3WVG

Time-Resolved Crystal Structure of HindIII with 0sec soaking

Summary for 3WVG

• Entry DOI: 10.2210/pdb3wvg/pdb
• Related: 3WVH 3WVI 3WVK 3WVP
• Descriptor: Type-2 restriction enzyme HindIII, DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3'), SODIUM ION, ... (5 entities in total)
• Functional Keywords: freeze-trap, time-resolved, type iip restriction endonuclease, restriction endonuclease, hydrolase, nuclease, hydrolase-dna complex, hydrolase/dna
• Biological source: Haemophilus influenzae; More
• Total number of polymer chains: 12
• Total formula weight: 169760.03

Authors

Kawamura, T.,Kobayashi, T.,Watanabe, N. (deposition date: 2014-05-21, release date: 2015-04-08, Last modification date: 2023-11-08)

Primary citation

Kawamura, T.,Kobayashi, T.,Watanabe, N.
Analysis of the HindIII-catalyzed reaction by time-resolved crystallography
Acta Crystallogr.,Sect.D, 71:256-265, 2015

PubMed Abstract: 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.

PubMed: 25664735
DOI: 10.1107/S1399004714025188

Experimental method

X-RAY DIFFRACTION (2.25 Å)