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PDBsum entry 1fpi
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protein ligands metals Protein-protein interface(s) links
Hydrolase (phosphoric monoester) PDB id
1fpi

 

 

 

 

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Contents
Protein chains
317 a.a. *
Ligands
AMP ×2
AHG ×2
Metals
__K ×6
Waters ×111
* Residue conservation analysis
PDB id:
1fpi
Name: Hydrolase (phosphoric monoester)
Title: Fructose-1,6-bisphosphatase (d-fructose-1,6-bisphosphate 1- phosphohydrolase) complexed with amp, 2,5-anhydro-d-glucitol-1,6- bisphosphate and potassium ions (100 mm)
Structure: Fructose-1,6-bisphosphatase. Chain: a, b. Synonym: d-fructose-1,6-bisphosphate 1-phosphohydrolase. Ec: 3.1.3.11
Source: Sus scrofa. Pig. Organism_taxid: 9823. Organ: kidney
Biol. unit: Tetramer (from PQS)
Resolution:
2.30Å     R-factor:   0.199    
Authors: V.Villeret,W.N.Lipscomb
Key ref: V.Villeret et al. (1995). Crystallographic evidence for the action of potassium, thallium, and lithium ions on fructose-1,6-bisphosphatase. Proc Natl Acad Sci U S A, 92, 8916-8920. PubMed id: 7568043 DOI: 10.1073/pnas.92.19.8916
Date:
02-Jun-95     Release date:   20-Jun-96    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00636  (F16P1_PIG) -  Fructose-1,6-bisphosphatase 1 from Sus scrofa
Seq:
Struc: 		338 a.a.
317 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.1.3.11  - fructose-bisphosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway: 		Pentose Phosphate Pathway (later stages)
      Reaction: beta-D-fructose 1,6-bisphosphate + H2O = beta-D-fructose 6-phosphate + phosphate
beta-D-fructose 1,6-bisphosphate
Bound ligand (Het Group name = AHG)
matches with 95.00% similarity 		+ H2O
 = beta-D-fructose 6-phosphate
 + phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1073/pnas.92.19.8916 Proc Natl Acad Sci U S A 92:8916-8920 (1995)
PubMed id: 7568043  
 
 
Crystallographic evidence for the action of potassium, thallium, and lithium ions on fructose-1,6-bisphosphatase.
V.Villeret, S.Huang, H.J.Fromm, W.N.Lipscomb.
 
  ABSTRACT  
 
Fructose-1,6-bisphosphatase (Fru-1,6-Pase; D-fructose-1,6-bisphosphate 1-phosphohydrolase, EC 3.1.3.11) requires two divalent metal ions to hydrolyze alpha-D-fructose 1,6-bisphosphate. Although not required for catalysis, monovalent cations modify the enzyme activity; K+ and Tl+ ions are activators, whereas Li+ ions are inhibitors. Their mechanisms of action are still unknown. We report here crystallographic structures of pig kidney Fru-1,6-Pase complexed with K+, Tl+, or both Tl+ and Li+. In the T form Fru-1,6-Pase complexed with the substrate analogue 2,5-anhydro-D-glucitol 1,6-bisphosphate (AhG-1,6-P2) and Tl+ or K+ ions, three Tl+ or K+ binding sites are found. Site 1 is defined by Glu-97, Asp-118, Asp-121, Glu-280, and a 1-phosphate oxygen of AhG-1,6-P2; site 2 is defined by Glu-97, Glu-98, Asp-118, and Leu-120. Finally, site 3 is defined by Arg-276, Glu-280, and the 1-phosphate group of AhG-1,6-P2. The Tl+ or K+ ions at sites 1 and 2 are very close to the positions previously identified for the divalent metal ions. Site 3 is specific to K+ or Tl+. In the divalent metal ion complexes, site 3 is occupied by the guanidinium group of Arg-276. These observations suggest that Tl+ or K+ ions can substitute for Arg-276 in the active site and polarize the 1-phosphate group, thus facilitating nucleophilic attack on the phosphorus center. In the T form complexed with both Tl+ and Li+ ions, Li+ replaces Tl+ at metal site 1. Inhibition by lithium very likely occurs as it binds to this site, thus retarding turnover or phosphate release. The present study provides a structural basis for a similar mechanism of inhibition for inositol monophosphatase, one of the potential targets of lithium ions in the treatment of manic depression.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
  19851000 P.D.Kiser, G.H.Lorimer, and K.Palczewski (2009).
Use of thallium to identify monovalent cation binding sites in GroEL.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 967-971.
PDB code: 3e76
17855404 M.Ganguly, F.Wang, M.Kaushik, M.P.Stone, L.A.Marky, and B.Gold (2007).
A study of 7-deaza-2'-deoxyguanosine 2'-deoxycytidine base pairing in DNA.
  Nucleic Acids Res, 35, 6181-6195.  
17270011 R.An, Q.J.Chen, M.F.Chai, P.L.Lu, Z.Su, Z.X.Qin, J.Chen, and X.C.Wang (2007).
AtNHX8, a member of the monovalent cation: proton antiporter-1 family in Arabidopsis thaliana, encodes a putative Li/H antiporter.
  Plant J, 49, 718-728.  
17112226 B.Gold, L.M.Marky, M.P.Stone, and L.D.Williams (2006).
A review of the role of the sequence-dependent electrostatic landscape in DNA alkylation patterns.
  Chem Res Toxicol, 19, 1402-1414.  
15858264 R.Gill, F.Mohammed, R.Badyal, L.Coates, P.Erskine, D.Thompson, J.Cooper, M.Gore, and S.Wood (2005).
High-resolution structure of myo-inositol monophosphatase, the putative target of lithium therapy.
  Acta Crystallogr D Biol Crystallogr, 61, 545-555.
PDB code: 2bji
12755692 L.Ramírez-Silva, and J.Oria-Hernández (2003).
Selectivity of pyruvate kinase for Na+ and K+ in water/dimethylsulfoxide mixtures.
  Eur J Biochem, 270, 2377-2385.  
12717724 S.B.Howerton, A.Nagpal, and L.D.Williams (2003).
Surprising roles of electrostatic interactions in DNA-ligand complexes.
  Biopolymers, 69, 87-99.
PDB code: 1p20
14612565 S.Prasad, K.J.Wright, D.Banerjee Roy, L.A.Bush, A.M.Cantwell, and E.Di Cera (2003).
Redesigning the monovalent cation specificity of an enzyme.
  Proc Natl Acad Sci U S A, 100, 13785-13790.  
11264477 C.J.Phiel, and P.S.Klein (2001).
Molecular targets of lithium action.
  Annu Rev Pharmacol Toxicol, 41, 789-813.  
10913263 J.Y.Choe, H.J.Fromm, and R.B.Honzatko (2000).
Crystal structures of fructose 1,6-bisphosphatase: mechanism of catalysis and allosteric inhibition revealed in product complexes.
  Biochemistry, 39, 8565-8574.
PDB codes: 1eyi 1eyj 1eyk
10841532 S.L.De Wall, E.S.Meadows, L.J.Barbour, and G.W.Gokel (2000).
Synthetic receptors as models for alkali metal cation-pi binding sites in proteins.
  Proc Natl Acad Sci U S A, 97, 6271-6276.  
10089399 C.M.Weeks, A.W.Roszak, M.Erman, R.Kaiser, H.Jörnvall, and D.Ghosh (1999).
Structure of rabbit liver fructose 1,6-bisphosphatase at 2.3 A resolution.
  Acta Crystallogr D Biol Crystallogr, 55, 93.
PDB code: 1bk4
9708979 J.Y.Choe, B.W.Poland, H.J.Fromm, and R.B.Honzatko (1998).
Role of a dynamic loop in cation activation and allosteric regulation of recombinant porcine fructose-1,6-bisphosphatase.
  Biochemistry, 37, 11441-11450.
PDB codes: 1bfl 1cnq
9808044 S.Basu, R.P.Rambo, J.Strauss-Soukup, J.H.Cate, A.R.Ferré-D'Amaré, S.A.Strobel, and J.A.Doudna (1998).
A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor.
  Nat Struct Biol, 5, 986-992.  
9585559 S.M.Wilbanks, and D.B.McKay (1998).
Structural replacement of active site monovalent cations by the epsilon-amino group of lysine in the ATPase fragment of bovine Hsc70.
  Biochemistry, 37, 7456-7462.
PDB codes: 1ba0 1ba1
9354627 G.R.Bishop, and V.L.Davidson (1997).
Catalytic role of monovalent cations in the mechanism of proton transfer which gates an interprotein electron transfer reaction.
  Biochemistry, 36, 13586-13592.  
9428713 L.Ramírez-Silva, J.Oria, A.Gómez-Puyou, and M.Tuena de Gómez-Puyou (1997).
The contribution of water to the selectivity of pyruvate kinase for Na+ and K+.
  Eur J Biochem, 250, 583-589.  
8688415 E.R.Guinto, and E.Di Cera (1996).
Large heat capacity change in a protein-monovalent cation interaction.
  Biochemistry, 35, 8800-8804.  
8608143 R.Zhang, V.Villeret, W.N.Lipscomb, and H.J.Fromm (1996).
Kinetics and mechanisms of activation and inhibition of porcine liver fructose-1,6-bisphosphatase by monovalent cations.
  Biochemistry, 35, 3038-3043.  
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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