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6  structures 5366  species 4  interactions 5777  sequences 18  architectures

Family: PP_kinase (PF02503)

Summary: Polyphosphate kinase middle domain

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Polyphosphate kinase Edit Wikipedia article

polyphosphate kinase
Identifiers
EC number 2.7.4.1
CAS number 9026-44-2
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 / QuickGO
Polyphosphate kinase
Identifiers
Symbol PP_kinase
Pfam PF02503
InterPro IPR003414

In enzymology, a polyphosphate kinase (EC 2.7.4.1), or polyphosphate polymerase, is an enzyme that catalyzes the formation of polyphosphate from ATP, with chain lengths of up to a thousand or more orthophosphate moieties.[1]

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

Thus, the two substrates of this enzyme are ATP and polyphosphate [(phosphate)n], whereas its two products are ADP and polyphosphate extended by one phosphate moiety [(phosphate)n+1].

This enzyme 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 acyl residue through an N-P bond.

Several enzymes catalyze polyphosphate polymerization. Some of these enzymes couple phosphotransfer to transmembrane transport. These enzyme/transporters are categorized in the Transporter Classification Database (TCDB) under the Polyphosphate Polymerase/YidH Superfamily (TC# 4.E.1) and are transferases that transfer phosphoyl groups (phosphotransferases) with polyphosphate as the acceptor. The systematic name of this enzyme class is ATP:polyphosphate phosphotransferase. This enzyme is also called polyphosphoric acid kinase.

Families

The Polyphosphate Polymerase Superfamily (TC# 4.E.1) includes the following families:

  • 4.E.1 - The Vacuolar (Acidocalcisome) Polyphosphate Polymerase (V-PPP) Family
  • 9.B.51 - The Uncharacterized DUF202/YidH (YidH) Family

The Vacuolar (Acidocalcisome) Polyphosphate Polymerase (V-PPP) Family

Eukaryotes contain inorganic polyphosphate (polyP) and acidocalcisomes, which sequester polyP and store amino acids and divalent cations.[2][3] Gerasimaitė et al.[4] showed that polyP produced in the cytosol of yeast is toxic. Reconstitution of polyP translocation with purified vacuoles, the acidocalcisomes of yeast, showed that cytosolic polyP cannot be imported whereas polyP produced by the vacuolar transporter chaperone (VTC) complex, an endogenous vacuolar polyP polymerase, is efficiently imported and does not interfere with growth. PolyP synthesis and import require an electrochemical gradient, probably as a (partial) driving force for polyP translocation. VTC exposes its catalytic domain to the cytosol and has nine vacuolar transmembrane segments (TMSs). Mutations in the VTC transmembrane regions, which may constitute the translocation channel, block not only polyP translocation but also synthesis. Since these mutations are far from the cytosolic catalytic domain of VTC, this suggests that the VTC complex obligatorily couples synthesis of polyP to its vesicular import in order to avoid toxic intermediates in the cytosol. The process therefore conforms to the classical definition of Group Translocation, where the substrate is modified during transport. Sequestration of otherwise toxic polyP may be one reason for the existence of this mechanism in acidocalcisomes.[4] The vacuolar polyphosphate kinase (polymerase) is described in TCDB with family TC# 4.E.1.[5]

Function

CYTH-like superfamily enzymes, which include polyphosphate polymerases, hydrolyze triphosphate-containing substrates and require metal cations as cofactors. They have a unique active site located at the center of an eight-stranded antiparallel beta barrel tunnel (the triphosphate tunnel). The name CYTH originated from the gene designation for bacterial class IV adenylyl cyclases (CyaB), and from thiamine triphosphatase (THTPA). Class IV adenylate cyclases catalyze the conversion of ATP to 3',5'-cyclic AMP (cAMP) and PPi. Thiamine triphosphatase is a soluble cytosolic enzyme which converts thiamine triphosphate to thiamine diphosphate. This domain superfamily also contains RNA triphosphatases, membrane-associated polyphosphate polymerases, tripolyphosphatases, nucleoside triphosphatases, nucleoside tetraphosphatases and other proteins with unknown functions.

The generalized reaction catalyzed by the vectorial polyphosphate polymerases is:[5]

ATP + (phosphate)n in the cytoplasm ADP + (phosphate)n+1 in the vacuolar lumen

Structure

VTC2 has three recognized domains: an N-terminal SPX domain, a large central CYTH-like domain and a smaller transmembrane VTC1 (DUF202) domain. The SPX domain is found in Syg1, Pho81, XPR1 (SPX), and related proteins. This domain is found at the amino termini of a variety of proteins. In the yeast protein, Syg1, the N-terminus directly binds to the G-protein beta subunit and inhibits transduction of the mating pheromone signal. Similarly, the N-terminus of the human XPR1 protein binds directly to the beta subunit of the G-protein heterotrimer, leading to increased production of cAMP. Thus, this domain is involved in G-protein associated signal transduction. The N-termini of several proteins involved in the regulation of phosphate transport, including the putative phosphate level sensors, Pho81 from Saccharomyces cerevisiae and NUC-2 from Neurospora crassa, have this domain.

The SPX domains of the S. cerevisiae low-affinity phosphate transporters, Pho87 and Pho90, auto-regulate uptake and prevent efflux. This SPX-dependent inhibition is mediated by a physical interaction with Spl2. NUC-2 contains several ankyrin repeats. Several members of this family are annotated as XPR1 proteins: the xenotropic and polytropic retrovirus receptor confers susceptibility to infection with xenotropic and polytropic murine leukaemia viruses (MLV). Infection by these retroviruses can inhibit XPR1-mediated cAMP signaling and result in cell toxicity and death. The similarity between Syg1 phosphate regulators and XPR1 sequences has been noted, as has the additional similarity to several predicted proteins of unknown function, from Drosophila melanogaster, Arabidopsis thaliana, Caenorhabditis elegans, Schizosaccharomyces pombe, S. cerevisiae, and many other diverse organisms.[5]

As of 2015, several structures have been solved for this class of enzymes, with PDB accession codes 1XDO, 1XDP, 2O8R, 3CZP, 3CZQ, 3RHF.

The Uncharacterized DUF202/YidH (YidH) Family

Members of the YidH Family are found in bacteria, archaea and eukaryotes. Members of this family include YidH of E. coli (TC# 9.B.51.1.1) which has 115 amino acyl residues and 3 TMSs of α-helical nature.[6] The first TMS has a low level of hydrophobicity, the second has a moderate level of hydrophobicity, and the third has very hydrophobic character. These traits appear to be characteristic of all members of this family. A representative list of proteins belonging to this family can be found in the Transporter Classification Database. In fungi, a long homologue of 351 aas has a similar 3 TMS DUF202 domain at its extreme C-terminus.

References

  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. 
  2. ^ Docampo, Roberto; Moreno, Silvia N. J. (August 2011). "Acidocalcisomes". Cell Calcium. 50 (2): 111–119. doi:10.1016/j.ceca.2011.05.012. PMC 3156361Freely accessible. PMID 21752464. 
  3. ^ Docampo, Roberto; et al. (2013). "New insights into the roles of acidocalcisomes and the Contractile Vacuole Complex in osmoregulation in Protists". International review of cell and molecular biology. 305: 69–113. doi:10.1016/B978-0-12-407695-2.00002-0. PMC 3818246Freely accessible. PMID 23890380. 
  4. ^ a b Gerasimaitė, R.; Sharma, S.; Desfougères, Y.; Schmidt, A.; Mayer, A. (October 2014). "Coupled synthesis and translocation restrains polyphosphate to acidocalcisome-like vacuoles and prevents its toxicity". J Cell Sci. 127 (23): 5093–104. doi:10.1242/jcs.159772. PMID 25315834. 
  5. ^ a b c Saier, Milton. "Transporter Classification Database: 4.E.1. The Vacuolar (Acidocalcisome) Polyphosphate Polymerase (V-PPP) Family". tcdb.org. Retrieved 26 December 2015. 
  6. ^ Eichmann, Cédric; Orts, Julien; Tzitzilonis, Christos; Vögeli, Beat; Smrt, Sean; Lorieau, Justin; Riek, Roland (2014-12-11). "Intermolecular detergent-membrane protein noes for the characterization of the dynamics of membrane protein-detergent complexes". The Journal of Physical Chemistry B. 118 (49): 14288–14301. doi:10.1021/jp509137q. ISSN 1520-5207. PMID 25419869. 

Further reading

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


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

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Alignments

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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
(668)
Full
(5777)
Representative proteomes UniProt
(18317)
NCBI
(24998)
Meta
(1005)
RP15
(1177)
RP35
(3543)
RP55
(5588)
RP75
(8120)
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PP/heatmap 1                

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

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

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  Seed
(668)
Full
(5777)
Representative proteomes UniProt
(18317)
NCBI
(24998)
Meta
(1005)
RP15
(1177)
RP35
(3543)
RP55
(5588)
RP75
(8120)
Alignment:
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  Seed
(668)
Full
(5777)
Representative proteomes UniProt
(18317)
NCBI
(24998)
Meta
(1005)
RP15
(1177)
RP35
(3543)
RP55
(5588)
RP75
(8120)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download   Download  

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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.

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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
Sequence Ontology: SO:0000417
Author: Mian N , Bateman A
Number in seed: 668
Number in full: 5777
Average length of the domain: 201.60 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 28.27 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 26.0 25.0
Noise cut-off 23.4 23.1
Model length: 202
Family (HMM) version: 17
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Interactions

There are 4 interactions for this family. More...

PP_kinase_N PP_kinase_C PP_kinase_C PP_kinase

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 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 sequence.

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