2F3D

Mechanism of displacement of a catalytically essential loop from the active site of fructose-1,6-bisphosphatase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.6 of the entry. See complete history

Literature

Mechanism of displacement of a catalytically essential loop from the active site of mammalian fructose-1,6-bisphosphatase.

Gao, Y.Iancu, C.V.Mukind, S.Choe, J.Y.Honzatko, R.B.

(2013) Biochemistry 52: 5206-5216

  • DOI: 10.1021/bi400532n
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • AMP triggers a 15° subunit-pair rotation in fructose-1,6-bisphosphatase (FBPase) from its active R state to its inactive T state. During this transition, a catalytically essential loop (residues 50-72) leaves its active (engaged) conformation. Here, ...

    AMP triggers a 15° subunit-pair rotation in fructose-1,6-bisphosphatase (FBPase) from its active R state to its inactive T state. During this transition, a catalytically essential loop (residues 50-72) leaves its active (engaged) conformation. Here, the structures of Ile(10) → Asp FBPase and molecular dynamic simulations reveal factors responsible for loop displacement. The AMP/Mg(2+) and AMP/Zn(2+) complexes of Asp(10) FBPase are in intermediate quaternary conformations (completing 12° of the subunit-pair rotation), but the complex with Zn(2+) provides the first instance of an engaged loop in a near-T quaternary state. The 12° subunit-pair rotation generates close contacts involving the hinges (residues 50-57) and hairpin turns (residues 58-72) of the engaged loops. Additional subunit-pair rotation toward the T state would make such contacts unfavorable, presumably causing displacement of the loop. Targeted molecular dynamics simulations reveal no steric barriers to subunit-pair rotations of up to 14° followed by the displacement of the loop from the active site. Principal component analysis reveals high-amplitude motions that exacerbate steric clashes of engaged loops in the near-T state. The results of the simulations and crystal structures are in agreement: subunit-pair rotations just short of the canonical T state coupled with high-amplitude modes sterically displace the dynamic loop from the active site.


    Organizational Affiliation

    Department of Biochemistry, Biophysics, and Molecular Biology, 4206 Molecular Biology Building, Iowa State University , Ames, Iowa 50011-3260, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fructose-1,6-bisphosphatase 1
A
338Sus scrofaMutation(s): 1 
Gene Names: FBP1 (FBP)
EC: 3.1.3.11
Find proteins for P00636 (Sus scrofa)
Go to Gene View: FBP1
Go to UniProtKB:  P00636
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
AMP
Query on AMP

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Download CCD File 
A
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
F6P
Query on F6P

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Download CCD File 
A
FRUCTOSE-6-PHOSPHATE
C6 H13 O9 P
BGWGXPAPYGQALX-ARQDHWQXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.222 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 55.840α = 90.00
b = 82.502β = 90.00
c = 165.025γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEdata reduction
DENZOdata reduction
AMoREphasing
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-04-25
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model
  • Version 1.4: 2013-07-24
    Type: Database references
  • Version 1.5: 2014-02-05
    Type: Database references
  • Version 1.6: 2017-10-18
    Type: Refinement description