3R1M

Structure of bifunctional fructose 1,6-bisphosphate aldolase/phosphatase (aldolase form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural basis for the bifunctionality of fructose-1,6-bisphosphate aldolase/phosphatase.

Fushinobu, S.Nishimasu, H.Hattori, D.Song, H.-J.Wakagi, T.

(2011) Nature 478: 538-541

  • DOI: 10.1038/nature10457
  • Primary Citation of Related Structures:  
    3R1M

  • PubMed Abstract: 
  • Enzymes catalyse specific reactions and are essential for maintaining life. Although some are referred to as being bifunctional, they consist of either two distinct catalytic domains or a single domain that displays promiscuous substrate specificity. Thus, one enzyme active site is generally responsible for one biochemical reaction ...

    Enzymes catalyse specific reactions and are essential for maintaining life. Although some are referred to as being bifunctional, they consist of either two distinct catalytic domains or a single domain that displays promiscuous substrate specificity. Thus, one enzyme active site is generally responsible for one biochemical reaction. In contrast to this conventional concept, archaeal fructose-1,6-bisphosphate (FBP) aldolase/phosphatase (FBPA/P) consists of a single catalytic domain, but catalyses two chemically distinct reactions of gluconeogenesis: (1) the reversible aldol condensation of dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (GA3P) to FBP; (2) the dephosphorylation of FBP to fructose-6-phosphate (F6P). Thus, FBPA/P is fundamentally different from ordinary enzymes whose active sites are responsible for a specific reaction. However, the molecular mechanism by which FBPA/P achieves its unusual bifunctionality remains unknown. Here we report the crystal structure of FBPA/P at 1.5-Å resolution in the aldolase form, where a critical lysine residue forms a Schiff base with DHAP. A structural comparison of the aldolase form with a previously determined phosphatase form revealed a dramatic conformational change in the active site, demonstrating that FBPA/P metamorphoses its active-site architecture to exhibit dual activities. Thus, our findings expand the conventional concept that one enzyme catalyses one biochemical reaction.


    Organizational Affiliation

    Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative uncharacterized protein ST0318A385Sulfurisphaera tokodaii str. 7Mutation(s): 0 
Gene Names: ST0318fbpSTK_03180
EC: 3.1.3.11 (UniProt), 4.1.2.13 (UniProt)
UniProt
Find proteins for F9VMT6 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7))
Explore F9VMT6 
Go to UniProtKB:  F9VMT6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF9VMT6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
13P
Query on 13P

Download Ideal Coordinates CCD File 
B [auth A]1,3-DIHYDROXYACETONEPHOSPHATE
C3 H7 O6 P
GNGACRATGGDKBX-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download Ideal Coordinates CCD File 
F [auth A](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.543α = 90
b = 112.543β = 90
c = 153.608γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-12
    Type: Initial release
  • Version 1.1: 2011-10-26
    Changes: Structure summary
  • Version 1.2: 2011-11-09
    Changes: Database references
  • Version 1.3: 2017-02-08
    Changes: Structure summary