4JNA | pdb_00004jna

Crystal structure of the DepH complex with dimethyl-FK228

• PDB DOI: https://doi.org/10.2210/pdb4JNA/pdb

• Classification: Oxidoreductase/Oxidoreductase inhibitor
• Organism(s): Chromobacterium violaceum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-03-14 Released: 2014-03-05 
• Deposition Author(s): Li, J., Wang, C., Zhang, Z.M., Zhou, J.H., Cheng, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.222 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.155 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Starting Model: experimental

Literature

The structural basis of an NADP+-independent dithiol oxidase in FK228 biosynthesis.

Li, J., Wang, C., Zhang, Z.M., Cheng, Y.Q., Zhou, J.

(2014) Sci Rep 4: 4145-4145

• PubMed: 24553401 
• DOI: https://doi.org/10.1038/srep04145
• Primary Citation Related Structures: 
  4JN9, 4JNA


• PubMed Abstract: 
  

  The disulfide bond is unusual in natural products and critical for thermal stability, cell permeability and bioactivity. DepH from Chromobacterium violaceum No. 968 is an FAD-dependent enzyme responsible for catalyzing the disulfide bond formation of FK228, an anticancer prodrug approved for the treatment of cutaneous T-cell lymphoma. Here we report the crystal structures of DepH and DepH complexed with a substrate analogue S,S'-dimethyl FK228 at 1.82 Å and 2.00 Å, respectively. Structural and biochemical analyses revealed that DepH, in contrast to the well characterized low molecular weight thioredoxin reductases (LMW TrxRs), is an NADP(+)-independent dithiol oxidase. DepH not only lacks a conserved GGGDXAXE motif necessary for NADP(+) binding in the canonical LMW TrxRs, but also contains a 11-residue sequence which physically impedes the binding of NADP(+). These observations explain the difference between NADP(+)-independent small molecule dithiol oxidases and NADP(+)-dependent thioredoxin reductases and provide insights for understanding the catalytic mechanism of dithiol oxidases involved in natural product biosynthesis.

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Organizational Affiliation: 
• 1] State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China [2].
1] Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53201, USA [2].
State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China.
1] Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53201, USA [2] UNT System College of Pharmacy, University of North Texas Health Science Center, Forth Worth, TX 76107, USA.
1] State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China [2] Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 185 East Lake Road, Wuhan 430071, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 76.76 kDa 
• Atom Count: 5,012 
• Modeled Residue Count: 599 
• Deposited Residue Count: 690 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DepH	A, B	340	Chromobacterium violaceum	Mutation(s): 0  Gene Names: depH
UniProt
Find proteins for A4ZPY8 (Chromobacterium violaceum) Explore A4ZPY8  Go to UniProtKB:  A4ZPY8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Dimethyl FK228	C [auth H], D [auth I]	5	N/A	Mutation(s): 0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	E [auth A], J [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
PO4	I [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	N [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	G [auth A], H [auth A], L [auth B], M [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	F [auth A], K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
060	C [auth H], D [auth I]	D-PEPTIDE LINKING	C4 H9 N O2 S		--
DBU	C [auth H], D [auth I]	PEPTIDE LINKING	C4 H7 N O2		THR
DVA	C [auth H], D [auth I]	D-PEPTIDE LINKING	C5 H11 N O2		--

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001184	C [auth H], D [auth I]	Dimethyl FK228	Cyclic depsipeptide / Antibiotic

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.222 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.155 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.283	α = 90
b = 154.283	β = 90
c = 71.828	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-05 
Deposition Author(s): Li, J., Wang, C., Zhang, Z.M., Zhou, J.H., Cheng, E.

Revision History  

• Version 1.0: 2014-03-05
  Type: Initial release
  
• Version 1.1: 2014-04-09
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Advisory, Refinement description
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations