4M9V

Zfp57 mutant (E182Q) in complex with 5-carboxylcytosine DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.97 Å
  • R-Value Free: 0.143 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.131 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

DNA recognition of 5-carboxylcytosine by a zfp57 mutant at an atomic resolution of 0.97 angstrom.

Liu, Y.Olanrewaju, Y.O.Zhang, X.Cheng, X.

(2013) Biochemistry 52: 9310-9317

  • DOI: https://doi.org/10.1021/bi401360n
  • Primary Citation of Related Structures:  
    4M9V

  • PubMed Abstract: 

    The Zfp57 gene encodes a KRAB (Krüppel-associated box) domain-containing C2H2 zinc finger transcription factor that is expressed in early development. Zfp57 protein recognizes methylated CpG dinucleotide within GCGGCA elements at multiple imprinting control regions. In the previously determined structure of the mouse Zfp57 DNA-binding domain in complex with DNA containing 5-methylcytosine (5mC), the side chains of Arg178 and Glu182 contact the methyl group via hydrophobic and van der Waals interactions. We examined the role of Glu182 in recognition of 5mC by mutagenesis. The majority of mutants examined lose selectivity of methylated (5mC) over unmodified (C) and oxidative derivatives, 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine (5caC), suggesting that the side chain of Glu182 (the size and the charge) is dispensable for methyl group recognition but negatively impacts the binding of unmodified cytosine as well as oxidized derivatives of 5mC to achieve 5mC selectivity. Substitution of Glu182 with its corresponding amide (E182Q) had no effect on methylated DNA binding but gained significant binding affinity for 5caC DNA, resulting in a binding affinity for 5caC DNA comparable to that of the wild-type protein for 5mC. We show structurally that the uncharged amide group of E182Q interacts favorably with the carboxylate group of 5caC. Furthermore, introducing a positively charged arginine at position 182 resulted in a mutant (E182R) having higher selectivity for the negatively charged 5caC.


  • Organizational Affiliation

    Department of Biochemistry, Emory University School of Medicine , 1510 Clifton Road, Atlanta, Georgia 30322, United States.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc finger protein 57
C, F
64Mus musculusMutation(s): 1 
Gene Names: Zfp57
UniProt
Find proteins for Q8C6P8 (Mus musculus)
Explore Q8C6P8 
Go to UniProtKB:  Q8C6P8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8C6P8
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*AP*TP*TP*GP*CP*(5CM)P*GP*CP*AP*G)-3')
A, D
11N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*CP*TP*GP*(1CC)P*GP*GP*CP*AP*AP*T)-3')
B, E
11N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download Ideal Coordinates CCD File 
G [auth B],
L [auth C],
O [auth E],
T [auth F]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
J [auth C],
K [auth C],
R [auth F],
S [auth F]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
H [auth B],
M [auth C],
N [auth C],
P [auth E]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA
Query on CA

Download Ideal Coordinates CCD File 
I [auth B],
Q [auth E]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.97 Å
  • R-Value Free: 0.143 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.131 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.388α = 90
b = 96.093β = 113.14
c = 36.408γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-27
    Type: Initial release
  • Version 1.1: 2014-01-22
    Changes: Database references
  • Version 2.0: 2020-06-24
    Changes: Advisory, Atomic model, Database references, Derived calculations
  • Version 2.1: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description