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 1.2 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 taurusGene 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 taurusGene 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 taurusGene 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 taurusGene 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 taurusGene 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 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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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

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Download CCD File 
C
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NDG
Query on NDG

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C, D
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-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

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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
CNSrefinement
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



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