4BKM | pdb_00004bkm

Crystal structure of the murine AUM (phosphoglycolate phosphatase) capping domain as a fusion protein with the catalytic core domain of murine chronophin (pyridoxal phosphate phosphatase)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 
    0.256 (Depositor) 
  • R-Value Work: 
    0.198 (Depositor) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.2 of the entry. See complete history

Literature

Evolutionary and Structural Analyses of the Mammalian Haloacid Dehalogenase-Type Phosphatases Aum and Chronophin Provide Insight Into the Basis of Their Different Substrate Specificities.

Seifried, A.Knobloch, G.Duraphe, P.S.Segerer, G.Manhard, J.Schindelin, H.Schultz, J.Gohla, A.

(2014) J Biological Chem 289: 3416

  • DOI: https://doi.org/10.1074/jbc.M113.503359
  • Primary Citation Related Structures: 
    4BKM

  • PubMed Abstract: 

    Mammalian haloacid dehalogenase (HAD)-type phosphatases are an emerging family of phosphatases with important functions in physiology and disease, yet little is known about the basis of their substrate specificity. Here, we characterize a previously unexplored HAD family member (gene annotation, phosphoglycolate phosphatase), which we termed AUM, for aspartate-based, ubiquitous, Mg(2+)-dependent phosphatase. AUM is a tyrosine-specific paralog of the serine/threonine-specific protein and pyridoxal 5'-phosphate-directed HAD phosphatase chronophin. Comparative evolutionary and biochemical analyses reveal that a single, differently conserved residue in the cap domain of either AUM or chronophin is crucial for phosphatase specificity. We have solved the x-ray crystal structure of the AUM cap fused to the catalytic core of chronophin to 2.65 Å resolution and present a detailed view of the catalytic clefts of AUM and chronophin that explains their substrate preferences. Our findings identify a small number of cap domain residues that encode the different substrate specificities of AUM and chronophin.


  • Organizational Affiliation
    • From the Institute for Pharmacology and Toxicology.

Macromolecule Content 

  • Total Structure Weight: 134.07 kDa 
  • Atom Count: 9,450 
  • Modeled Residue Count: 1,216 
  • Deposited Residue Count: 1,236 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PYRIDOXAL PHOSPHATE PHOSPHATASE, PHOSPHOGLYCOLATE PHOSPHATASE, PYRIDOXAL PHOSPHATE PHOSPHATASE
A, B, C, D
309Mus musculusMutation(s): 0 
EC: 3.1.3.3 (PDB Primary Data), 3.1.3.74 (PDB Primary Data), 3.1.3.18 (PDB Primary Data), 3.1.3.21 (UniProt), 3.1.3.16 (UniProt), 3.1.3.48 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P60487 (Mus musculus)
Explore P60487 
Go to UniProtKB:  P60487
IMPC:  MGI:1919282
Find proteins for Q8CHP8 (Mus musculus)
Explore Q8CHP8 
Go to UniProtKB:  Q8CHP8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP60487Q8CHP8
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free:  0.256 (Depositor) 
  • R-Value Work:  0.198 (Depositor) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.5α = 90
b = 91.96β = 90.2
c = 105.92γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-25
    Type: Initial release
  • Version 1.1: 2014-02-19
    Changes: Database references
  • Version 1.2: 2017-03-15
    Changes: Source and taxonomy
  • Version 2.0: 2017-06-28
    Changes: Atomic model, Data collection
  • Version 2.1: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 2.2: 2024-10-09
    Changes: Structure summary