4RIF | pdb_00004rif

Landomycin Glycosyltransferase LanGT2, carbasugar substrate complex

• PDB DOI: https://doi.org/10.2210/pdb4RIF/pdb

• Classification: TRANSFERASE
• Organism(s): Streptomyces cyanogenus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-10-06 Released: 2015-01-28 
• Deposition Author(s): Tam, H.K., Gerhardt, S., Breit, B., Bechthold, A., Einsle, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.198 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

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

• PubMed: 25581707 
• DOI: https://doi.org/10.1002/anie.201409792
• Primary Citation 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.

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 81.87 kDa 
• Atom Count: 5,884 
• Modeled Residue Count: 749 
• Deposited Residue Count: 758 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyl transferase homolog	A, B	379	Streptomyces cyanogenus	Mutation(s): 0  Gene Names: lanGT2
UniProt
Find proteins for Q9ZGC0 (Streptomyces cyanogenus) Explore Q9ZGC0  Go to UniProtKB:  Q9ZGC0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3R2	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 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.97	α = 87.3
b = 59.71	β = 73.97
c = 71.99	γ = 64.92

Software Package:

Software Name	Purpose
MOLREP	phasing
BUSTER	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-28 
Deposition Author(s): Tam, H.K., Gerhardt, S., Breit, B., Bechthold, A., Einsle, O.

Revision History  

• 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