4CN1 | pdb_00004cn1

GlgE isoform 1 from Streptomyces coelicolor D394A mutant with maltose- 1-phosphate bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 
    0.215 (Depositor), 0.221 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4CN1

This is version 2.1 of the entry. See complete history

Literature

Structural Insight Into How Streptomyces Coelicolor Maltosyl Transferase Glge Binds Alpha-Maltose 1-Phosphate and Forms a Maltosyl-Enzyme Intermediate.

Syson, K.Stevenson, C.E.M.Rashid, A.M.Saalbach, G.Tang, M.Tuukkanen, A.Svergun, D.I.Withers, S.G.Lawson, D.M.Bornemann, S.

(2014) Biochemistry 53: 2494

  • DOI: https://doi.org/10.1021/bi500183c
  • Primary Citation Related Structures: 
    4CN1, 4CN4, 4CN6

  • PubMed Abstract: 

    GlgE (EC 2.4.99.16) is an α-maltose 1-phosphate:(1→4)-α-d-glucan 4-α-d-maltosyltransferase of the CAZy glycoside hydrolase 13_3 family. It is the defining enzyme of a bacterial α-glucan biosynthetic pathway and is a genetically validated anti-tuberculosis target. It catalyzes the α-retaining transfer of maltosyl units from α-maltose 1-phosphate to maltooligosaccharides and is predicted to use a double-displacement mechanism. Evidence of this mechanism was obtained using a combination of site-directed mutagenesis of Streptomyces coelicolor GlgE isoform I, substrate analogues, protein crystallography, and mass spectrometry. The X-ray structures of α-maltose 1-phosphate bound to a D394A mutein and a β-2-deoxy-2-fluoromaltosyl-enzyme intermediate with a E423A mutein were determined. There are few examples of CAZy glycoside hydrolase family 13 members that have had their glycosyl-enzyme intermediate structures determined, and none before now have been obtained with a 2-deoxy-2-fluoro substrate analogue. The covalent modification of Asp394 was confirmed using mass spectrometry. A similar modification of wild-type GlgE proteins from S. coelicolor and Mycobacterium tuberculosis was also observed. Small-angle X-ray scattering of the M. tuberculosis enzyme revealed a homodimeric assembly similar to that of the S. coelicolor enzyme but with slightly differently oriented monomers. The deeper understanding of the structure-function relationships of S. coelicolor GlgE will aid the development of inhibitors of the M. tuberculosis enzyme.


  • Organizational Affiliation
    • Department of Biological Chemistry, John Innes Centre, Norwich Research Park , Norwich NR4 7UH, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 155.89 kDa 
  • Atom Count: 10,785 
  • Modeled Residue Count: 1,298 
  • Deposited Residue Count: 1,390 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ALPHA-1,4-GLUCAN\: MALTOSE-1-PHOSPHATE MALTOSYLTRANSFERASE 1
A, B
695Streptomyces coelicolorMutation(s): 1 
EC: 2.4.99.16
UniProt
Find proteins for Q9L1K2 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Explore Q9L1K2 
Go to UniProtKB:  Q9L1K2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9L1K2
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-glucopyranose-(1-4)-1-O-phosphono-alpha-D-glucopyranose
C, D
2N/A
Glycosylation Resources
GlyTouCan: G71823NC
GlyCosmos: G71823NC

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free:  0.215 (Depositor), 0.221 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.52α = 90
b = 113.52β = 90
c = 313.6γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-21
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
  • Version 2.1: 2023-12-20
    Changes: Data collection, Database references, Refinement description, Structure summary