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: 2.7 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.257 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history. 

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


  • 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 ...

    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).

    Related Citations: 
    • Purification of Bovine Lysosomal A-Mannosidase, Characterization of its Gene and Determination of Two Mutations that Cause A- Mannosidosis
      Tollersrud, O.-K.,Berg, T.,Healy, P.,Evjen, G.,Ramachandran, U.
      (1997) Eur.J.Biochem. 246: 410

    Organizational Affiliation: 

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysosomal alpha-mannosidase
A
298Bos taurusMutation(s): 0 
Gene Names: MAN2B1 (MANB)
EC: 3.2.1.24
Find proteins for Q29451 (Bos taurus)
Go to Gene View: MAN2B1
Go to UniProtKB:  Q29451
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Lysosomal alpha-mannosidase
B
84Bos taurusMutation(s): 0 
Gene Names: MAN2B1 (MANB)
EC: 3.2.1.24
Find proteins for Q29451 (Bos taurus)
Go to Gene View: MAN2B1
Go to UniProtKB:  Q29451
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Lysosomal alpha-mannosidase
C
159Bos taurusMutation(s): 0 
Gene Names: MAN2B1 (MANB)
EC: 3.2.1.24
Find proteins for Q29451 (Bos taurus)
Go to Gene View: MAN2B1
Go to UniProtKB:  Q29451
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Lysosomal alpha-mannosidase
D
282Bos taurusMutation(s): 0 
Gene Names: MAN2B1 (MANB)
EC: 3.2.1.24
Find proteins for Q29451 (Bos taurus)
Go to Gene View: MAN2B1
Go to UniProtKB:  Q29451
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Lysosomal alpha-mannosidase
E
126Bos taurusMutation(s): 0 
Gene Names: MAN2B1 (MANB)
EC: 3.2.1.24
Find proteins for Q29451 (Bos taurus)
Go to Gene View: MAN2B1
Go to UniProtKB:  Q29451
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4
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Download CCD File 
A, E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MAN
Query on MAN
Download SDF File 
Download CCD File 
C
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA
Download SDF File 
Download CCD File 
C
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG
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Download CCD File 
A, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
TRS
Query on TRS
Download SDF File 
Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.257 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 117.880α = 90.00
b = 117.880β = 90.00
c = 582.040γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
CNSrefinement
AMoREphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-03-20
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 2.0: 2018-07-11
    Type: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Source and taxonomy, Structure summary