4RIF

Landomycin Glycosyltransferase LanGT2, carbasugar substrate complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structural Characterization of O- and C-Glycosylating Variants of the Landomycin Glycosyltransferase LanGT2.

Tam, H.K.Harle, J.Gerhardt, S.Rohr, J.Wang, G.Thorson, J.S.Bigot, A.Lutterbeck, M.Seiche, W.Breit, B.Bechthold, A.Einsle, O.

(2015) Angew Chem Int Ed Engl 54: 2811-2815

  • DOI: https://doi.org/10.1002/anie.201409792
  • Primary Citation of Related Structures:  
    4RIE, 4RIF, 4RIG, 4RIH, 4RII

  • PubMed Abstract: 

    The structures of the O-glycosyltransferase LanGT2 and the engineered, C-C bond-forming variant LanGT2S8Ac show how the replacement of a single loop can change the functionality of the enzyme. Crystal structures of the enzymes in complex with a nonhydrolyzable nucleotide-sugar analogue revealed that there is a conformational transition to create the binding sites for the aglycon substrate. This induced-fit transition was explored by molecular docking experiments with various aglycon substrates.


  • Organizational Affiliation

    Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg (Germany).


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycosyl transferase homolog
A, B
379Streptomyces cyanogenusMutation(s): 0 
Gene Names: lanGT2
UniProt
Find proteins for Q9ZGC0 (Streptomyces cyanogenus)
Explore Q9ZGC0 
Go to UniProtKB:  Q9ZGC0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ZGC0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3R2
Query on 3R2

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
2'-deoxy-5'-O-[(R)-{[(R)-{[(1S,3R,4R,5S)-3,4-dihydroxy-5-methylcyclohexyl]oxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-3,4-dihydrothymidine
C17 H28 N2 O13 P2
CWVOKCJHBPKJQP-PVMIAKCWSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.97α = 87.3
b = 59.71β = 73.97
c = 71.99γ = 64.92
Software Package:
Software NamePurpose
MOLREPphasing
BUSTERrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-28
    Type: Initial release
  • Version 1.1: 2015-03-04
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-04-03
    Changes: Refinement description