6ZXX

Catabolic reductive dehalogenase NpRdhA, N-terminally tagged.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B12 (Subject of Investigation/LOI)
Query on B12

Download Ideal Coordinates CCD File 
F [auth A],
M [auth B],
T [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]
K [auth B]
L [auth B]
R [auth C]
D [auth A],
E [auth A],
K [auth B],
L [auth B],
R [auth C],
S [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
QSH (Subject of Investigation/LOI)
Query on QSH

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H [auth A],
O [auth B],
V [auth C]
3,5-bis(bromanyl)-4-oxidanyl-benzoic acid
C7 H4 Br2 O3
PHWAJJWKNLWZGJ-UHFFFAOYSA-N
QSB (Subject of Investigation/LOI)
Query on QSB

Download Ideal Coordinates CCD File 
I [auth A],
P [auth B],
W [auth C]
3 bromo 4 hydroxybenzoic acid
C7 H5 Br O3
XMEQDAIDOBVHEK-UHFFFAOYSA-N
BR
Query on BR

Download Ideal Coordinates CCD File 
J [auth A],
Q [auth B],
X [auth C]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
NA
Query on NA

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G [auth A],
N [auth B],
U [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 180.182α = 90
b = 170.391β = 99.16
c = 107.957γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
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