7XQA

Orf1-glycine complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.192 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

N-Formimidoylation/-iminoacetylation modification in aminoglycosides requires FAD-dependent and ligand-protein NOS bridge dual chemistry.

Wang, Y.L.Chang, C.Y.Hsu, N.S.Lo, I.W.Lin, K.H.Chen, C.L.Chang, C.F.Wang, Z.C.Ogasawara, Y.Dairi, T.Maruyama, C.Hamano, Y.Li, T.L.

(2023) Nat Commun 14: 2528-2528

  • DOI: https://doi.org/10.1038/s41467-023-38218-w
  • Primary Citation of Related Structures:  
    7XQA, 7XX0, 7XXC, 7XXD, 7XXM, 7XXP, 7XXR, 7XYE, 7XYL, 7Y0X, 7YPU, 7YPV, 8GRI

  • PubMed Abstract: 

    Oxidized cysteine residues are highly reactive and can form functional covalent conjugates, of which the allosteric redox switch formed by the lysine-cysteine NOS bridge is an example. Here, we report a noncanonical FAD-dependent enzyme Orf1 that adds a glycine-derived N-formimidoyl group to glycinothricin to form the antibiotic BD-12. X-ray crystallography was used to investigate this complex enzymatic process, which showed Orf1 has two substrate-binding sites that sit 13.5 Å apart unlike canonical FAD-dependent oxidoreductases. One site could accommodate glycine and the other glycinothricin or glycylthricin. Moreover, an intermediate-enzyme adduct with a NOS-covalent linkage was observed in the later site, where it acts as a two-scissile-bond linkage facilitating nucleophilic addition and cofactor-free decarboxylation. The chain length of nucleophilic acceptors vies with bond cleavage sites at either N-O or O-S accounting for N-formimidoylation or N-iminoacetylation. The resultant product is no longer sensitive to aminoglycoside-modifying enzymes, a strategy that antibiotic-producing species employ to counter drug resistance in competing species.


  • Organizational Affiliation

    Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-formimidoyl fortimicin A synthase
A, B, C, D, E
A, B, C, D, E, F, G
512Streptomyces luteocolorMutation(s): 0 
UniProt
Find proteins for A0A125SZC1 (Streptomyces luteocolor)
Explore A0A125SZC1 
Go to UniProtKB:  A0A125SZC1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A125SZC1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
N-formimidoyl fortimicin A synthase512Streptomyces luteocolorMutation(s): 0 
UniProt
Find proteins for A0A125SZC1 (Streptomyces luteocolor)
Explore A0A125SZC1 
Go to UniProtKB:  A0A125SZC1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A125SZC1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
I [auth A]
L [auth B]
N [auth C]
P [auth D]
R [auth E]
I [auth A],
L [auth B],
N [auth C],
P [auth D],
R [auth E],
T [auth F],
W [auth G],
Y [auth H]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
GLY
Query on GLY

Download Ideal Coordinates CCD File 
J [auth A]
K [auth A]
M [auth B]
O [auth C]
Q [auth D]
J [auth A],
K [auth A],
M [auth B],
O [auth C],
Q [auth D],
S [auth E],
U [auth F],
V [auth F],
X [auth G],
Z [auth H]
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
GQI
Query on GQI
H
L-PEPTIDE LINKINGC5 H8 N2 O5 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.192 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.386α = 89.853
b = 107.803β = 89.989
c = 134.754γ = 83.575
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentTaiwan--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-31
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-05-08
    Changes: Database references