8ILA

Crystal structure of LmbT from Streptomyces lincolnensis NRRL ISP-5355 in complex with substrates


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Structural Basis of Low-Molecular-Weight Thiol Glycosylation in Lincomycin A Biosynthesis.

Dai, Y.Cheng, Y.Ding, W.Qiao, H.Zhang, D.Zhong, G.Xia, M.Tao, J.Sun, P.Fang, P.Liu, W.

(2023) ACS Chem Biol 18: 1271-1277

  • DOI: https://doi.org/10.1021/acschembio.3c00185
  • Primary Citation of Related Structures:  
    8IL0, 8ILA

  • PubMed Abstract: 

    The involvement of low-molecular-weight thiols in the biosynthesis of natural products is rarely reported. During lincomycin A biosynthesis, ergothioneine (EGT) is incorporated in the S -glycosylation catalyzed by LmbT. In contrast to the widely reported glycosylation of nitrogen and oxygen atoms, the glycosylation of sulfur atoms is less studied. In particular, the crystal structure of enzymes that glycosylate thiols on small molecules rather than peptides has not been reported. Here, we report the crystal structures of LmbT in apo form and in complex with GDP and EGT S -conjugated lincosamine. We found that LmbT has a characteristic glycosyltransferase type B fold, which forms a symmetric homotetramer. The substrates are bound deeply in the catalytic cleft. Consistent with the substrate structure, LmbT does not have the large peptide binding groove of the previously reported S -glycosyltransferase. Combined with site-directed mutagenesis, we propose a catalytic mechanism for the unusual EGT-mediated S -glycosylation in natural product biosynthesis.


  • Organizational Affiliation

    Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou 450052, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GlycosyltransferaseA,
B [auth C],
C [auth B],
D
457Streptomyces lincolnensisMutation(s): 0 
Gene Names: GJU35_01490
UniProt
Find proteins for A9Y8T1 (Streptomyces lincolnensis)
Explore A9Y8T1 
Go to UniProtKB:  A9Y8T1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9Y8T1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download Ideal Coordinates CCD File 
E [auth A],
G [auth C],
I [auth B],
K [auth D]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
Q3L (Subject of Investigation/LOI)
Query on Q3L

Download Ideal Coordinates CCD File 
F [auth A],
H [auth C],
J [auth B],
L [auth D]
(2~{S})-3-[2-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-[(1~{R},2~{R})-1-azanyl-2-oxidanyl-propyl]-3,4,5-tris(oxidanyl)oxan-2-yl]sulfanyl-1~{H}-imidazol-5-yl]-2-(trimethyl-$l^{4}-azanyl)propanoic acid
C17 H31 N4 O7 S
MZDFOQLXMBUKGA-HNXDCMGUSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.382α = 90
b = 137.739β = 90
c = 146.101γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China22277132
National Natural Science Foundation of China (NSFC)China21977107

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-20
    Type: Initial release