6LVV

N, N-dimethylformamidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A 2-Tyr-1-carboxylate Mononuclear Iron Center Forms the Active Site of a Paracoccus Dimethylformamidase.

Arya, C.K.Yadav, S.Fine, J.Casanal, A.Chopra, G.Ramanathan, G.Vinothkumar, K.R.Subramanian, R.

(2020) Angew Chem Int Ed Engl 59: 16961-16966

  • DOI: https://doi.org/10.1002/anie.202005332
  • Primary Citation of Related Structures:  
    6LVB, 6LVC, 6LVD, 6LVE, 6LVV

  • PubMed Abstract: 

    N,N-dimethyl formamide (DMF) is an extensively used organic solvent but is also a potent pollutant. Certain bacterial species from genera such as Paracoccus, Pseudomonas, and Alcaligenes have evolved to use DMF as a sole carbon and nitrogen source for growth via degradation by a dimethylformamidase (DMFase). We show that DMFase from Paracoccus sp. strain DMF is a halophilic and thermostable enzyme comprising a multimeric complex of the α 2 β 2 or (α 2 β 2 ) 2 type. One of the three domains of the large subunit and the small subunit are hitherto undescribed protein folds of unknown evolutionary origin. The active site consists of a mononuclear iron coordinated by two Tyr side-chain phenolates and one carboxylate from Glu. The Fe 3+ ion in the active site catalyzes the hydrolytic cleavage of the amide bond in DMF. Kinetic characterization reveals that the enzyme shows cooperativity between subunits, and mutagenesis and structural data provide clues to the catalytic mechanism.


  • Organizational Affiliation

    Department of Chemistry, Indian Institute of Technology, Kanpur, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N,N-dimethylformamidase large subunit
A, C, E, G, I
A, C, E, G, I, K, M, O
775Paracoccus sp. SSG05Mutation(s): 0 
Gene Names: dmfase2
EC: 3.5.1.56
UniProt
Find proteins for I6NT79 (Paracoccus sp. SSG05)
Explore I6NT79 
Go to UniProtKB:  I6NT79
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI6NT79
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
N,N-dimethylformamidase small subunit
B, D, F, H, J
B, D, F, H, J, L, N, P
132Paracoccus sp. SSG05Mutation(s): 0 
Gene Names: dmfase1
EC: 3.5.1.56
UniProt
Find proteins for I6NWZ0 (Paracoccus sp. SSG05)
Explore I6NWZ0 
Go to UniProtKB:  I6NWZ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI6NWZ0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
BA [auth L]
DA [auth N]
FA [auth P]
R [auth B]
T [auth D]
BA [auth L],
DA [auth N],
FA [auth P],
R [auth B],
T [auth D],
V [auth F],
X [auth H],
Z [auth J]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
FE (Subject of Investigation/LOI)
Query on FE

Download Ideal Coordinates CCD File 
AA [auth K]
CA [auth M]
EA [auth O]
Q [auth A]
S [auth C]
AA [auth K],
CA [auth M],
EA [auth O],
Q [auth A],
S [auth C],
U [auth E],
W [auth G],
Y [auth I]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 160.514α = 90
b = 142.553β = 92.92
c = 181.488γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-12
    Type: Initial release
  • Version 1.1: 2020-12-16
    Changes: Database references
  • Version 1.2: 2021-03-24
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Database references, Refinement description