7E36 | pdb_00007e36

A [6+4]-cycloaddition adduct is the biosynthetic intermediate in streptoseomycin biosynthesis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.205 (Depositor), 0.206 (DCC) 
  • R-Value Work: 
    0.165 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 
    0.166 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7E36

This is version 1.3 of the entry. See complete history

Literature

A [6+4]-cycloaddition adduct is the biosynthetic intermediate in streptoseomycin biosynthesis.

Wang, K.B.Wang, W.Zhang, B.Wang, X.Chen, Y.Zhu, H.J.Liang, Y.Tan, R.X.Ge, H.M.

(2021) Nat Commun 12: 2092-2092

  • DOI: https://doi.org/10.1038/s41467-021-22395-7
  • Primary Citation Related Structures: 
    7E36

  • PubMed Abstract: 

    Streptoseomycin (STM, 1) is a bacterial macrolactone that has a unique 5/14/10/6/6-pentacyclic ring with an ether bridge. We have previously identified the biosynthetic gene cluster for 1 and characterized StmD as [6 + 4]- and [4 + 2]-bispericyclase that catalyze a reaction leading to both 6/10/6- and 10/6/6-tricyclic adducts (6 and 7). The remaining steps, especially how to install and stabilize the required 10/6/6-tricyclic core for downstream modifications, remain unknown. In this work, we have identified three oxidoreductases that fix the required 10/6/6-tryciclic core. A pair of flavin-dependent oxidoreductases, StmO1 and StmO2, catalyze the direct hydroxylation at [6 + 4]-adduct (6). Subsequently, a spontaneous [3,3]-Cope rearrangement and an enol-ketone tautomerization result in the formation of 10/6/6-tricyclic intermediate 12b, which can be further converted to a stable 10/6/6-tricyclic alcohol 11 through a ketoreduction by StmK. Crystal structure of the heterodimeric complex NtfO1-NtfO2, homologues of StmO1-StmO2 with equivalent function, reveals protein-protein interactions. Our results demonstrate that the [6 + 4]-adduct instead of [4 + 2]-adduct is the bona fide biosynthetic intermediate.


  • Organizational Affiliation
    • State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, China.

Macromolecule Content 

  • Total Structure Weight: 81.58 kDa 
  • Atom Count: 5,989 
  • Modeled Residue Count: 714 
  • Deposited Residue Count: 745 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Alkanesulfonate monooxygenase SsuD/methylene tetrahydromethanopterin reductase-like flavin-dependent oxidoreductase (Luciferase family)324Nocardia tenerifensisMutation(s): 0 
Gene Names: DFR70_1157
UniProt
Find proteins for A0A318JWT9 (Nocardia tenerifensis)
Explore A0A318JWT9 
Go to UniProtKB:  A0A318JWT9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A318JWT9
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
FMN-dependent oxidoreductase (Nitrilotriacetate monooxygenase family)421Nocardia tenerifensisMutation(s): 0 
Gene Names: DFR70_1156
UniProt
Find proteins for A0A318JQQ2 (Nocardia tenerifensis)
Explore A0A318JQQ2 
Go to UniProtKB:  A0A318JQQ2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A318JQQ2
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MES

Query on MES



Download:Ideal Coordinates CCD File
L [auth B]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
TRS

Query on TRS



Download:Ideal Coordinates CCD File
N [auth B]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth A],
M [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL

Query on CL



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
O [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
K [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.205 (Depositor), 0.206 (DCC) 
  • R-Value Work:  0.165 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 0.166 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.28α = 90
b = 104.99β = 95.95
c = 75.95γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China21572100
National Natural Science Foundation of China (NSFC)China81522042
National Natural Science Foundation of China (NSFC)China81773591
National Natural Science Foundation of China (NSFC)China81421091
National Natural Science Foundation of China (NSFC)China81500059
National Natural Science Foundation of China (NSFC)China81673333
National Natural Science Foundation of China (NSFC)China21672101
National Natural Science Foundation of China (NSFC)China21661140001

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-10
    Type: Initial release
  • Version 1.1: 2021-03-17
    Changes: Database references, Structure summary
  • Version 1.2: 2021-04-21
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Database references, Refinement description