PDBsum entry 3hqg

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Hydrolase/DNA PDB id
Protein chain
222 a.a.
Waters ×67

References listed in PDB file
Key reference
Title Structural mechanisms for the 5'-Ccwgg sequence recognition by the n- And c-Terminal domains of ecorii.
Authors D.Golovenko, E.Manakova, G.Tamulaitiene, S.Grazulis, V.Siksnys.
Ref. Nucleic Acids Res, 2009, 37, 6613-6624.
PubMed id 19729506
EcoRII restriction endonuclease is specific for the 5'-CCWGG sequence (W stands for A or T); however, it shows no activity on a single recognition site. To activate cleavage it requires binding of an additional target site as an allosteric effector. EcoRII dimer consists of three structural units: a central catalytic core, made from two copies of the C-terminal domain (EcoRII-C), and two N-terminal effector DNA binding domains (EcoRII-N). Here, we report DNA-bound EcoRII-N and EcoRII-C structures, which show that EcoRII combines two radically different structural mechanisms to interact with the effector and substrate DNA. The catalytic EcoRII-C dimer flips out the central T:A base pair and makes symmetric interactions with the CC:GG half-sites. The EcoRII-N effector domain monomer binds to the target site asymmetrically in a single defined orientation which is determined by specific hydrogen bonding and van der Waals interactions with the central T:A pair in the major groove. The EcoRII-N mode of the target site recognition is shared by the large class of higher plant transcription factors of the B3 superfamily.
Secondary reference #1
Title Crystal structure of type iie restriction endonuclease ecorii reveals an autoinhibition mechanism by a novel effector-Binding fold.
Authors X.E.Zhou, Y.Wang, M.Reuter, M.Mücke, D.H.Krüger, E.J.Meehan, L.Chen.
Ref. J Mol Biol, 2004, 335, 307-319. [DOI no: 10.1016/j.jmb.2003.10.030]
PubMed id 14659759
Full text Abstract
Figure 6.
Figure 6. The N-domain structure and the effector-binding cleft. The secondary structural elements are labeled and so are some of the key amino acid residues in the proposed effector-binding cleft. Putative DNA-binding residues H36, Y41, K92, R94, E96, K97 and R98 are shown in ball-and-stick.
Figure 9.
Figure 9. The inactive dimer structure of EcoRII and a model of autoinhibition. The ribbon diagram is a back view of Figure 5 and related to Figure 5 by a 180° rotation about the vertical axis. The locations of the two effector clefts and the two catalytic half-sites are indicated. The catalytic half-sites are blocked by the N-domains and inaccessible by a substrate DNA. The two key residues Y41 and E96 in the effector clefts are shown in ball-and-stick and labeled. The a-helix H6 is also labeled.
The above figures are reproduced from the cited reference with permission from Elsevier
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