PDBsum entry 4rd5

Hydrolase/DNA

PDB id: 4rd5

Contents

Protein chains

160 a.a.

DNA/RNA

Waters ×86

PDB id:

4rd5

Name:

Hydrolase/DNA

Title:

Crystal structure of r.Ngoavii restriction endonuclease b3 domain with cognate DNA

Structure:

Restriction endonuclease r.Ngovii. Chain: a, b. Engineered: yes. DNA (5'-d( Cp Cp Cp Tp Ap Ap Gp Cp Gp Gp Cp Ap Ap Tp Cp C)- 3'). Chain: c, e. Engineered: yes. DNA (5'-d( Gp Gp Gp Ap Tp Tp Gp Cp Cp Gp Cp Tp Tp Ap Gp G)- 3').

Source:

Neisseria gonorrhoeae. Organism_taxid: 242231. Strain: atcc 700825 / fa 1090. Gene: ngo0364. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: synthetic construct. Other_details: synthetic construct

Resolution:

2.70Å R-factor: 0.218 R-free: 0.250

Authors:

G.Tamulaitiene,A.Silanskas,S.Grazulis,M.Zaremba,V.Siksnys

Key ref:

G.Tamulaitiene et al. (2014). Crystal structure of the R-protein of the multisubunit ATP-dependent restriction endonuclease NgoAVII. Nucleic Acids Res, 42, 14022-14030. PubMed id: 25429979 DOI: 10.1093/nar/gku1237

Date:

18-Sep-14 Release date: 24-Dec-14

Protein chains

Q5F9M9  (Q5F9M9_NEIG1) -  Restriction endonuclease NgoFVII from Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090)

Seq: 345 a.a.

Struc: 160 a.a.

DNA/RNA chains

C-C-T-A-A-G-C-G-G-C-A-A-T-C-C 15 bases

G-G-G-A-T-T-G-C-C-G-C-T-T-A-G 15 bases

C-C-T-A-A-G-C-G-G-C-A-A-T-C-C 15 bases

G-G-G-A-T-T-G-C-C-G-C-T-T-A-G 15 bases

Enzyme reactions

• Enzyme class: E.C.3.1.21.4 - type Ii site-specific deoxyribonuclease.
• Reaction: Endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates.
• Cofactor: Mg(2+)

DOI no: 10.1093/nar/gku1237

Nucleic Acids Res 42:14022-14030 (2014)

PubMed id: 25429979

Crystal structure of the R-protein of the multisubunit ATP-dependent restriction endonuclease NgoAVII.

G.Tamulaitiene, A.Silanskas, S.Grazulis, M.Zaremba, V.Siksnys.

ABSTRACT

The restriction endonuclease (REase) NgoAVII is composed of two proteins, R.NgoAVII and N.NgoAVII, and shares features of both Type II restriction enzymes and Type I/III ATP-dependent restriction enzymes (see accompanying paper Zaremba et al., 2014). Here we present crystal structures of the R.NgoAVII apo-protein and the R.NgoAVII C-terminal domain bound to a specific DNA. R.NgoAVII is composed of two domains: an N-terminal nucleolytic PLD domain; and a C-terminal B3-like DNA-binding domain identified previously in BfiI and EcoRII REases, and in plant transcription factors. Structural comparison of the B3-like domains of R.NgoAVII, EcoRII, BfiI and the plant transcription factors revealed a conserved DNA-binding surface comprised of N- and C-arms that together grip the DNA. The C-arms of R.NgoAVII, EcoRII, BfiI and plant B3 domains are similar in size, but the R.NgoAVII N-arm which makes the majority of the contacts to the target site is much longer. The overall structures of R.NgoAVII and BfiI are similar; however, whilst BfiI has stand-alone catalytic activity, R.NgoAVII requires an auxiliary cognate N.NgoAVII protein and ATP hydrolysis in order to cleave DNA at the target site. The structures we present will help formulate future experiments to explore the molecular mechanisms of intersubunit crosstalk that control DNA cleavage by R.NgoAVII and related endonucleases.