1NV7 | pdb_00001nv7

Fructose-1,6-Bisphosphatase Complex With AMP, Magnesium, Fructose-6-Phosphate, Phosphate and Thallium (20 mM)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.251 (Depositor) 
  • R-Value Work: 
    0.182 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

Interaction of Tl+ with product complexes of fructose-1,6-bisphosphatase

Choe, J.Y.Nelson, S.W.Fromm, H.J.Honzatko, R.B.

(2003) J Biological Chem 278: 16008-16014

  • DOI: https://doi.org/10.1074/jbc.M212394200
  • Primary Citation Related Structures: 
    1NUZ, 1NV0, 1NV1, 1NV2, 1NV3, 1NV4, 1NV5, 1NV6, 1NV7

  • PubMed Abstract: 

    Fructose-1,6-bisphosphatase requires divalent cations (Mg2+, Mn2+, or Zn2+) for catalysis, but a diverse set of monovalent cations (K+, Tl+, Rb+, or NH(4)(+)) will further enhance enzyme activity. Here, the interaction of Tl+ with fructose-1,6-bisphosphatase is explored under conditions that support catalysis. On the basis of initial velocity kinetics, Tl+ enhances catalysis by 20% with a K(a) of 1.3 mm and a Hill coefficient near unity. Crystal structures of enzyme complexes with Mg2+, Tl+, and reaction products, in which the concentration of Tl+ is 1 mm or less, reveal Mg2+ at metal sites 1, 2, and 3 of the active site, but little or no bound Tl+. Intermediate concentrations of Tl+ (5-20 mm) displace Mg2+ from site 3 and the 1-OH group of fructose 6-phosphate from in-line geometry with respect to bound orthophosphate. Loop 52-72 appears in a new conformational state, differing from its engaged conformation by disorder in residues 61-69. Tl+ does not bind to metal sites 1 or 2 in the presence of Mg2+, but does bind to four other sites with partial occupancy. Two of four Tl+ sites probably represent alternative binding sites for the site 3 catalytic Mg2+, whereas the other sites could play roles in monovalent cation activation.


  • Organizational Affiliation
    • Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA.

Macromolecule Content 

  • Total Structure Weight: 76.47 kDa 
  • Atom Count: 5,515 
  • Modeled Residue Count: 654 
  • Deposited Residue Count: 674 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fructose-1,6-Bisphosphatase
A, B
337Sus scrofaMutation(s): 0 
EC: 3.1.3.11
UniProt
Find proteins for P00636 (Sus scrofa)
Explore P00636 
Go to UniProtKB:  P00636
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00636
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AMP

Query on AMP



Download:Ideal Coordinates CCD File
F [auth A],
N [auth B]
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
F6P

Query on F6P



Download:Ideal Coordinates CCD File
C [auth A],
K [auth B]
6-O-phosphono-beta-D-fructofuranose
C6 H13 O9 P
BGWGXPAPYGQALX-ARQDHWQXSA-N
TL

Query on TL



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth A]
J [auth A]
O [auth B]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
O [auth B],
P [auth B],
Q [auth B],
R [auth B]
THALLIUM (I) ION
Tl
ZLUSCZLCHQSJRU-UHFFFAOYSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
E [auth A],
M [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG

Query on MG



Download:Ideal Coordinates CCD File
D [auth A],
L [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.251 (Depositor) 
  • R-Value Work:  0.182 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.95α = 90
b = 166.15β = 90
c = 79.29γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
SHELXL-97refinement
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-07-08
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-11-20
    Changes: Derived calculations
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.5: 2023-10-25
    Changes: Data collection, Database references, Refinement description, Structure summary