5DBJ | pdb_00005dbj

Crystal structure of halogenase PltA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 
    0.292 (Depositor), 0.293 (DCC) 
  • R-Value Work: 
    0.239 (Depositor), 0.239 (DCC) 
  • R-Value Observed: 
    0.241 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history

Literature

Crystal structure of halogenase PltA from the pyoluteorin biosynthetic pathway.

Pang, A.H.Garneau-Tsodikova, S.Tsodikov, O.V.

(2015) J Struct Biol 192: 349-357

  • DOI: https://doi.org/10.1016/j.jsb.2015.09.013
  • Primary Citation Related Structures: 
    5DBJ

  • PubMed Abstract: 

    Pyoluteorin is an antifungal agent composed of a 4,5-dichlorinated pyrrole group linked to a resorcinol moiety. The pyoluteorin biosynthetic gene cluster in Pseudomonas fluorescens Pf-5 encodes the halogenase PltA, which has been previously demonstrated to perform both chlorinations in vitro. PltA selectively accepts as a substrate a pyrrole moiety covalently tethered to a nonribosomal peptide thiolation domain PltL (pyrrolyl-S-PltL) for FAD-dependent di-chlorination, yielding 4,5-dichloropyrrolyl-S-PltL. We report a 2.75 Å-resolution crystal structure of PltA in complex with FAD and chloride. PltA is a dimeric enzyme, containing a flavin-binding fold conserved in flavin-dependent halogenases and monooxygenases, and an additional unique helical region at the C-terminus. This C-terminal region blocks a putative substrate-binding cleft, suggesting that a conformational change involving repositioning of this region is necessary to allow binding of the pyrrolyl-S-PltL substrate for its dichlorination by PltA.


  • Organizational Affiliation
    • Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536-0596, USA.

Macromolecule Content 

  • Total Structure Weight: 261.2 kDa 
  • Atom Count: 17,754 
  • Modeled Residue Count: 2,177 
  • Deposited Residue Count: 2,275 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
FADH2-dependent halogenase PltAA [auth E],
B [auth A],
C [auth B],
D [auth C],
E [auth D]
455Pseudomonas protegens Pf-5Mutation(s): 0 
Gene Names: pltAPFL_2787
EC: 3.8.1.1 (PDB Primary Data), 1.14.19.56 (UniProt)
UniProt
Find proteins for Q4KCZ0 (Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5))
Explore Q4KCZ0 
Go to UniProtKB:  Q4KCZ0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4KCZ0
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
F [auth E],
I [auth A],
L [auth B],
O [auth C],
R [auth D]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
G [auth E]
H [auth E]
J [auth A]
K [auth A]
M [auth B]
G [auth E],
H [auth E],
J [auth A],
K [auth A],
M [auth B],
N [auth B],
P [auth C],
Q [auth C],
S [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free:  0.292 (Depositor), 0.293 (DCC) 
  • R-Value Work:  0.239 (Depositor), 0.239 (DCC) 
  • R-Value Observed: 0.241 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 242.934α = 90
b = 94.981β = 91.21
c = 102.145γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-07
    Type: Initial release
  • Version 1.1: 2015-10-14
    Changes: Database references
  • Version 1.2: 2015-11-25
    Changes: Database references
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description