6ZY1

Catabolic reductive dehalogenase NpRdhA, N-terminally tagged in complex with 3-bromo-4-hydroxybenzoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.177 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Catabolic Reductive Dehalogenase Substrate Complex Structures Underpin Rational Repurposing of Substrate Scope.

Halliwell, T.Fisher, K.Payne, K.A.P.Rigby, S.E.J.Leys, D.

(2020) Microorganisms 8

  • DOI: https://doi.org/10.3390/microorganisms8091344
  • Primary Citation of Related Structures:  
    6ZXU, 6ZXX, 6ZY0, 6ZY1

  • PubMed Abstract: 

    Reductive dehalogenases are responsible for the reductive cleavage of carbon-halogen bonds during organohalide respiration. A variety of mechanisms have been proposed for these cobalamin and [4Fe-4S] containing enzymes, including organocobalt, radical, or cobalt-halide adduct based catalysis. The latter was proposed for the oxygen-tolerant Nitratireductor pacificus pht-3B cataboli c reductive dehalogenase (NpRdhA). Here, we present the first substrate bound NpRdhA crystal structures, confirming a direct cobalt-halogen interaction is established and providing a rationale for substrate preference. Product formation is observed in crystallo due to X-ray photoreduction. Protein engineering enables rational alteration of substrate preference, providing a future blue print for the application of this and related enzymes in bioremediation.


  • Organizational Affiliation

    Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Oxidoreductase, NAD-binding/iron-sulfur cluster-binding protein
A, B, C
725Nitratireductor pacificus pht-3BMutation(s): 0 
Gene Names: NA2_14372
UniProt
Find proteins for K2MB66 (Nitratireductor pacificus pht-3B)
Explore K2MB66 
Go to UniProtKB:  K2MB66
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK2MB66
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B12 (Subject of Investigation/LOI)
Query on B12

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B],
P [auth C]
COBALAMIN
C62 H89 Co N13 O14 P
LKVIQTCSMMVGFU-DWSMJLPVSA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
I [auth B]
J [auth B]
N [auth C]
D [auth A],
E [auth A],
I [auth B],
J [auth B],
N [auth C],
O [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
QSB (Subject of Investigation/LOI)
Query on QSB

Download Ideal Coordinates CCD File 
H [auth A],
M [auth B],
R [auth C]
3 bromo 4 hydroxybenzoic acid
C7 H5 Br O3
XMEQDAIDOBVHEK-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B],
Q [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.177 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 175.871α = 90
b = 170.104β = 98.35
c = 107.651γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/M007316/1

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-16
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Database references, Refinement description