6UKF

HhaI endonuclease in Complex with DNA at 1 Angstrom Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of HhaI endonuclease with cognate DNA at an atomic resolution of 1.0 angstrom.

Horton, J.R.Yang, J.Zhang, X.Petronzio, T.Fomenkov, A.Wilson, G.G.Roberts, R.J.Cheng, X.

(2019) Nucleic Acids Res. --: --

  • DOI: 10.1093/nar/gkz1195
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • HhaI, a Type II restriction endonuclease, recognizes the symmetric sequence 5'-GCG↓C-3' in duplex DNA and cleaves ('↓') to produce fragments with 2-base, 3'-overhangs. We determined the structure of HhaI in complex with cognate DNA at an ultra-high a ...

    HhaI, a Type II restriction endonuclease, recognizes the symmetric sequence 5'-GCG↓C-3' in duplex DNA and cleaves ('↓') to produce fragments with 2-base, 3'-overhangs. We determined the structure of HhaI in complex with cognate DNA at an ultra-high atomic resolution of 1.0 Å. Most restriction enzymes act as dimers with two catalytic sites, and cleave the two strands of duplex DNA simultaneously, in a single binding event. HhaI, in contrast, acts as a monomer with only one catalytic site, and cleaves the DNA strands sequentially, one after the other. HhaI comprises three domains, each consisting of a mixed five-stranded β sheet with a defined function. The first domain contains the catalytic-site; the second contains residues for sequence recognition; and the third contributes to non-specific DNA binding. The active-site belongs to the 'PD-D/EXK' superfamily of nucleases and contains the motif SD-X11-EAK. The first two domains are similar in structure to two other monomeric restriction enzymes, HinP1I (G↓CGC) and MspI (C↓CGG), which produce fragments with 5'-overhangs. The third domain, present only in HhaI, shifts the positions of the recognition residues relative to the catalytic site enabling this enzyme to cleave the recognition sequence at a different position. The structure of M.HhaI, the biological methyltransferase partner of HhaI, was determined earlier. Together, these two structures represent the first natural pair of restriction-modification enzymes to be characterized in atomic detail.


    Organizational Affiliation

    New England Biolabs, Inc., Ipswich, MA 01938, USA.,Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HhaI Restriction Endonuclease
X
258Haemophilus parahaemolyticus HK385Mutation(s): 0 
Find proteins for I3DBY6 (Haemophilus parahaemolyticus HK385)
Go to UniProtKB:  I3DBY6
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*CP*CP*AP*AP*GP*CP*GP*CP*AP*AP*CP*G)-3')A13Haemophilus parahaemolyticus
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*(5IT)P*TP*GP*CP*GP*CP*TP*(5IT)P*GP*GP*A)-3')B13Haemophilus parahaemolyticus
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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Download CCD File 
X
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
X
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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X
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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A, B, X
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5IU
Query on 5IU
B
DNA LINKINGC9 H12 I N2 O8 PDU
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 61.018α = 90.00
b = 37.317β = 109.77
c = 69.027γ = 90.00
Software Package:
Software NamePurpose
SERGUIdata collection
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM049245-23

Revision History 

  • Version 1.0: 2019-12-18
    Type: Initial release
  • Version 1.1: 2020-01-08
    Type: Database references