3A4K image
Deposition Date 2009-07-09
Release Date 2009-10-20
Last Version Date 2023-11-01
Entry Detail
PDB ID:
3A4K
Keywords:
HYDROLASE/DNA
Title:
Crystal structural analysis of HindIII restriction endonuclease in complex with cognate DNA and divalent cations at 2.17 angstrom resolution
Biological Source:
Source Organism:
Haemophilus influenzae (Taxon ID: 71421)
(Taxon ID: )
Host Organism:
Escherichia coli BL21(DE3)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.17 Å
R-Value Free:
0.22
R-Value Work:
0.17
R-Value Observed:
0.18
Space Group:
P 1 21 1
3A4K validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Type-2 restriction enzyme HindIII
Gene (Uniprot):hindIIIR
Chain IDs:A, B (auth: C), C (auth: B), D
Chain Length:301
Number of Molecules:4
Biological Source:Haemophilus influenzae
UniProt ID:P43870 Pfam ID:PF09518 EC:3.1.21.4
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3')
Chain IDs:M, N
Chain Length:12
Number of Molecules:2
Biological Source:
Ligand Molecules
ACT
GOL
MG
MN
Primary Citation
Structures of restriction endonuclease HindIII in complex with its cognate DNA and divalent cations
Acta Crystallogr.,Sect.D 65 1326 1333 (2009)
PMID: 19966419 DOI: 10.1107/S0907444909041134

Abstact

The three-dimensional crystal structures of HindIII bound to its cognate DNA with and without divalent cations were solved at 2.17 and 2.00 A resolution, respectively. HindIII forms a dimer. The structures showed that HindIII belongs to the EcoRI-like (alpha-class) subfamily of type II restriction endonucleases. The cognate DNA-complex structures revealed the specific DNA-recognition mechanism of HindIII by which it recognizes the palindromic sequence A/AGCTT. In the Mg(2+) ion-soaked structure the DNA was cleaved and two ions were bound at each active site, corresponding to the two-metal-ion mechanism.

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Protein

Chemical

Disease

Primary Citation of related structures
2E52