3WVH: Time-resolved Crystal Structure Of Hindiii With 25sec Soaking

In order to investigate the mechanism of the reaction catalyzed by HindIII, structures of HindIII-DNA complexes with varying durations of soaking time in cryoprotectant buffer containing manganese ions were determined by the freeze-trap method. In the crystal structures of the complexes obtained after soaking for a longer duration, two manganese ions, indicated by relatively higher electron density, are clearly observed at the two metal ion-binding sites in the active site of HindIII. The increase in the electron density of the two metal-ion peaks followed distinct pathways with increasing soaking times, suggesting variation in the binding rate constant for the two metal sites. DNA cleavage is observed when the second manganese ion appears, suggesting that HindIII uses the two-metal-ion mechanism, or alternatively that its reactivity is enhanced by the binding of the second metal ion. In addition, conformational change in a loop near the active site accompanies the catalytic reaction.
PDB ID: 3WVHDownload
MMDB ID: 128335
PDB Deposition Date: 2014/5/21
Updated in MMDB: 2015/04
Experimental Method:
x-ray diffraction
Resolution: 2.54  Å
Source Organism:
Haemophilus influenzae Rd KW20
Similar Structures:
Biological Unit for 3WVH: tetrameric; determined by author and by software (PISA)
Molecular Components in 3WVH
Label Count Molecule
Proteins (2 molecules)
Type-2 Restriction Enzyme Hindiii(Gene symbol: hindIIIR)
Molecule annotation
Nucleotide(1 molecule)
DNA (5'-d(*gp*cp*cp*ap*ap*gp*cp*tp*tp*gp*gp*c)-3')
Molecule annotation
Chemicals (6 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB