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PDBsum entry 1eip
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protein Protein-protein interface(s) links
Acid anhydride hydrolase PDB id
1eip

 

 

 

 

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Contents
Protein chains
169 a.a.
Obsolete entry
PDB id:
1eip
Name: Acid anhydride hydrolase
Title: The structure of e. Coli soluble pyrophosphatase at 2.7 angstroms resolution
Structure: Chain: a, b. Engineered: yes
Source: not given
Resolution:
2.70Å     R-factor:   0.209    
Authors: J.A.Kankare,T.Salminen,A.Goldman
Key ref: J.Kankare et al. (1994). The structure of E.coli soluble inorganic pyrophosphatase at 2.7 A resolution. Protein Eng, 7, 823-830. PubMed id: 7971944
Date:
29-Mar-94     Release date:   31-Aug-94    
PROCHECK
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 Headers
 References

Protein chains
No UniProt id for this chain
Struc: 169 a.a.
Key:    Secondary structure  CATH domain

 

 
Protein Eng 7:823-830 (1994)
PubMed id: 7971944  
 
 
The structure of E.coli soluble inorganic pyrophosphatase at 2.7 A resolution.
J.Kankare, G.S.Neal, T.Salminen, T.Glumoff, T.].Glumhoff T [corrected to Glumoff, B.S.Cooperman, R.Lahti, A.Goldman.
 
  ABSTRACT  
 
The structure of E.coli soluble inorganic pyrophosphatase has been refined at 2.7 A resolution to an R-factor of 20.9%. The overall fold of the molecule is essentially the same as yeast pyrophosphatase, except that yeast pyrophosphatase is longer at both the N- and C-termini. Escherichia coli pyrophosphatase is a mixed alpha + beta protein with a complicated topology. The active site cavity, which is also very similar to the yeast enzyme, is formed by seven beta-strands and an alpha-helix and has a rather asymmetric distribution of charged residues. Our structure-based alignment extends and improves upon earlier sequence alignment studies; it shows that probably no more than 14, not 15-17 charged and polar residues are part of the conserved enzyme mechanism of pyrophosphatases. Six of these conserved residues, at the bottom of the active site cavity, form a tight group centred on Asp70 and probably bind the two essential Mg2+ ions. The others, more spreadout and more positively charged, presumably bind substrate. Escherichia coli pyrophosphatase has an extra aspartate residue in the active site cavity, which may explain why the two enzymes bind divalent cation differently. Based on the structure, we have identified a sequence motif that seems to occur only in soluble inorganic pyrophosphatases.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
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.  
  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.  
14695284 B.Liu, M.Bartlam, R.Gao, W.Zhou, H.Pang, Y.Liu, Y.Feng, and Z.Rao (2004).
Crystal structure of the hyperthermophilic inorganic pyrophosphatase from the archaeon Pyrococcus horikoshii.
  Biophys J, 86, 420-427.
PDB code: 1ude
11339880 J.A.Triccas, and B.Gicquel (2001).
Analysis of stress- and host cell-induced expression of the Mycobacterium tuberculosis inorganic pyrophosphatase.
  BMC Microbiol, 1, 3.  
11294631 T.Hyytiä, P.Halonen, A.Salminen, A.Goldman, R.Lahti, and B.S.Cooperman (2001).
Ligand binding sites in Escherichia coli inorganic pyrophosphatase: effects of active site mutations.
  Biochemistry, 40, 4645-4653.  
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.  
  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
9485300 P.Pohjanjoki, R.Lahti, A.Goldman, and B.S.Cooperman (1998).
Evolutionary conservation of enzymatic catalysis: quantitative comparison of the effects of mutation of aligned residues in Saccharomyces cerevisiae and Escherichia coli inorganic pyrophosphatases on enzymatic activity.
  Biochemistry, 37, 1754-1761.  
9972267 T.Wakagi, T.Oshima, H.Imamura, and H.Matsuzawa (1998).
Cloning of the gene for inorganic pyrophosphatase from a thermoacidophilic archaeon, Sulfolobus sp. strain 7, and overproduction of the enzyme by coexpression of tRNA for arginine rare codon.
  Biosci Biotechnol Biochem, 62, 2408-2414.  
  9423859 Y.Abu Kwaik (1998).
Induced expression of the Legionella pneumophila gene encoding a 20-kilodalton protein during intracellular infection.
  Infect Immun, 66, 203-212.  
9188741 A.V.Efimov (1997).
Structural trees for protein superfamilies.
  Proteins, 28, 241-260.  
9147131 T.Shimizu, M.Imai, S.Araki, K.Kishida, Y.Terasawa, and A.Hachimori (1997).
Some properties of inorganic pyrophosphatase from Bacillus subtilis.
  Int J Biochem Cell Biol, 29, 303-310.  
8664254 A.A.Baykov, T.Hyytia, S.E.Volk, V.N.Kasho, A.V.Vener, A.Goldman, R.Lahti, and B.S.Cooperman (1996).
Catalysis by Escherichia coli inorganic pyrophosphatase: pH and Mg2+ dependence.
  Biochemistry, 35, 4655-4661.  
8706712 E.H.Harutyunyan, I.P.Kuranova, B.K.Vainshtein, W.E.Höhne, V.S.Lamzin, Z.Dauter, A.V.Teplyakov, and K.S.Wilson (1996).
X-ray structure of yeast inorganic pyrophosphatase complexed with manganese and phosphate.
  Eur J Biochem, 239, 220-228.
PDB code: 1ypp
8664256 J.Kankare, T.Salminen, R.Lahti, B.S.Cooperman, A.A.Baykov, and A.Goldman (1996).
Crystallographic identification of metal-binding sites in Escherichia coli inorganic pyrophosphatase.
  Biochemistry, 35, 4670-4677.
PDB codes: 1ipw 1ipx 1ipy 1ipz
8994974 P.Heikinheimo, J.Lehtonen, A.Baykov, R.Lahti, B.S.Cooperman, and A.Goldman (1996).
The structural basis for pyrophosphatase catalysis.
  Structure, 4, 1491-1508.
PDB codes: 1wgi 1wgj
8706698 P.Heikinheimo, P.Pohjanjoki, A.Helminen, M.Tasanen, B.S.Cooperman, A.Goldman, A.Baykov, and R.Lahti (1996).
A site-directed mutagenesis study of Saccharomyces cerevisiae pyrophosphatase. Functional conservation of the active site of soluble inorganic pyrophosphatases.
  Eur J Biochem, 239, 138-143.  
8664255 S.E.Volk, V.Y.Dudarenkov, J.Käpylä, V.N.Kasho, O.A.Voloshina, T.Salminen, A.Goldman, R.Lahti, A.A.Baykov, and B.S.Cooperman (1996).
Effect of E20D substitution in the active site of Escherichia coli inorganic pyrophosphatase on its quaternary structure and catalytic properties.
  Biochemistry, 35, 4662-4669.  
  8062829 G.Gaudino, A.Follenzi, L.Naldini, C.Collesi, M.Santoro, K.A.Gallo, P.J.Godowski, and P.M.Comoglio (1994).
RON is a heterodimeric tyrosine kinase receptor activated by the HGF homologue MSP.
  EMBO J, 13, 3524-3532.  
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 code is shown on the right.

 

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