PDBsum entry 2w00

Hydrolase

PDB id: 2w00

Contents

Protein chains

842 a.a. *

Ligands

ATP ×2

Metals

_MG ×2

Waters ×582

* Residue conservation analysis

PDB id:

2w00

Name:

Hydrolase

Title:

Crystal structure of the hsdr subunit of the ecor124i restriction enzyme in complex with atp

Structure:

Hsdr. Chain: a, b. Synonym: r.Ecor124i. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Strain: b834(de3). Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.60Å R-factor: 0.221 R-free: 0.265

Authors:

M.Lapkouski,S.Panjikar,I.Kuta Smatanova,R.Ettrich,E.Csefalvay

Key ref:

M.Lapkouski et al. (2009). Structure of the motor subunit of type I restriction-modification complex EcoR124I. Nat Struct Biol, 16, 94-95. PubMed id: 19079266 DOI: 10.1038/nsmb.1523

Date:

08-Aug-08 Release date: 16-Dec-08

Protein chains

P10486  (T1R1_ECOLX) -  Type I restriction enzyme EcoR124I/EcoR124II endonuclease subunit from Escherichia coli

Seq: 1038 a.a.

Struc: 842 a.a.

Enzyme reactions

• Enzyme class: E.C.3.1.21.3 - type I site-specific deoxyribonuclease.
• Reaction: Endonucleolytic cleavage of DNA to give random double-stranded fragments with terminal 5'-phosphate; ATP is simultaneously hydrolyzed.

DOI no: 10.1038/nsmb.1523

Nat Struct Biol 16:94-95 (2009)

PubMed id: 19079266

Structure of the motor subunit of type I restriction-modification complex EcoR124I.

M.Lapkouski, S.Panjikar, P.Janscak, I.K.Smatanova, J.Carey, R.Ettrich, E.Csefalvay.

ABSTRACT

Type I restriction-modification enzymes act as conventional adenine methylases on hemimethylated DNAs, but unmethylated recognition targets induce them to translocate thousands of base pairs before cleaving distant sites nonspecifically. The first crystal structure of a type I motor subunit responsible for translocation and cleavage suggests how the pentameric translocating complex is assembled and provides a structural framework for translocation of duplex DNA by RecA-like ATPase motors.

Selected figure(s)

Figure 1.
(a) Planar domain assembly. 'Front' view with helices numbered and strands lettered sequentially from the N to the C terminus. Dashed lines indicate short regions of disorder; unresolved residues 893 to 1038 are not shown. Endonuclease active-site residues and ATP are shown as skeletal models; the black sphere represents Mg^2+. (b) ATP binding. ATP, Lys220 and Glu409 electron density are shown in blue mesh; the white sphere represents Mg^2+; red spheres represent water oxygens. Dashed lines connect atoms that are close enough for bonding.

Figure 2.
(a) Electrostatic potential surface. Blue, positive; red, negative. Shown is the top view onto the helicase cleft with the front of the subunit facing upward; canonical sequence motifs are numbered in helicase domains 1 and 2 (light blue and pink, respectively). (b) DNA path. Ribbon model of view in a. The DNA backbone model is shown in gray ribbon; the open circle shows the closest approach to the active site. (c) Active site. Front view shown, with the top of the subunit at the right. Spheres represent residue side chain atoms: yellow, catalytic (Asp151 unlabeled); green, exit. (d) DNA exit. Bottom view with the front of the subunit facing upward. The positions of unresolved Lys865 and 866 between helices 39 and 40 were determined by loop modeling as described in Supplementary Methods.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2009, 16, 94-95) copyright 2009.