Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 99.27 kDa 
• Atom Count: 7,920 
• Modelled Residue Count: 852 
• Deposited Residue Count: 852 
• Unique protein chains: 1

 3QPF

Analysis of a New Family of Widely Distributed Metal-independent alpha-Mannosidases Provides Unique Insight into the Processing of N-linked Glycans, Streptococcus pneumoniae SP_2144 apo-structure

• PDB DOI:  https://doi.org/10.2210/pdb3QPF/pdb

• Classification: HYDROLASE
• Organism(s): Streptococcus pneumoniae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-02-12 Released: 2011-03-09 
• Deposition Author(s): Gregg, K.J., Zandberg, W.F., Hehemann, J.-H., Whitworth, G.E., Deng, L.E., Vocadlo, D.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.217 
• R-Value Work: 0.156 
• R-Value Observed: 0.159 

Literature

Analysis of a New Family of Widely Distributed Metal-independent {alpha}-Mannosidases Provides Unique Insight into the Processing of N-Linked Glycans.

Gregg, K.J., Zandberg, W.F., Hehemann, J.H., Whitworth, G.E., Deng, L., Vocadlo, D.J., Boraston, A.B.

(2011) J Biol Chem 286: 15586-15596

• PubMed: 21388958 
• DOI: https://doi.org/10.1074/jbc.M111.223172
• Primary Citation of Related Structures:  
  3QPF, 3QRY, 3QSP, 3QT3, 3QT9


• PubMed Abstract: 
  

The modification of N-glycans by α-mannosidases is a process that is relevant to a large number of biologically important processes, including infection by microbial pathogens and colonization by microbial symbionts. At present, the described mannosidases specific for α1,6-mannose linkages are very limited in number. Through structural and functional analysis of two sequence-related enzymes, one from Streptococcus pneumoniae (SpGH125) and one from Clostridium perfringens (CpGH125), a new glycoside hydrolase family, GH125, is identified and characterized. Analysis of SpGH125 and CpGH125 reveal them to have exo-α1,6-mannosidase activity consistent with specificity for N-linked glycans having their α1,3-mannose branches removed. The x-ray crystal structures of SpGH125 and CpGH125 obtained in apo-, inhibitor-bound, and substrate-bound forms provide both mechanistic and molecular insight into how these proteins, which adopt an (α/α)(6)-fold, recognize and hydrolyze the α1,6-mannosidic bond by an inverting, metal-independent catalytic mechanism. A phylogenetic analysis of GH125 proteins reveals this to be a relatively large and widespread family found frequently in bacterial pathogens, bacterial human gut symbionts, and a variety of fungi. Based on these studies we predict this family of enzymes will primarily comprise such exo-α1,6-mannosidases.

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Organizational Affiliation: 

Department of Biochemistry and Microbiology, University of Victoria, P.O. Box 3055 STN CSC, Victoria, British Columbia V8W 3P6, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A, B	426	Streptococcus pneumoniae	Mutation(s): 0  Gene Names: SP_2144
UniProt
Find proteins for A0A0H2URZ6 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore A0A0H2URZ6  Go to UniProtKB:  A0A0H2URZ6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.217 
• R-Value Work: 0.156 
• R-Value Observed: 0.159 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.04	α = 90
b = 101.61	β = 90
c = 158.89	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-09 
Deposition Author(s): Gregg, K.J., Zandberg, W.F., Hehemann, J.-H., Whitworth, G.E., Deng, L.E., Vocadlo, D.J.

Revision History  

• Version 1.0: 2011-03-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description