PDBsum entry 1wgi

Go to PDB code: 
protein metals Protein-protein interface(s) links
Hydrolase PDB id
Protein chains
283 a.a. *
_MN ×4
Waters ×195
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Structure of inorganic pyrophosphatase
Structure: Inorganic pyrophosphatase. Chain: a, b. Synonym: ppase. Engineered: yes. Other_details: metal complex
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: ppa1. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Homo-Dimer (from PDB file)
2.20Å     R-factor:   0.172     R-free:   0.211
Authors: P.Heikinheimo,A.Goldman
Key ref:
P.Heikinheimo et al. (1996). The structural basis for pyrophosphatase catalysis. Structure, 4, 1491-1508. PubMed id: 8994974 DOI: 10.1016/S0969-2126(96)00155-4
24-Oct-96     Release date:   19-Nov-97    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P00817  (IPYR_YEAST) -  Inorganic pyrophosphatase
287 a.a.
283 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Inorganic diphosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Diphosphate + H2O = 2 phosphate
+ H(2)O
= 2 × phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     phosphate-containing compound metabolic process   1 term 
  Biochemical function     protein binding     5 terms  


    Added reference    
DOI no: 10.1016/S0969-2126(96)00155-4 Structure 4:1491-1508 (1996)
PubMed id: 8994974  
The structural basis for pyrophosphatase catalysis.
P.Heikinheimo, J.Lehtonen, A.Baykov, R.Lahti, B.S.Cooperman, A.Goldman.
BACKGROUND: Soluble inorganic pyrophosphatase (PPase), an essential enzyme central to phosphorus metabolism, catalyzes the hydrolysis of the phosphoanhydride bond in inorganic pyrophosphate. Catalysis requires divalent metal ions which affect the apparent pKas of the essential general acid and base on the enzyme, and the pKa of the substrate. Three to five metal ions are required for maximal activity, depending on pH and enzyme source. A detailed understanding of catalysis would aid both in understanding the nature of biological mechanisms of phosphoryl transfer, and in understanding the role of divalent cations. Without a high-resolution complex structure such a model has previously been unobtainable. RESULTS: We report the first two high-resolution structures of yeast PPase, at 2.2 and 2.0 A resolution with R factors of around 17%. One structure contains the two activating metal ions; the other, the product (MnPi)2 as well. The latter structure shows an extensive network of hydrogen bond and metal ion interactions that account for virtually every lone pair on the product phosphates. It also contains a water molecule/hydroxide ion bridging two metal ions and, uniquely, a phosphate bound to four Mn2+ ions. CONCLUSIONS: Our structure-based model of the PPase mechanism posits that the nucleophile is the hydroxide ion mentioned above. This aspect of the mechanism is formally analogous to the "two-metal ion' mechanism of alkaline phosphatase, exonucleases and polymerases. A third metal ion coordinates another water molecule that is probably the required general acid. Extensive Lewis acid coordination and hydrogen bonds provide charge shielding of the electrophile and lower the pKa of the leaving group. This "three-metal ion' mechanism is in detail different from that of other phosphoryl transfer enzymes, presumably reflecting how ancient the reaction is.
  Selected figure(s)  
Figure 7.
Figure 7. The proposed PPase mechanism. The activesite coordination is shown in two dimensions; hydrogen bonding is shown with grey lines and metal coordination with dashed lines. The flow of electrons is indicated with arrows. The reaction involves a hydroxide ion (Wat1), coordinated to metals Mn1 and Mn2, which hydrolyzes the substrate P[2]O[7]-Mn[2]. P1 and P2 are labels for the leaving and electrophilic phosphoryl groups, respectively. The required general acid is a water molecule (Wat6) coordinated to Mn3 and hydrogen bonded to P1 in the Mn[2]ˇY-PPaseˇ(MnP[i])[2] structure. (The two-dimensional presentation of the mechanism was initially created using LIGPLOT [72] and edited using CorelDRAW 4.0.)
  The above figure is reprinted by permission from Cell Press: Structure (1996, 4, 1491-1508) copyright 1996.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21190293 A.Srivastava, and A.K.Sau (2010).
Biochemical studies on Helicobacter pylori arginase: insight into the difference in activity compared to other arginases.
  IUBMB Life, 62, 906-915.  
  19916164 D.Koutsioulis, A.Lyskowski, S.Mäki, E.Guthrie, G.Feller, V.Bouriotis, and P.Heikinheimo (2010).
Coordination sphere of the third metal site is essential to the activity and metal selectivity of alkaline phosphatases.
  Protein Sci, 19, 75-84.
PDB codes: 2w5v 2w5w 2w5x
19882151 S.Y.Park, B.Lee, K.S.Park, Y.Chong, M.Y.Yoon, S.J.Jeon, and D.E.Kim (2010).
Facilitation of polymerase chain reaction with thermostable inorganic pyrophosphatase from hyperthermophilic archaeon Pyrococcus horikoshii.
  Appl Microbiol Biotechnol, 85, 807-812.  
19608746 E.M.Warren, H.Huang, E.Fanning, W.J.Chazin, and B.F.Eichman (2009).
Physical interactions between Mcm10, DNA, and DNA polymerase alpha.
  J Biol Chem, 284, 24662-24672.
PDB code: 3h15
17095506 I.P.Fabrichniy, L.Lehtiö, M.Tammenkoski, A.B.Zyryanov, E.Oksanen, A.A.Baykov, R.Lahti, and A.Goldman (2007).
A trimetal site and substrate distortion in a family II inorganic pyrophosphatase.
  J Biol Chem, 282, 1422-1431.
PDB codes: 2haw 2iw4
17598086 M.J.Lee, H.Huang, W.Lin, R.R.Yang, C.L.Liu, and C.Y.Huang (2007).
Activation of Helicobacter pylori inorganic pyrophosphatase and the importance of Cys16 in thermostability, enzyme activation and quaternary structure.
  Arch Microbiol, 188, 473-482.  
17505113 M.K.Rantanen, L.Lehtiö, L.Rajagopal, C.E.Rubens, and A.Goldman (2007).
Structure of the Streptococcus agalactiae family II inorganic pyrophosphatase at 2.80 A resolution.
  Acta Crystallogr D Biol Crystallogr, 63, 738-743.
PDB code: 2enx
17635582 M.R.Gómez-García, M.Losada, and A.Serrano (2007).
Comparative biochemical and functional studies of family I soluble inorganic pyrophosphatases from photosynthetic bacteria.
  FEBS J, 274, 3948-3959.  
16291745 B.Espiau, G.Lemercier, A.Ambit, F.Bringaud, G.Merlin, T.Baltz, and N.Bakalara (2006).
A soluble pyrophosphatase, a key enzyme for polyphosphate metabolism in Leishmania.
  J Biol Chem, 281, 1516-1523.  
16988955 T.C.Chao, H.Huang, J.Y.Tsai, C.Y.Huang, and Y.J.Sun (2006).
Kinetic and structural properties of inorganic pyrophosphatase from the pathogenic bacterium Helicobacter pylori.
  Proteins, 65, 670-680.
PDB codes: 2bqx 2bqy
16239722 C.A.Wu, N.K.Lokanath, D.Y.Kim, H.J.Park, H.Y.Hwang, S.T.Kim, S.W.Suh, and K.K.Kim (2005).
Structure of inorganic pyrophosphatase from Helicobacter pylori.
  Acta Crystallogr D Biol Crystallogr, 61, 1459-1464.
PDB code: 1ygz
16092891 J.L.Hougland, A.V.Kravchuk, D.Herschlag, and J.A.Piccirilli (2005).
Functional identification of catalytic metal ion binding sites within RNA.
  PLoS Biol, 3, e277.  
16239227 M.Tammenkoski, S.Benini, N.N.Magretova, A.A.Baykov, and R.Lahti (2005).
An unusual, His-dependent family I pyrophosphatase from Mycobacterium tuberculosis.
  J Biol Chem, 280, 41819-41826.  
  16243777 S.J.Jeon, and K.Ishikawa (2005).
Characterization of the Family I inorganic pyrophosphatase from Pyrococcus horikoshii OT3.
  Archaea, 1, 385-389.  
16212541 V.M.Moiseev, E.V.Rodina, S.A.Kurilova, N.N.Vorobyeva, T.I.Nazarova, and S.M.Avaeva (2005).
Substitutions of glycine residues Gly100 and Gly147 in conservative loops decrease rates of conformational rearrangements of Escherichia coli inorganic pyrophosphatase.
  Biochemistry (Mosc), 70, 858-866.  
15107429 A.M.Malinen, G.A.Belogurov, M.Salminen, A.A.Baykov, and R.Lahti (2004).
Elucidating the role of conserved glutamates in H+-pyrophosphatase of Rhodospirillum rubrum.
  J Biol Chem, 279, 26811-26816.  
14993708 V.U.Tuominen, D.A.Myles, M.T.Dauvergne, R.Lahti, P.Heikinheimo, and A.Goldman (2004).
Production and preliminary analysis of perdeuterated yeast inorganic pyrophosphatase crystals suitable for neutron diffraction.
  Acta Crystallogr D Biol Crystallogr, 60, 606-609.  
12823552 M.K.Islam, T.Miyoshi, H.Kasuga-Aoki, T.Isobe, T.Arakawa, Y.Matsumoto, and N.Tsuji (2003).
Inorganic pyrophosphatase in the roundworm Ascaris and its role in the development and molting process of the larval stage parasites.
  Eur J Biochem, 270, 2814-2826.  
12596267 T.Hamelryck (2003).
Efficient identification of side-chain patterns using a multidimensional index tree.
  Proteins, 51, 96.  
11854292 A.Salminen, A.N.Parfenyev, K.Salli, I.S.Efimova, N.N.Magretova, A.Goldman, A.A.Baykov, and R.Lahti (2002).
Modulation of dimer stability in yeast pyrophosphatase by mutations at the subunit interface and ligand binding to the active site.
  J Biol Chem, 277, 15465-15471.  
11432753 E.V.Rodina, Y.P.Vainonen, N.N.Vorobyeva, S.A.Kurilova, T.I.Nazarova, and S.M.Avaeva (2001).
The role of Asp42 in Escherichia coli inorganic pyrophosphatase functioning.
  Eur J Biochem, 268, 3851-3857.  
11525166 M.C.Merckel, I.P.Fabrichniy, A.Salminen, N.Kalkkinen, A.A.Baykov, R.Lahti, and A.Goldman (2001).
Crystal structure of Streptococcus mutans pyrophosphatase: a new fold for an old mechanism.
  Structure, 9, 289-297.
PDB code: 1i74
11248042 P.Heikinheimo, V.Tuominen, A.K.Ahonen, A.Teplyakov, B.S.Cooperman, A.A.Baykov, R.Lahti, and A.Goldman (2001).
Toward a quantum-mechanical description of metal-assisted phosphoryl transfer in pyrophosphatase.
  Proc Natl Acad Sci U S A, 98, 3121-3126.
PDB codes: 1e6a 1e9g
10712586 V.C.Wasinger, J.D.Pollack, and I.Humphery-Smith (2000).
The proteome of Mycoplasma genitalium. Chaps-soluble component.
  Eur J Biochem, 267, 1571-1582.  
11118200 W.Blankenfeldt, M.Asuncion, J.S.Lam, and J.H.Naismith (2000).
The structural basis of the catalytic mechanism and regulation of glucose-1-phosphate thymidylyltransferase (RmlA).
  EMBO J, 19, 6652-6663.
PDB codes: 1fxo 1fzw 1g0r 1g1l 1g23 1g2v 1g3l
10095764 A.A.Baykov, T.Hyytiä, M.V.Turkina, I.S.Efimova, V.N.Kasho, A.Goldman, B.S.Cooperman, and R.Lahti (1999).
Functional characterization of Escherichia coli inorganic pyrophosphatase in zwitterionic buffers.
  Eur J Biochem, 260, 308-317.  
10567351 A.Salminen, I.S.Efimova, A.N.Parfenyev, N.N.Magretova, K.Mikalahti, A.Goldman, A.A.Baykov, and R.Lahti (1999).
Reciprocal effects of substitutions at the subunit interfaces in hexameric pyrophosphatase of Escherichia coli. Dimeric and monomeric forms of the enzyme.
  J Biol Chem, 274, 33898-33904.  
10872443 D.W.Christianson, and J.D.Cox (1999).
Catalysis by metal-activated hydroxide in zinc and manganese metalloenzymes.
  Annu Rev Biochem, 68, 33-57.  
9920869 I.S.Efimova, A.Salminen, P.Pohjanjoki, J.Lapinniemi, N.N.Magretova, B.S.Cooperman, A.Goldman, R.Lahti, and A.A.Baykov (1999).
Directed mutagenesis studies of the metal binding site at the subunit interface of Escherichia coli inorganic pyrophosphatase.
  J Biol Chem, 274, 3294-3299.  
  10386872 V.M.Leppänen, H.Nummelin, T.Hansen, R.Lahti, G.Schäfer, and A.Goldman (1999).
Sulfolobus acidocaldarius inorganic pyrophosphatase: structure, thermostability, and effect of metal ion in an archael pyrophosphatase.
  Protein Sci, 8, 1218-1231.
PDB code: 1qez
9761898 A.Carfi, E.Duée, M.Galleni, J.M.Frère, and O.Dideberg (1998).
1.85 A resolution structure of the zinc (II) beta-lactamase from Bacillus cereus.
  Acta Crystallogr D Biol Crystallogr, 54, 313-323.
PDB code: 1bvt
10089488 G.J.Kleywegt, and T.A.Jones (1998).
Databases in protein crystallography.
  Acta Crystallogr D Biol Crystallogr, 54, 1119-1131.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.