5MR6 | pdb_00005mr6

XiaF from Streptomyces sp. in complex with FADH2 and Glycerol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.229 (Depositor), 0.186 (DCC) 
  • R-Value Work: 
    0.198 (Depositor) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Cryptic indole hydroxylation by a non-canonical terpenoid cyclase parallels bacterial xenobiotic detoxification.

Kugel, S.Baunach, M.Baer, P.Ishida-Ito, M.Sundaram, S.Xu, Z.Groll, M.Hertweck, C.

(2017) Nat Commun 8: 15804-15804

  • DOI: https://doi.org/10.1038/ncomms15804
  • Primary Citation Related Structures: 
    5LVU, 5LVW, 5MR6

  • PubMed Abstract: 

    Terpenoid natural products comprise a wide range of molecular architectures that typically result from C-C bond formations catalysed by classical type I/II terpene cyclases. However, the molecular diversity of biologically active terpenoids is substantially increased by fully unrelated, non-canonical terpenoid cyclases. Their evolutionary origin has remained enigmatic. Here we report the in vitro reconstitution of an unusual flavin-dependent bacterial indoloterpenoid cyclase, XiaF, together with a designated flavoenzyme-reductase (XiaP) that mediates a key step in xiamycin biosynthesis. The crystal structure of XiaF with bound FADH 2 (at 2.4 Å resolution) and phylogenetic analyses reveal that XiaF is, surprisingly, most closely related to xenobiotic-degrading enzymes. Biotransformation assays show that XiaF is a designated indole hydroxylase that can be used for the production of indigo and indirubin. We unveil a cryptic hydroxylation step that sets the basis for terpenoid cyclization and suggest that the cyclase has evolved from xenobiotics detoxification enzymes.


  • Organizational Affiliation
    • Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany.

Macromolecule Content 

  • Total Structure Weight: 1,082.82 kDa 
  • Atom Count: 77,543 
  • Modeled Residue Count: 9,504 
  • Deposited Residue Count: 9,912 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
XiaF protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
413Streptomyces sp.Mutation(s): 0 
Gene Names: xiaF
UniProt
Find proteins for I7IIA9 (Streptomyces sp. HKI0576)
Explore I7IIA9 
Go to UniProtKB:  I7IIA9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI7IIA9
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD

Query on FAD



Download:Ideal Coordinates CCD File
AA [auth B]
AB [auth O]
CA [auth C]
CB [auth P]
EA [auth D]
AA [auth B],
AB [auth O],
CA [auth C],
CB [auth P],
EA [auth D],
EB [auth Q],
GA [auth E],
GB [auth R],
IA [auth F],
IB [auth S],
KA [auth G],
KB [auth T],
MA [auth H],
MB [auth U],
OA [auth I],
OB [auth V],
QA [auth J],
QB [auth W],
SA [auth K],
SB [auth X],
UA [auth L],
WA [auth M],
Y [auth A],
YA [auth N]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
BA [auth B]
BB [auth O]
DA [auth C]
DB [auth P]
FA [auth D]
BA [auth B],
BB [auth O],
DA [auth C],
DB [auth P],
FA [auth D],
FB [auth Q],
HA [auth E],
HB [auth R],
JA [auth F],
JB [auth S],
LA [auth G],
LB [auth T],
NA [auth H],
NB [auth U],
PA [auth I],
PB [auth V],
RA [auth J],
RB [auth W],
TA [auth K],
TB [auth X],
VA [auth L],
XA [auth M],
Z [auth A],
ZA [auth N]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.229 (Depositor), 0.186 (DCC) 
  • R-Value Work:  0.198 (Depositor) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 166.93α = 89.96
b = 167.09β = 90.18
c = 200.94γ = 119.82
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB749

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-07-05
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Author supporting evidence, Data collection, Database references, Refinement description