenolpyruvate carboxylase". More...

Phosphoenolpyruvate carboxylase Edit Wikipedia article

phosphoenolpyruvate carboxylase
Identifiers
EC number 4.1.1.31
CAS number 9067-77-0
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
Phosphoenolpyruvate carboxylase
Identifiers
Symbol PEPcase
Pfam PF00311
InterPro IPR001449
PROSITE PDOC00330
SCOP 1fiy
SUPERFAMILY 1fiy

Phosphoenolpyruvate carboxylase (also known as PEP carboxylase, PEPCase, or PEPC; EC 4.1.1.31) is an enzyme in the family of carboxy-lyases that catalyzes the addition of bicarbonate to phosphoenolpyruvate (PEP) to form the four-carbon compound oxaloacetate:

PEP + HCO3- → oxaloacetate + Pi

This reaction is used for carbon fixation in CAM and C4 plants where it plays a key role in photosynthesis. The enzyme is also found in some bacteria, but not in animals or fungi.[1]

Enzyme regulation[edit]

This protein may use the morpheein model of allosteric regulation. [2]

PEP carboxylase in photosynthesis[edit]

After conversion of CO2 to bicarbonate by carbonic anhydrase, PEP carboxylase assimilates the available bicarbonate into a four-carbon compound (oxaloacetate, which is further converted to malate) that can be stored or shuttled between plant cells. This allows for a separation of initial carbon fixation by contact with air and secondary carbon fixation into sugars by RuBisCO during the light-independent reactions of photosynthesis.

In succulent CAM plants adapted for growth in very dry conditions, PEP carboxylase fixes bicarbonate during the night when the plant opens its stomata to allow for gas exchange. During the day time, the plant closes the stomata to preserve water and releases CO2 inside the leaf from the storage compounds produced during the night. This allows the plants to thrive in dry climates by conducting photosynthesis without losing water through open stomata during the day.

In C4 plants, for example maize, PEP carboxylase fixes bicarbonate in the mesophyll cells of the leaf and the resulting four-carbon compound, malate, is shuttled into the bundle sheath cells where it releases CO2 for fixation by RuBisCO. Thus, the two processes are separated spatially, allowing for RuBisCO to operate in a low-oxygen environment to circumvent photorespiration. Photorespiration occurs due to the inherent oxygenase activity of RuBisCO in which the enzyme uses oxygen instead of carbon dioxide without incorporating carbon into sugars or generating ATP. As such, it is a wasteful reaction for the plant. By comparison, C4 carbon fixation via PEP carboxylase is more efficient.

Notes[edit]

External links[edit]

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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No Pfam abstract.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR021135

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.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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 PK_TIM (CL0151), which contains the following 10 members:

C-C_Bond_Lyase HpcH_HpaI ICL Malate_synthase Pantoate_transf PEP-utilizers_C PEP_mutase PEPcase PEPcase_2 PK

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
(65)
Full
(4128)
Representative proteomes NCBI
(3411)
Meta
(2728)
RP15
(201)
RP35
(483)
RP55
(654)
RP75
(773)
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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
(65)
Full
(4128)
Representative proteomes NCBI
(3411)
Meta
(2728)
RP15
(201)
RP35
(483)
RP55
(654)
RP75
(773)
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
(65)
Full
(4128)
Representative proteomes NCBI
(3411)
Meta
(2728)
RP15
(201)
RP35
(483)
RP55
(654)
RP75
(773)
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:

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 View help on the curation process

Seed source: Prosite
Previous IDs: none
Type: Family
Author: Finn RD, Coggill P
Number in seed: 65
Number in full: 4128
Average length of the domain: 540.50 aa
Average identity of full alignment: 36 %
Average coverage of the sequence by the domain: 85.56 %

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 20.6 20.6
Trusted cut-off 20.8 20.6
Noise cut-off 20.2 20.5
Model length: 794
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

PEPcase

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 PEPcase domain has been found. There are 5 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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