5G3S | pdb_00005g3s

The structure of the L-tryptophan oxidase VioA from Chromobacterium violaceum - Samarium derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 
    0.188 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.165 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.166 (Depositor) 

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This is version 1.4 of the entry. See complete history

Literature

Biosynthesis of Violacein: Structure and Function of L-Tryptophan Oxidase Vioa Chromobacterium Violaceum

Fuller, J.Roepke, R.Krausze, J.Rennhack, K.E.Daniel, N.P.Blankenfeldt, W.Schulz, S.Jahn, D.Moser, J.

(2016) J Biological Chem 291: 20068

  • DOI: https://doi.org/10.1074/jbc.M116.741561
  • Primary Citation Related Structures: 
    5G3S, 5G3T, 5G3U

  • PubMed Abstract: 

    Violacein is a natural purple pigment of Chromobacterium violaceum with potential medical applications as antimicrobial, antiviral, and anticancer drugs. The initial step of violacein biosynthesis is the oxidative conversion of l-tryptophan into the corresponding α-imine catalyzed by the flavoenzyme l-tryptophan oxidase (VioA). A substrate-related (3-(1H-indol-3-yl)-2-methylpropanoic acid) and a product-related (2-(1H-indol-3-ylmethyl)prop-2-enoic acid) competitive VioA inhibitor was synthesized for subsequent kinetic and x-ray crystallographic investigations. Structures of the binary VioA·FADH2 and of the ternary VioA·FADH2·2-(1H-indol-3-ylmethyl)prop-2-enoic acid complex were resolved. VioA forms a "loosely associated" homodimer as indicated by small-angle x-ray scattering experiments. VioA belongs to the glutathione reductase family 2 of FAD-dependent oxidoreductases according to the structurally conserved cofactor binding domain. The substrate-binding domain of VioA is mainly responsible for the specific recognition of l-tryptophan. Other canonical amino acids were efficiently discriminated with a minor conversion of l-phenylalanine. Furthermore, 7-aza-tryptophan, 1-methyl-tryptophan, 5-methyl-tryptophan, and 5-fluoro-tryptophan were efficient substrates of VioA. The ternary product-related VioA structure indicated involvement of protein domain movement during enzyme catalysis. Extensive structure-based mutagenesis in combination with enzyme kinetics (using l-tryptophan and substrate analogs) identified Arg(64), Lys(269), and Tyr(309) as key catalytic residues of VioA. An increased enzyme activity of protein variant H163A in the presence of l-phenylalanine indicated a functional role of His(163) in substrate binding. The combined structural and mutational analyses lead to the detailed understanding of VioA substrate recognition. Related strategies for the in vivo synthesis of novel violacein derivatives are discussed.


  • Organizational Affiliation
    • From the Institute of Microbiology and.

Macromolecule Content 

  • Total Structure Weight: 100.79 kDa 
  • Atom Count: 6,908 
  • Modeled Residue Count: 819 
  • Deposited Residue Count: 846 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
L-TRYPTOPHAN OXIDASE VIOA
A, B
423Chromobacterium violaceumMutation(s): 1 
EC: 1.4.3.23
UniProt
Find proteins for Q9S3V1 (Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / CCUG 213 / NBRC 12614 / NCIMB 9131 / NCTC 9757 / MK))
Explore Q9S3V1 
Go to UniProtKB:  Q9S3V1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9S3V1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FDA

Query on FDA



Download:Ideal Coordinates CCD File
GA [auth B],
P [auth A]
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE
C27 H35 N9 O15 P2
YPZRHBJKEMOYQH-UYBVJOGSSA-N
HG

Query on HG



Download:Ideal Coordinates CCD File
AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
EA [auth B]
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
EA [auth B],
FA [auth B],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A]
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
SM

Query on SM



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
SAMARIUM (III) ION
Sm
DOSGOCSVHPUUIA-UHFFFAOYSA-N
TRS

Query on TRS



Download:Ideal Coordinates CCD File
KA [auth B],
V [auth A]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
NO3

Query on NO3



Download:Ideal Coordinates CCD File
HA [auth B],
IA [auth B],
Q [auth A],
R [auth A],
S [auth A]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
JA [auth B],
T [auth A],
U [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSS
Query on CSS
A, B
L-PEPTIDE LINKINGC3 H7 N O2 S2CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free:  0.188 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.165 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 0.166 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.88α = 90
b = 87.07β = 112.95
c = 78.02γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
SHELXCDEphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-03
    Type: Initial release
  • Version 1.1: 2016-08-10
    Changes: Database references
  • Version 1.2: 2016-10-05
    Changes: Database references
  • Version 1.3: 2019-03-06
    Changes: Data collection, Derived calculations, Experimental preparation, Other
  • Version 1.4: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary