3MX4 | pdb_00003mx4

DNA binding and cleavage by the GIY-YIG endonuclease R.Eco29KI inactive variant E142Q

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.274 (Depositor), 0.275 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

Starting Model: other
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wwPDB Validation 3D Report Full Report

Validation slider image for 3MX4

This is version 1.3 of the entry. See complete history. 

Literature

Folding, DNA Recognition, and Function of GIY-YIG Endonucleases: Crystal Structures of R.Eco29kI.

Mak, A.N., Lambert, A.R., Stoddard, B.L.

(2010) Structure 18: 1321-1331

  • DOI: https://doi.org/10.1016/j.str.2010.07.006
  • Primary Citation Related Structures: 
    3MX1, 3MX4, 3NIC

  • PubMed Abstract: 

    The GIY-YIG endonuclease family comprises hundreds of diverse proteins and a multitude of functions; none have been visualized bound to DNA. The structure of the GIY-YIG restriction endonuclease R.Eco29kI has been solved both alone and bound to its target site. The protein displays a domain-swapped homodimeric structure with several extended surface loops encircling the DNA. Only three side chains from each protein subunit contact DNA bases, two directly and one via a bridging solvent molecule. Both tyrosine residues within the GIY-YIG motif are positioned in the catalytic center near a putative nucleophilic water; the remainder of the active site resembles the HNH endonuclease family. The structure illustrates how the GIY-YIG scaffold has been adapted for the highly specific recognition of a DNA restriction site, in contrast to nonspecific DNA cleavage by GIY-YIG domains in homing endonucleases or structure-specific cleavage by DNA repair enzymes such as UvrC.

    • Organizational Affiliation: 
    • Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

Macromolecule Content 

  • Total Structure Weight: 268.53 kDa 
  • Atom Count: 17,406 
  • Modeled Residue Count: 1,856 
  • Deposited Residue Count: 2,056 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 2

Macromolecules


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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Eco29kIR
A, B, C, D, E
A, B, C, D, E, F, G, H
235Escherichia coliMutation(s): 2 
Gene Names: eco29kIR
EC: 3.1.21.4
UniProt
Find proteins for Q46944 (Escherichia coli)
Explore Q46944 
Go to UniProtKB:  Q46944
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ46944
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*GP*GP*GP*AP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*GP*CP*CP*GP*C)-3')
I, K, M, O
22N/A
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*CP*GP*GP*CP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*TP*CP*CP*CP*G)-3')
J, L, N, P
22N/A
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.274 (Depositor), 0.275 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.855α = 90
b = 101.463β = 110.19
c = 144.403γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references
  • Version 1.3: 2024-04-03
    Changes: Refinement description