6M5B

X-ray crystal structure of cyclic-PIP and DNA complex in a reverse binding orientation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.184 

wwPDB Validation 3D Report Full Report



Literature

X-ray Crystal Structure of a Cyclic-PIP-DNA Complex in the Reverse-Binding Orientation.

Abe, K.Hirose, Y.Eki, H.Takeda, K.Bando, T.Endo, M.Sugiyama, H.

(2020) J Am Chem Soc 142: 10544-10549

  • DOI: 10.1021/jacs.0c03972
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Elucidation of the details of the associating mode is one of the major concerns for the precise design of DNA-binding molecules that are used for gene regulation. Pyrrole-imidazole polyamide (PIP) is a well-established synthetic DNA-binding molecule ...

    Elucidation of the details of the associating mode is one of the major concerns for the precise design of DNA-binding molecules that are used for gene regulation. Pyrrole-imidazole polyamide (PIP) is a well-established synthetic DNA-binding molecule that has sequence-specificity for duplex DNA. By the design of the sequence of pyrrole, imidazole, and other synthetic units, PIP is bound to the target DNA sequence selectively. Here, we report the X-ray crystal structure of newly synthesized chiral cyclic PIP (cPIP) complexed with DNA at 1.5 Å resolution and reveal that cPIP binds in the reverse orientation in the DNA minor groove. Analysis of the crystal structure revealed that the positions of the hydrogen bonds between the bases and the pyrrole-imidazole moieties of cPIP were similar for both forward- and reverse-binding orientations and that the distortion of the B-form DNA structure caused by cPIP binding was also similar for both orientations. We further found that new hydrogen bonds formed between the amino groups on the γ-turn units and DNA at both ends of the cPIP molecule. Additionally, by comparing the reverse PIP orientation with the forward orientation, we could clarify that the cause of the preference toward the reverse orientation in the S -form cPIP as used in this study is the overall conformation of the cPIP-DNA complex, particularly the configuration of hydrogen bonds. These results thus provide an explanation for the different stereoselectivity of cPIP binding in the minor groove.


    Organizational Affiliation

    Institute for Integrated Cell-Material Science, Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan.



Macromolecules
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*(CBR)P*AP*GP*GP*CP*CP*TP*GP*G)-3')A10synthetic construct
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
S7E
Query on S7E

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A
4-[[4-[(4-azanyl-1-methyl-pyrrol-2-yl)carbonylamino]-1-methyl-pyrrol-2-yl]carbonylamino]-~{N}-[2-[[(3~{S})-3-azanyl-4-oxidanylidene-butyl]carbamoyl]-1-methyl-imidazol-4-yl]-1-methyl-imidazole-2-carboxamide
C26 H32 N12 O5
UZFBAFZKKPMVCV-AWEZNQCLSA-N
 Ligand Interaction
EDO
Query on EDO

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A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.184 
  • Space Group: I 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.235α = 90
b = 82.235β = 90
c = 82.235γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
SOLVEphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan18KK0139
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan16H06356

Revision History 

  • Version 1.0: 2020-06-24
    Type: Initial release