Biological Assembly 1  

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - ABCDE 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 111685.16 
• Atom Count: 7346 
• Residue Count: 949 
• Unique protein chains: 5

1O7D

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

• DOI: 10.2210/pdb1O7D/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus


• Deposited: 2002-10-30 Released: 2003-03-20 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.289 
• R-Value Work: 0.257 

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: 12634058 


• 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).

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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




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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Lysosomal alpha-mannosidase	A	298	Bos taurus	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
Lysosomal alpha-mannosidase	B	84	Bos taurus	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
Lysosomal alpha-mannosidase	C	159	Bos taurus	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
Lysosomal alpha-mannosidase	D	282	Bos taurus	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
Lysosomal alpha-mannosidase	E	126	Bos taurus	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
SO4	A, E	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MAN	C	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
BMA	C	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
NAG	A, C, D	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
TRS	A	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL TRIS BUFFER C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

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 = 117.880	α = 90.00
b = 117.880	β = 90.00
c = 582.040	γ = 120.00

Software Package:

Software Name	Purpose
AMoRE	phasing
DENZO	data reduction
CNS	refinement
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-10-30 
• Released Date: 2003-03-20 
• Deposition Author(s): 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.

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