Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
6  structures 2906  species 1  interaction 3692  sequences 9  architectures

Family: PP_kinase (PF02503)

Summary: Polyphosphate kinase middle 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 "Polyphosphate kinase". More...

Polyphosphate kinase Edit Wikipedia article

polyphosphate kinase
EC number
CAS number 9026-44-2
IntEnz IntEnz view
ExPASy NiceZyme view
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / EGO
Polyphosphate kinase
Symbol PP_kinase
Pfam PF02503
InterPro IPR003414

In enzymology, a polyphosphate kinase (EC is an enzyme that catalyzes the formation of polyphosphate from ATP, with chain lengths of up to a thousand or more orthophosphate molecules.[1]

ATP + (phosphate)n \rightleftharpoons ADP + (phosphate)n+1

Thus, the two substrates of this enzyme are ATP and (phosphate)n, whereas its two products are ADP and (phosphate)n+1.

It is a membrane protein and goes through an intermediate stage during the reaction where it is autophosphorylated with a phosphate group covalently linked to a basic amino acid residue through an N-P bond.

This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with a phosphate group as acceptor. The systematic name of this enzyme class is ATP:polyphosphate phosphotransferase. This enzyme is also called polyphosphoric acid kinase. This enzyme participates in oxidative phosphorylation.

Structural studies[edit]

As of late 2007, 3 structures have been solved for this class of enzymes, with PDB accession codes 1XDO, 1XDP, and 2O8R.


  1. ^ Brown MR, Kornberg A (June 2008). "The long and short of it - polyphosphate, PPK and bacterial survival". Trends Biochem. Sci. 33 (6): 284–90. doi:10.1016/j.tibs.2008.04.005. PMID 18487048. 

Further reading[edit]

  • Hoffmann-Ostenhof O, Kenedy J, Keck K, Gabriel O, Schonfellinger HW (1954). "A new transphosphorylase from yeast.". Biochim. Biophys. Acta. 14 (2): 285. PMID 13172250. 
  • Kornberg A, Kornberg SR, Simms ES (1956). "Metaphosphate synthesis by an enzyme from Escherichia coli". Biochim. Biophys. Acta. 20 (1): 215–27. doi:10.1016/0006-3002(56)90280-3. PMID 13315368. 
  • Muhammed A (1961). "Studies on biosynthesis of polymetaphosphate by an enzyme from Corynebacterium xerosis". Biochim. Biophys. Acta 54: 121–132. doi:10.1016/0006-3002(61)90945-3. PMID 14476999. 

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.

Polyphosphate kinase middle domain Provide feedback

Polyphosphate kinase (Ppk) catalyses the formation of polyphosphate from ATP, with chain lengths of up to a thousand or more orthophosphate molecules.

Literature references

  1. Geissdorfer W, Ratajczak A, Hillen W; , Appl Environ Microbiol 1998;64:896-901.: Transcription of ppk from Acinetobacter sp. strain ADP1, encoding a putative polyphosphate kinase, is induced by phosphate starvation. PUBMED:9501429 EPMC:9501429

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR024953

Polyphosphate kinase (Ppk) catalyses the formation of polyphosphate from ATP, with chain lengths of up to a thousand or more orthophosphate molecules [PUBMED:9501429]. This entry represents the Ppk middle domain.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

Loading domain graphics...


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...

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.

Representative proteomes NCBI
Jalview View  View  View  View  View  View  View  View 
HTML View  View  View  View  View  View     
PP/heatmap 1 View  View  View  View  View     
Pfam viewer View  View             

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

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

Format an alignment

Representative proteomes NCBI

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.

Representative proteomes NCBI
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...


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: Pfam-B_2701 (release 5.4)
Previous IDs: none
Type: Domain
Author: Mian N, Bateman A
Number in seed: 173
Number in full: 3692
Average length of the domain: 200.80 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 31.95 %

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 25.0 25.0
Trusted cut-off 27.6 26.7
Noise cut-off 22.4 22.1
Model length: 207
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

Sunburst controls


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...

Loading sunburst data...

Tree controls


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


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.


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



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 PP_kinase 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 seqence.

Loading structure mapping...