1IVY

PHYSIOLOGICAL DIMER HPP PRECURSOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 

wwPDB Validation 3D Report Full Report



Literature

Three-dimensional structure of the human 'protective protein': structure of the precursor form suggests a complex activation mechanism.

Rudenko, G.Bonten, E.d'Azzo, A.Hol, W.G.

(1995) Structure 3: 1249-1259

  • DOI: 10.1016/s0969-2126(01)00260-x
  • Primary Citation of Related Structures:  
    1IVY

  • PubMed Abstract: 
  • The human 'protective protein' (HPP) forms a multi-enzyme complex with beta-galactosidase and neuraminidase in the lysosomes, protecting these two glycosidases from degradation. In humans, deficiency of HPP leads to the lysosomal storage disease gala ...

    The human 'protective protein' (HPP) forms a multi-enzyme complex with beta-galactosidase and neuraminidase in the lysosomes, protecting these two glycosidases from degradation. In humans, deficiency of HPP leads to the lysosomal storage disease galactosialidosis. Proteolytic cleavage of the precursor form of HPP involves removal of a 2 kDa excision peptide and results in a carboxypeptidase activity. The physiological relevance of this activity is, as yet, unknown.


    Related Citations: 
    • Structure Determination of the Human Protective Protein: Twofold Averaging Reveals the Three-Dimensional Structure of a Domain which Was Entirely Absent in the Initial Model
      Rudenko, G., Bonten, E., D'Azzo, A., Hol, W.G.J.
      (1996) Acta Crystallogr D Biol Crystallogr 52: 923
    • Expression of Cdna Encoding the Human 'Protective Protein' Associated with Lysosomal Beta-Galactosidase and Neuraminidase: Homology to Yeast Proteases
      Galjart, N.J., Gillemans, N., Harris, A., Van Der Horst, G.T., Verheijen, F.W., Galjaard, H., D'Azzo, A.
      (1988) Cell 54: 755

    Organizational Affiliation

    Department of Biological Structure, School of Medicine, University of Washington, Seattle 98195-7742, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HUMAN PROTECTIVE PROTEINAB452Homo sapiensMutation(s): 0 
Gene Names: HUPP54CTSAPPGB
EC: 3.4.16.5
Find proteins for P10619 (Homo sapiens)
Explore P10619 
Go to UniProtKB:  P10619
NIH Common Fund Data Resources
PHAROS  P10619
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2 N-Glycosylation
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
2 N-Glycosylation
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, B
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.04α = 90
b = 148.11β = 90
c = 80.97γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
ROTAVATAdata reduction
Agrovatadata reduction
TRUNCATEdata reduction
X-PLORmodel building
X-PLORrefinement
CCP4data scaling
ROTAVATAdata scaling
TRUNCATEdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-04-21
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Refinement description, Structure summary