| inorganic pyrophosphatase | |||||||||
|---|---|---|---|---|---|---|---|---|---|
 Pyrophosphatase (inorganic) hexamer, E.Coli | |||||||||
| Identifiers | |||||||||
| EC no. | 3.6.1.1 | ||||||||
| CAS no. | 9024-82-2 | ||||||||
| Databases | |||||||||
| IntEnz | IntEnz view | ||||||||
| BRENDA | BRENDA entry | ||||||||
| ExPASy | NiceZyme view | ||||||||
| KEGG | KEGG entry | ||||||||
| MetaCyc | metabolic pathway | ||||||||
| PRIAM | profile | ||||||||
| PDB structures | RCSB PDBPDBePDBsum | ||||||||
| Gene Ontology | AmiGO /QuickGO | ||||||||
| |||||||||
| Soluble inorganic pyrophosphatase | |||||||||
|---|---|---|---|---|---|---|---|---|---|
 Structure of soluble inorganic pyrophosphatase, isolated fromThermococcus litoralis (PDB:2PRD). | |||||||||
| Identifiers | |||||||||
| Symbol | Pyrophosphatase | ||||||||
| Pfam | PF00719 | ||||||||
| InterPro | IPR008162 | ||||||||
| PROSITE | PS00387 | ||||||||
| CATH | 2prd | ||||||||
| SCOP2 | 2prd /SCOPe /SUPFAM | ||||||||
| CDD | cd00412 | ||||||||
| |||||||||
| pyrophosphatase (inorganic) 1 | |||||||
|---|---|---|---|---|---|---|---|
| Identifiers | |||||||
| Symbol | PPA1 | ||||||
| Alt. symbols | PP | ||||||
| NCBI gene | 5464 | ||||||
| HGNC | 9226 | ||||||
| OMIM | 179030 | ||||||
| RefSeq | NM_021129 | ||||||
| UniProt | Q15181 | ||||||
| Other data | |||||||
| Locus | Chr. 10q11.1-q24 | ||||||
| |||||||
| pyrophosphatase (inorganic) 2 | |||||||
|---|---|---|---|---|---|---|---|
| Identifiers | |||||||
| Symbol | PPA2 | ||||||
| NCBI gene | 27068 | ||||||
| HGNC | 28883 | ||||||
| OMIM | 609988 | ||||||
| RefSeq | NM_176869 | ||||||
| UniProt | Q9H2U2 | ||||||
| Other data | |||||||
| Locus | Chr. 4q25 | ||||||
| |||||||
Inorganic pyrophosphatase (orinorganic diphosphatase,PPase) is anenzyme (EC3.6.1.1) that catalyzes the conversion of one ion ofpyrophosphate to twophosphate ions.[1] This is a highlyexergonic reaction, and therefore can be coupled to unfavorable biochemical transformations in order to drive these transformations to completion.[2] The functionality of thisenzyme plays a critical role inlipid metabolism (including lipid synthesis and degradation), calcium absorption and bone formation,[3][4] and DNA synthesis,[5] as well as otherbiochemical transformations.[6][7]
Two types ofinorganic diphosphatase, very different in terms of bothamino acid sequence andstructure, have been characterised to date:soluble andtransmembraneproton-pumping pyrophosphatases (sPPases and H(+)-PPases, respectively). sPPases are ubiquitousproteins that hydrolysepyrophosphate to release heat, whereas H+-PPases, so far unidentified inanimal andfungal cells, couple the energy of PPihydrolysis toproton movement acrossbiologicalmembranes.[8]
Thermostable soluble pyrophosphatase had been isolated from theextremophileThermococcus litoralis. The 3-dimensional structure was determined usingx-ray crystallography, and was found to consist of twoalpha-helices, as well as anantiparallel closedbeta-sheet. The form of inorganic pyrophosphatase isolated fromThermococcus litoralis was found to contain a total of 174amino acid residues and have ahexamericoligomeric organization (Image 1).[9]
Humans possess two genes encoding pyrophosphatase, PPA1 and PPA2.[10] PPA1 has been assigned to agene locus on humanchromosome 10,[11] and PPA2 tochromosome 4.[12]
Though the precise mechanism ofcatalysis via inorganic pyrophosphatase in most organisms remains uncertain, site-directedmutagenesis studies inEscherichia coli have allowed for analysis of theenzymeactive site and identification of keyamino acids. In particular, this analysis has revealed 17 residues of that may be of functional importance incatalysis.[13]
Further research suggests that theprotonation state of Asp67 is responsible for modulating the reversibility of thereaction inEscherichia coli. Thecarboxylate functional group of this residue has been shown to perform anucleophilic attack on thepyrophosphatesubstrate when fourmagnesiumions are present. Direct coordination with these fourmagnesiumions andhydrogen bonding interactions with Arg43, Lys29, and Lys142 (all positively charged residues) have been shown to anchor the substrate to theactive site. The fourmagnesiumions are also suggested to be involved in the stabilization of thetrigonal bipyramidtransition state, which lowers the energetic barrier for the aforementionednucleophilic attack.[13]
Several studies have also identified additionalsubstrates that can act asallosteric effectors. In particular, the binding ofpyrophosphate (PPi) to the effector site of inorganic pyrophosphatase increases its rate ofhydrolysis at theactive site.[14]ATP has also been shown to function as anallosteric activator inEscherichia coli,[15] whilefluoride has been shown to inhibithydrolysis ofpyrophosphate inyeast.[16]
The hydrolysis of inorganicpyrophosphate (PPi) to twophosphate ions is utilized in many biochemical pathways to render reactions effectively irreversible.[17] This process is highlyexergonic (accounting for approximately a −19kJ change infree energy), and therefore greatly increases the energetic favorability of reaction system when coupled with a typically less-favorable reaction.[18]
Inorganic pyrophosphatase catalyzes thishydrolysis reaction in the early steps oflipid degradation, a prominent example of this phenomenon. By promoting the rapidhydrolysis ofpyrophosphate (PPi), Inorganic pyrophosphatase provides the driving force for the activation offatty acids destined forbeta oxidation.[18]
Beforefatty acids can undergo degradation to fulfill the metabolic needs of an organism, they must first be activated via a thioester linkage tocoenzyme A. This process is catalyzed by the enzymeacyl-CoA synthetase, and occurs on the outermitochondrial membrane. This activation is accomplished in two reactive steps: (1) the fatty acid reacts with a molecule ofATP to form an enzyme-boundacyl adenylate andpyrophosphate (PPi), and (2) the sulfhydryl group of CoA attacks the acyl adenylate, formingacyl CoA and a molecule ofAMP. Each of these two steps is reversible under biological conditions, save for the additional hydrolysis of PPi by inorganic pyrophosphatase.[18] This coupledhydrolysis provides the driving force for the overall forward activation reaction, and serves as a source ofinorganic phosphate used in other biological processes.
Examination ofprokaryotic andeukaryotic forms of soluble inorganic pyrophosphatase (sPPase,PfamPF00719) has shown that they differ significantly in bothamino acid sequence, number of residues, andoligomeric organization. Despite differing structural components, recent work has suggested a large degree ofevolutionary conservation ofactive site structure as well asreaction mechanism, based onkinetic data.[19] Analysis of approximately one million genetic sequences taken fromorganisms in theSargasso Sea identified a 57 residue sequence within the regions coding forproton-pumping inorganic pyrophosphatase (H+-PPase) that appears to be highly conserved; this region primarily consisted of the four earlyamino acid residuesGly,Ala,Val andAsp, suggesting an evolutionarily ancient origin for theprotein.[20]
