1O7D

The structure of the bovine lysosomal a-mannosidase suggests a novel mechanism for low pH activation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.257 

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Literature

The Structure of Bovine Lysosomal Alpha-Mannosidase Suggests a Novel Mechanism for Low-Ph Activation

Heikinheimo, P.Helland, R.Leiros, H.S.Leiros, I.Karlsen, S.Evjen, G.Ravelli, R.Schoehn, G.Ruigrok, R.Tollersrud, O.-K.Mcsweeney, S.Hough, E.

(2003) J Mol Biol 327: 631

  • DOI: https://doi.org/10.1016/s0022-2836(03)00172-4
  • Primary Citation of Related Structures:  
    1O7D

  • PubMed Abstract: 

    Lysosomal alpha-mannosidase (LAM: EC 3.2.1.24) belongs to the sequence-based glycoside hydrolase family 38 (GH38). Two other mammalian GH38 members, Golgi alpha-mannosidase II (GIIAM) and cytosolic alpha-mannosidase, are expressed in all tissues. In humans, cattle, cat and guinea pig, lack of lysosomal alpha-mannosidase activity causes the autosomal recessive disease alpha-mannosidosis. Here, we describe the three-dimensional structure of bovine lysosomal alpha-mannosidase (bLAM) at 2.7A resolution and confirm the solution state dimer by electron microscopy. We present the first structure of a mammalian GH38 enzyme that offers indications for the signal areas for mannose phosphorylation, suggests a previously undetected mechanism of low-pH activation and provides a template for further biochemical studies of the family 38 glycoside hydrolases as well as lysosomal transport. Furthermore, it provides a basis for understanding the human form of alpha-mannosidosis at the atomic level. The atomic coordinates and structure factors have been deposited in the Protein Data Bank (accession codes 1o7d and r1o7dsf).


  • Organizational Affiliation

    Institutt for Kjemi, Universitetet i Tromsø, N-9037, Tromsø, Norway.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysosomal alpha-mannosidase298Bos taurusMutation(s): 0 
EC: 3.2.1.24
UniProt
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UniProt GroupQ29451
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Lysosomal alpha-mannosidase84Bos taurusMutation(s): 0 
EC: 3.2.1.24
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Lysosomal alpha-mannosidase159Bos taurusMutation(s): 0 
EC: 3.2.1.24
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Lysosomal alpha-mannosidase282Bos taurusMutation(s): 0 
EC: 3.2.1.24
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Lysosomal alpha-mannosidase126Bos taurusMutation(s): 0 
EC: 3.2.1.24
UniProt
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Oligosaccharides

Help

Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F
9N-Glycosylation
Glycosylation Resources
GlyTouCan:  G83161QT
GlyCosmos:  G83161QT
GlyGen:  G83161QT
Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, H, I
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.257 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.88α = 90
b = 117.88β = 90
c = 582.04γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2003-03-20
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2018-07-11
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Source and taxonomy, Structure summary
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 3.1: 2023-12-13
    Changes: Data collection, Database references, Refinement description, Structure summary