5F5N | pdb_00005f5n

The structure of monooxygenase KstA11 in complex with NAD and its substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 
    0.166 (Depositor), 0.168 (DCC) 
  • R-Value Work: 
    0.143 (Depositor), 0.148 (DCC) 
  • R-Value Observed: 
    0.145 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Hydroxyl regioisomerization of anthracycline catalyzed by a four-enzyme cascade

Zhang, Z.Gong, Y.-K.Zhou, Q.Hu, Y.Ma, H.-M.Chen, Y.-S.Igarashi, Y.Pan, L.Tang, G.-L.

(2017) Proc Natl Acad Sci U S A 114: 1554-1559

  • DOI: https://doi.org/10.1073/pnas.1610097114
  • Primary Citation Related Structures: 
    5F5L, 5F5N

  • PubMed Abstract: 

    Ranking among the most effective anticancer drugs, anthracyclines represent an important family of aromatic polyketides generated by type II polyketide synthases (PKSs). After formation of polyketide cores, the post-PKS tailoring modifications endow the scaffold with various structural diversities and biological activities. Here we demonstrate an unprecedented four-enzyme-participated hydroxyl regioisomerization process involved in the biosynthesis of kosinostatin. First, KstA15 and KstA16 function together to catalyze a cryptic hydroxylation of the 4-hydroxyl-anthraquinone core, yielding a 1,4-dihydroxyl product, which undergoes a chemically challenging asymmetric reduction-dearomatization subsequently acted by KstA11; then, KstA10 catalyzes a region-specific reduction concomitant with dehydration to afford the 1-hydroxyl anthraquinone. Remarkably, the shunt product identifications of both hydroxylation and reduction-dehydration reactions, the crystal structure of KstA11 with bound substrate and cofactor, and isotope incorporation experiments reveal mechanistic insights into the redox dearomatization and rearomatization steps. These findings provide a distinguished tailoring paradigm for type II PKS engineering.


  • Organizational Affiliation
    • State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China.

Macromolecule Content 

  • Total Structure Weight: 64.98 kDa 
  • Atom Count: 5,747 
  • Modeled Residue Count: 578 
  • Deposited Residue Count: 578 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Monooxygenase
A, B
289Micromonospora okiiMutation(s): 0 
UniProt
Find proteins for A0A023GUL3 (Micromonospora okii)
Explore A0A023GUL3 
Go to UniProtKB:  A0A023GUL3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A023GUL3
Sequence Annotations
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Reference Sequence

Small Molecules

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

Query on NAD



Download:Ideal Coordinates CCD File
C [auth A],
J [auth B]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
5VD

Query on 5VD



Download:Ideal Coordinates CCD File
D [auth A],
K [auth B]
methyl (1~{R},2~{R},4~{S})-2-methyl-2,4,5,7,10-pentakis(oxidanyl)-6,11-bis(oxidanylidene)-3,4-dihydro-1~{H}-tetracene-1-carboxylate
C21 H18 O9
ZBSRQGXAWDQXFX-SBOBAANCSA-N
EPE

Query on EPE



Download:Ideal Coordinates CCD File
Q [auth B],
R [auth B]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG

Query on MG



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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free:  0.166 (Depositor), 0.168 (DCC) 
  • R-Value Work:  0.143 (Depositor), 0.148 (DCC) 
  • R-Value Observed: 0.145 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.476α = 90
b = 66.025β = 90
c = 176.319γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data processing
Cootmodel building
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Basic Research Program of ChinaChina2013CB836900
a Shanghai Rising Star Scholar awardChina13QA1404300

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-21
    Type: Initial release
  • Version 1.1: 2017-02-08
    Changes: Database references
  • Version 1.2: 2017-03-01
    Changes: Database references
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Refinement description