3QSP

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 non-productive substrate complex with alpha-1,6-mannobiose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.160 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


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

  • DOI: 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative uncharacterized proteinA, B426Streptococcus pneumoniaeMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2URZ6
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranoseC, D 2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G71124KE
GlyCosmos:  G71124KE
GlyGen:  G71124KE
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth B],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth B],
J [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.160 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.51α = 90
b = 159.04β = 106.74
c = 60.13γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
MOLREPphasing
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-03-07
    Changes: Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary