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PDBsum entry 3f3k

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protein ligands Protein-protein interface(s) links
Structural genomics, unknown function PDB id
3f3k
Jmol
Contents
Protein chains
260 a.a. *
Ligands
GOL ×6
Waters ×939
* Residue conservation analysis
PDB id:
3f3k
Name: Structural genomics, unknown function
Title: The structure of uncharacterized protein ykr043c from saccha cerevisiae.
Structure: Uncharacterized protein ykr043c. Chain: a, b. Engineered: yes
Source: Saccharomyces cerevisiae. Brewer's yeast,lager beer yeast,yeast. Organism_taxid: 4932. Strain: s288c. Gene: ykr043c. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.75Å     R-factor:   0.143     R-free:   0.170
Authors: M.Cuff,X.Xu,H.Cui,A.Edwards,A.Savchenko,A.Joachimiak,Midwest For Structural Genomics (Mcsg)
Key ref: E.Kuznetsova et al. (2010). Structure and activity of the metal-independent fructose-1,6-bisphosphatase YK23 from Saccharomyces cerevisiae. J Biol Chem, 285, 21049-21059. PubMed id: 20427268 DOI: 10.1074/jbc.M110.118315
Date:
30-Oct-08     Release date:   09-Dec-08    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P36136  (SHB17_YEAST) -  Sedoheptulose 1,7-bisphosphatase
Seq:
Struc:
271 a.a.
260 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.1.3.37  - Sedoheptulose-bisphosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Calvin Cycle
      Reaction: Sedoheptulose 1,7-bisphosphate + H2O = sedoheptulose 7-phosphate + phosphate
Sedoheptulose 1,7-bisphosphate
+ H(2)O
= sedoheptulose 7-phosphate
+ phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   2 terms 
  Biological process     oxidation-reduction process   5 terms 
  Biochemical function     oxidoreductase activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M110.118315 J Biol Chem 285:21049-21059 (2010)
PubMed id: 20427268  
 
 
Structure and activity of the metal-independent fructose-1,6-bisphosphatase YK23 from Saccharomyces cerevisiae.
E.Kuznetsova, L.Xu, A.Singer, G.Brown, A.Dong, R.Flick, H.Cui, M.Cuff, A.Joachimiak, A.Savchenko, A.F.Yakunin.
 
  ABSTRACT  
 
Fructose-1,6-bisphosphatase (FBPase), a key enzyme of gluconeogenesis and photosynthetic CO(2) fixation, catalyzes the hydrolysis of fructose 1,6-bisphosphate (FBP) to produce fructose 6-phosphate, an important precursor in various biosynthetic pathways. All known FBPases are metal-dependent enzymes, which are classified into five different classes based on their amino acid sequences. Eukaryotes are known to contain only the type-I FBPases, whereas all five types exist in various combinations in prokaryotes. Here we demonstrate that the uncharacterized protein YK23 from Saccharomyces cerevisiae efficiently hydrolyzes FBP in a metal-independent reaction. YK23 is a member of the histidine phosphatase (phosphoglyceromutase) superfamily with homologues found in all organisms. The crystal structure of the YK23 apo-form was solved at 1.75-A resolution and revealed the core domain with the alpha/beta/alpha-fold covered by two small cap domains. Two liganded structures of this protein show the presence of two phosphate molecules (an inhibitor) or FBP (a substrate) bound to the active site. FBP is bound in its linear, open conformation with the cleavable C1-phosphate positioned deep in the active site. Alanine replacement mutagenesis of YK23 identified six conserved residues absolutely required for activity and suggested that His(13) and Glu(99) are the primary catalytic residues. Thus, YK23 represents the first family of metal-independent FBPases and a second FBPase family in eukaryotes.