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14  structures 3966  species 1  interaction 5137  sequences 26  architectures

Family: H_PPase (PF03030)

Summary: Inorganic H+ pyrophosphatase

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This is the Wikipedia entry entitled "H%2B, Na%2B-translocating pyrophosphatase family". More...

H%2B, Na%2B-translocating pyrophosphatase family Edit Wikipedia article

H+, Na+-translocating pyrophosphatase
Identifiers
Symbol?
PfamPF03030
InterProIPR004131
TCDB3.A.10
OPM superfamily390
OPM protein4av3

Members of the H+, Na+-translocating Pyrophosphatase (M+-PPase) Family (TC# 3.A.10) are found in the vacuolar (tonoplast) membranes of higher plants, algae, and protozoa, and in both bacteria and archaea. They are therefore ancient enzymes.

Two types of inorganic diphosphatase, very different in terms of both amino acid sequence and structure, have been characterised to date: soluble and transmembrane proton-pumping pyrophosphatases (sPPases and H(+)-PPases, respectively). sPPases are ubiquitous proteins that hydrolyse pyrophosphate to release heat, whereas H+-PPases, so far unidentified in animal and fungal cells, couple the energy of PPi hydrolysis to proton movement across biological membranes.[1][2] The latter type is represented by this group of proteins. H+-PPases vacuolar-type inorganic pyrophosphatases (V-PPase) or pyrophosphate-energised vacuolar membrane proton pumps.[3] In plants, vacuoles contain two enzymes for acidifying the interior of the vacuole, the V-ATPase and the V-PPase (V is for vacuolar).[2]

Two distinct biochemical subclasses of H+-PPases have been characterised to date: K+-stimulated and K+-insensitive.[1][3]

Classification

Full-length members of the H+-PPase family have been sequenced from numerous bacteria, archaea and eukaryotes. These H+ pumping enzymes, which are probably homodimeric, have been reported to fall into two phylogenetic subfamilies.[4] One subfamily invariably contains a conserved cysteine (Cys222) and includes all known K+-independent H+-PPases, while the other has another conserved cysteine (Cys573) but lacks Cys222 and includes all known K+-dependent H+-PPases.[4][5] All H+-PPases require Mg2+, and those from plant vacuoles, acidocalcisomes of protozoa and fermentative bacteria require mM K+. Those from respiratory and photosynthetic bacteria as well as archaea are less dependent upon K+. However, exceptions may exist.[4] It is not sure whether K+ is transported.

The archaeon, Methanosarcina mazei Gö1, encodes within its genome two H+-translocating pyrophosphatases (PPases), Mvp1 and Mvp2. Mvp1 resembles bacterial PPases while Mvp2 resembles plant PPases.[6] Mvp2 was shown to translocate 1 H+ per pyrophosphate hydrolyzed.

Some PPases from Anaerostipes caccae, Chlorobium limicola, Clostridium tetani, and Desulfuromonas acetoxidans have been identified as K+-dependent Na+ transporters.[7] Phylogenetic analysis led to the identification of a monophyletic clade comprising characterized and predicted Na+-transporting PPases (Na+-PPases) within the K+-dependent subfamily. H+-transporting PPases (H+-PPases) are more heterogeneous and form at least three independent clades in both subfamilies.[7]

Function

The plant enzymes probably pump one H+ upon hydrolysis of pyrophosphate, thereby generating a proton motive force, positive and acidic in the tonoplast lumen. They establish a pmf of similar magnitude to that generated by the H+-translocating ATPases in the same vacuolar membrane. The bacterial and archaeal proteins may catalyze fully reversible reactions, thus being able to synthesize pyrophosphate when the pmf is sufficient. The enzyme from R. rubrum contributes to the pmf when light intensity is insufficient to generate a pmf sufficient in magnitude to support rapid ATP synthesis. Both C-termini of the dimeric subunits of V-PPase are on the same side of the membrane, and they are close to each other.[8] Transmembrane domain 6 of vacuolar H+-pyrophosphatase appears to mediate both protein targeting and proton transport.[9]

The generalized transport reaction catalyzed by H+-PPases is:

pyrophosphate (P2) + H2O + H+ (cytoplasm) → inorganic phosphate (2 Pi) + H+ (external milieu or vacuolar lumen).

Structure

Eukaryotic members of the H+-PPase family are large proteins of about 770 amino acyl residues (aas) with 15 or 16 putative transmembrane α-helical spanners (TMSs). The N-termini are predicted to be in the vacuolar lumen while the C-termini are thought to be in the cytoplasm. These proteins exhibit a region that shows convincing sequence similarity to the regions surrounding the DCCD-sensitive glutamate in the C-terminal regions of the c-subunits of F-type ATPases (TC #3.A.2). The H+-pyrophosphatase of Streptomyces coelicolor has been shown to have a 17 TMS topology with the substrate binding domain exposed to the cytoplasm. The C-terminus is hydrophilic with a single C-terminal TMS. The basic structure is believed to have 16 TMSs with several large cytoplasmic loops containing functional motifs.[10] Several acidic residues in the Arabidopsis H+-PPase have been shown to be important for function. Some plants possess closely related H+-PPase isoforms. These enzymes have the enzyme commission number EC 3.6.1.1.

Lin et al. (2012) reported the crystal structure of a Vigna radiata H+-PPase (VrH+-PPase) in complex with a non-hydrolysable substrate analogue, imidodiphosphate (IDP), at 2.35 Å resolution. Each VrH+-PPase subunit consists of an integral membrane domain formed by 16 transmembrane helices.[11] IDP is bound in the cytosolic region of each subunit and trapped by numerous charged residues and five Mg2+ ions. A previously undescribed proton translocation pathway is formed by six core transmembrane helices. Proton pumping can be initialized by PP(i) hydrolysis, and H+ is then transported into the vacuolar lumen through a pathway consisting of Arg 242, Asp 294, Lys 742 and Glu 301. Lin et al. (2012) proposed a working model of the mechanism for the coupling between proton pumping and PP(i) hydrolysis by H+-PPases. Membrane-integral pyrophosphatases (M-PPases) are crucial for the survival of plants, bacteria, and protozoan parasites. They couple pyrophosphate hydrolysis or synthesis to Na+ or H+ pumping.[11] The 2.6Å structure of Thermotoga maritima H+-PPase in the resting state revealed a previously unknown solution for ion pumping.[12] The hydrolytic center, 20 angstroms above the membrane, is coupled to the gate formed by the conserved Asp(243), Glu(246), and Lys(707) by an unusual 'coupling funnel' of six α helices. Helix 12 slides down upon substrate binding to open the gate by a simple binding-change mechanism. Below the gate, four helices form the exit channel. Superimposing helices 3 to 6, 9 to 12, and 13 to 16 suggests that M-PPases arose through gene triplication.[12] By comparing the active sites, fluoride inhibition data and the various models for ion transport, Kajander et al. concluded that membrane-integral PPases probably use binding of pyrophosphate to drive pumping.[13]

See also

References

  1. ^ a b Perez-Castineira JR, Lopez-Marques RL, Villalba JM, Losada M, Serrano A (December 2002). "Functional complementation of yeast cytosolic pyrophosphatase by bacterial and plant H+-translocating pyrophosphatases". Proc. Natl. Acad. Sci. U.S.A. 99 (25): 15914–9. doi:10.1073/pnas.242625399. hdl:11441/26079. PMC 138539. PMID 12451180.
  2. ^ a b Baltscheffsky M, Schultz A, Baltscheffsky H (September 1999). "H+ -PPases: a tightly membrane-bound family". FEBS Lett. 457 (3): 527–33. doi:10.1016/S0014-5793(99)90617-8. PMID 10523139.
  3. ^ a b Perez-Castineira JR, Lopez-Marques RL, Losada M, Serrano A (May 2001). "A thermostable K(+)-stimulated vacuolar-type pyrophosphatase from the hyperthermophilic bacterium Thermotoga maritima". FEBS Lett. 496 (1): 6–11. doi:10.1016/S0014-5793(01)02390-0. PMID 11343697.
  4. ^ a b c Belogurov GA, Turkina MV, Penttinen A, Huopalahti S, Baykov AA, Lahti R (June 2002). "H+-pyrophosphatase of Rhodospirillum rubrum. High yield expression in Escherichia coli and identification of the Cys residues responsible for inactivation my mersalyl". The Journal of Biological Chemistry. 277 (25): 22209–14. doi:10.1074/jbc.M202951200. PMID 11956221.
  5. ^ Belogurov GA, Fabrichniy IP, Pohjanjoki P, Kasho VN, Lehtihuhta E, Turkina MV, Cooperman BS, Goldman A, Baykov AA, Lahti R (November 2000). "Catalytically important ionizations along the reaction pathway of yeast pyrophosphatase". Biochemistry. 39 (45): 13931–8. doi:10.1021/bi000895s. PMID 11076535.
  6. ^ Bäumer S, Lentes S, Gottschalk G, Deppenmeier U (March 2002). "Identification and analysis of proton-translocating pyrophosphatases in the methanogenic archaeon Methansarcina mazei". Archaea. 1 (1): 1–7. doi:10.1155/2002/371325. PMC 2685546. PMID 15803653.
  7. ^ a b Luoto HH, Belogurov GA, Baykov AA, Lahti R, Malinen AM (June 2011). "Na+-translocating membrane pyrophosphatases are widespread in the microbial world and evolutionarily precede H+-translocating pyrophosphatases". The Journal of Biological Chemistry. 286 (24): 21633–42. doi:10.1074/jbc.M111.244483. PMC 3283130. PMID 21527638.
  8. ^ Liu TH, Hsu SH, Huang YT, Lin SM, Huang TW, Chuang TH, Fan SK, Fu CC, Tseng FG, Pan RL (August 2009). "The proximity between C-termini of dimeric vacuolar H+-pyrophosphatase determined using atomic force microscopy and a gold nanoparticle technique". The FEBS Journal. 276 (16): 4381–94. doi:10.1111/j.1742-4658.2009.07146.x. PMID 19614743.
  9. ^ Pan YJ, Lee CH, Hsu SH, Huang YT, Lee CH, Liu TH, Chen YW, Lin SM, Pan RL (January 2011). "The transmembrane domain 6 of vacuolar H(+)-pyrophosphatase mediates protein targeting and proton transport". Biochimica et Biophysica Acta. 1807 (1): 59–67. doi:10.1016/j.bbabio.2010.10.006. PMID 20937245.
  10. ^ Mimura H, Nakanishi Y, Hirono M, Maeshima M (August 2004). "Membrane topology of the H+-pyrophosphatase of Streptomyces coelicolor determined by cysteine-scanning mutagenesis". The Journal of Biological Chemistry. 279 (33): 35106–12. doi:10.1074/jbc.M406264200. PMID 15187077.
  11. ^ a b Lin SM, Tsai JY, Hsiao CD, Huang YT, Chiu CL, Liu MH, Tung JY, Liu TH, Pan RL, Sun YJ (March 2012). "Crystal structure of a membrane-embedded H+-translocating pyrophosphatase". Nature. 484 (7394): 399–403. doi:10.1038/nature10963. PMID 22456709.
  12. ^ a b Kellosalo J, Kajander T, Kogan K, Pokharel K, Goldman A (July 2012). "The structure and catalytic cycle of a sodium-pumping pyrophosphatase". Science. 337 (6093): 473–6. doi:10.1126/science.1222505. PMID 22837527.
  13. ^ Kajander T, Kellosalo J, Goldman A (June 2013). "Inorganic pyrophosphatases: one substrate, three mechanisms". FEBS Letters. 587 (13): 1863–9. doi:10.1016/j.febslet.2013.05.003. PMID 23684653.
This article incorporates text from the public domain Pfam and InterPro: IPR004131

As of this edit, this article uses content from "3.A.10 The H+, Na+-translocating Pyrophosphatase (M+-PPase) Family", which is licensed in a way that permits reuse under the Creative Commons Attribution-ShareAlike 3.0 Unported License, but not under the GFDL. All relevant terms must be followed.

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Inorganic H+ pyrophosphatase Provide feedback

The H+ pyrophosphatase is an transmembrane proton pump involved in establishing the H+ electrochemical potential difference between the vacuole lumen and the cell cytosol. Vacuolar-type H(+)-translocating inorganic pyrophosphatases have long been considered to be restricted to plants and to a few species of photo-trophic bacteria. However, in recent investigations, these pyrophosphatases have been found in organisms as disparate as thermophilic Archaea and parasitic protists [1].

Literature references

  1. Drozdowicz YM, Rea PA; , Trends Plant Sci 2001;6:206-211.: Vacuolar H(+) pyrophosphatases: from the evolutionary backwaters into the mainstream. PUBMED:11335173 EPMC:11335173


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004131

Two types of proteins that hydrolyse inorganic pyrophosphate (PPi), very different in both amino acid sequence and structure, have been characterised to date: soluble and membrane-bound proton-pumping pyrophosphatases (sPPases and H(+)-PPases, respectively). sPPases are ubiquitous proteins that hydrolyse PPi to release heat, whereas H+-PPases, so far unidentified in animal and fungal cells, couple the energy of PPi hydrolysis to proton movement across biological membranes [PUBMED:12451180, PUBMED:10523139]. The latter type is represented by this group of proteins. H+-PPases (EC) are also called vacuolar-type inorganic pyrophosphatases (V-PPase) or pyrophosphate-energised vacuolar membrane proton pumps [PUBMED:11343697]. In plants, vacuoles contain two enzymes for acidifying the interior of the vacuole, the V-ATPase and the V-PPase (V is for vacuolar) [PUBMED:10523139].

Two distinct biochemical subclasses of H+-PPases have been characterised to date: K+-stimulated and K+-insensitive [PUBMED:12451180, PUBMED:11343697].

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  Seed
(323)
Full
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Representative proteomes UniProt
(12597)
NCBI
(13142)
Meta
(4993)
RP15
(1755)
RP35
(3768)
RP55
(5120)
RP75
(6497)
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  Seed
(323)
Full
(5137)
Representative proteomes UniProt
(12597)
NCBI
(13142)
Meta
(4993)
RP15
(1755)
RP35
(3768)
RP55
(5120)
RP75
(6497)
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Seed source: Pfam-B_1050 (release 6.4)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Griffiths-Jones SR
Number in seed: 323
Number in full: 5137
Average length of the domain: 633.60 aa
Average identity of full alignment: 44 %
Average coverage of the sequence by the domain: 92.62 %

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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 29.7 29.7
Trusted cut-off 30.0 31.1
Noise cut-off 28.8 29.5
Model length: 650
Family (HMM) version: 16
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H_PPase

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 H_PPase domain has been found. There are 14 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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