1K9Y | pdb_00001k9y

The PAPase Hal2p complexed with magnesium ions and reaction products: AMP and inorganic phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.203 (Depositor), 0.208 (DCC) 
  • R-Value Work: 
    0.156 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 
    0.158 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1K9Y

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structural enzymology of Li(+)-sensitive/Mg(2+)-dependent phosphatases.

Patel, S.Martinez-Ripoll, M.Blundell, T.L.Albert, A.

(2002) J Mol Biology 320: 1087-1094

  • DOI: https://doi.org/10.1016/s0022-2836(02)00564-8
  • Primary Citation Related Structures: 
    1K9Y, 1KA1

  • PubMed Abstract: 

    Li(+)-sensitive/Mg(2+)-dependent phosphatases have attracted considerable attention since they have been proposed as targets for lithium therapy in the treatment of manic-depressive patients. The members of this enzyme superfamily display low levels of sequence identity while possessing a common fold and active site. Extensive structural and biochemical data demonstrate the direct involvement of two metal ions in catalysis, and show that lithium exerts its inhibitory action by blocking the products at the active site. By exploiting the different inhibitory properties of magnesium and calcium, we have been able to solve the X-ray structures of the Li(+)-sensitive/Mg(2+)-dependent 3'-phosphoadenosine-5'-phosphatase in complex with its substrate and with its products. The structural comparison of these complexes provides a 3D picture of the different stages of the catalytic cycle. This gives new insights into the understanding of the biological function of this group of enzymes and their lithium inhibition, and should assist in the design of improved inhibitors of therapeutic value.


  • Organizational Affiliation
    • Department of Biochemistry, University of Cambridge, Cambridge, UK.

Macromolecule Content 

  • Total Structure Weight: 39.79 kDa 
  • Atom Count: 2,997 
  • Modeled Residue Count: 354 
  • Deposited Residue Count: 357 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Halotolerance protein HAL2357Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: HAL2
EC: 3.1.3.7
UniProt
Find proteins for P32179 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32179 
Go to UniProtKB:  P32179
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32179
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AMP

Query on AMP



Download:Ideal Coordinates CCD File
F [auth A]ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
E [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
BME

Query on BME



Download:Ideal Coordinates CCD File
G [auth A]BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
MG

Query on MG



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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.203 (Depositor), 0.208 (DCC) 
  • R-Value Work:  0.156 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 0.158 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.693α = 90
b = 45.075β = 110.96
c = 71.794γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
CCP4data 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: 2001-11-07
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description