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52  structures 6946  species 0  interactions 15831  sequences 80  architectures

# Summary: PEP-utilising enzyme, PEP-binding domain

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 "Pyruvate, phosphate dikinase". More...

# Pyruvate, phosphate dikinase

In enzymology, a pyruvate, phosphate dikinase (EC 2.7.9.1) is an enzyme that catalyzes the chemical reaction

ATP + pyruvate + phosphate ${\displaystyle \rightleftharpoons }$ AMP + phosphoenolpyruvate + diphosphate

The 3 substrates of this enzyme are ATP, pyruvate, and phosphate, whereas its 3 products are AMP, phosphoenolpyruvate, and diphosphate.

This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with paired acceptors. The systematic name of this enzyme class is ATP:pyruvate, phosphate phosphotransferase. Other names in common use include pyruvate, orthophosphate dikinase, pyruvate-phosphate dikinase (phosphorylating), pyruvate, phosphate dikinase, pyruvate-inorganic phosphate dikinase, pyruvate-phosphate dikinase, pyruvate-phosphate ligase, pyruvic-phosphate dikinase, pyruvic-phosphate ligase, pyruvate, Pi dikinase, and PPDK. This enzyme participates in pyruvate metabolism and carbon fixation.

## Structural studies

As of late 2007, 10 structures have been solved for this class of enzymes, with PDB accession codes 1DIK, 1GGO, 1H6Z, 1JDE, 1KBL, 1KC7, 1VBG, 1VBH, 2DIK, and 2FM4.

## References

• Hatch MD, Slack CR (1968). "A new enzyme for the interconversion of pyruvate and phosphopyruvate and its role in the C4 dicarboxylic acid pathway of photosynthesis". Biochem. J. 106: 141â€“6. PMIDÂ 4305612.
• Reeves RE (1968). "A new enzyme with the glycolytic function of pyruvate kinase". J. Biol. Chem. 243: 3202â€“4. PMIDÂ 4297474.
• Reeves RE (1971). "Pyruvate,phosphate dikinase from Bacteroides symbiosus". Biochem. J. 125: 531â€“9. PMIDÂ 5144757.
• Reeves RE, Menzies RA, Hsu DS (1968). "The pyruvate-phosphate dikinase reaction. The fate of phosphate and the equilibrium". J. Biol. Chem. 243: 5486â€“91. PMIDÂ 4302788.`{{cite journal}}`: CS1 maint: multiple names: authors list (link)

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.

# PEP-utilising enzyme, PEP-binding domain

This entry represents a TIM barrel domain found at the C terminus of a number of PEP (phosphoenolpyruvate)-utilising proteins. In PPDK (Pyruvate phosphate dikinase) this C-terminal domain has been shown to be a PEP-binding domain [1].

## Literature references

1. Lim K, Read RJ, Chen CC, Tempczyk A, Wei M, Ye D, Wu C, Dunaway-Mariano D, Herzberg O;, Biochemistry. 2007;46:14845-14853.: Swiveling domain mechanism in pyruvate phosphate dikinase. PUBMED:18052212 EPMC:18052212

This tab holds annotation information from the InterPro database.

# InterPro entry IPR000121

A number of enzymes that catalyze the transfer of a phosphoryl group from phosphoenolpyruvate (PEP) via a phospho-histidine intermediate have been shown to be structurally related [ PUBMED:7686067 , PUBMED:8973315 , PUBMED:2176881 , PUBMED:1557039 ]. All these enzymes share the same catalytic mechanism: they bind PEP and transfer the phosphoryl group from it to a histidine residue. The sequence around that residue is highly conserved. This C-terminal domain has been shown to be the PEP-binding domain [ PUBMED:18052212 ]. It is often found associated with the pyruvate phosphate dikinase, AMP/ATP-binding domain ( INTERPRO ) at its N terminus and the PEP-utilizing enzyme mobile domain.

### 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...

# Pfam Clan

This family is a member of clan PK_TIM (CL0151), which has the following description:

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:

PEP-utilizers_C

# 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 (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
(14)
Full
(15831)
Representative proteomes UniProt
(84787)
RP15
(2207)
RP35
(7998)
RP55
(16314)
RP75
(28577)
Jalview View  View  View  View  View  View  View
HTML View
PP/heatmap 1

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: available, not generated, not available.

## Format an alignment

Seed
(14)
Full
(15831)
Representative proteomes UniProt
(84787)
RP15
(2207)
RP35
(7998)
RP55
(16314)
RP75
(28577)
Alignment:
Format:
Order:
Sequence:
Gaps:

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
(14)
Full
(15831)
Representative proteomes UniProt
(84787)
RP15
(2207)
RP35
(7998)
RP55
(16314)
RP75
(28577)

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.

# 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: Prosite Previous IDs: none Type: Domain Sequence Ontology: SO:0000417 Author: Finn RD , Griffiths-Jones SR Number in seed: 14 Number in full: 15831 Average length of the domain: 309.1 aa Average identity of full alignment: 32 % Average coverage of the sequence by the domain: 42.64 %

## 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:
Parameter Sequence Domain
Gathering cut-off 22.8 22.8
Trusted cut-off 22.8 22.8
Noise cut-off 22.7 22.7
Model length: 294
Family (HMM) version: 21

# Species distribution

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### Colour assignments

 Archea Eukaryota Bacteria Other sequences Viruses Unclassified Viroids Unclassified sequence

### Selections

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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...

### Tree controls

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The tree shows the occurrence of this domain across different species. More...

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# 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 PEP-utilizers_C domain has been found. There are 52 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.

# 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