PDBsum entry: 1d02

Hydrolase/DNA

PDB id: 1d02

Contents

Protein chains

197 a.a.

DNA/RNA

Waters ×646

PDB id:

1d02

Name:

Hydrolase/DNA

Title:

Crystal structure of muni restriction endonuclease in comple cognate DNA

Structure:

DNA (5'-d( Gp Cp Cp Ap Ap Tp Tp Gp Gp C)-3'). Chain: c, d. Engineered: yes. Type ii restriction enzyme muni. Chain: a, b. Synonym: endonuclease muni. Engineered: yes. Mutation: yes

Source:

Synthetic: yes. Other_details: decameric oligonucleotide 5'-ds(gpcpcpapaptp was synthesized with standard procedures. Mycoplasma. Organism_taxid: 2093. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PQS)

Resolution:

1.70Å R-factor: 0.180 R-free: 0.213

Authors:

M.Deibert,S.Grazulis,A.Janulaitis,V.Siksnys,R.Huber

Key ref:

M.Deibert et al. (1999). Crystal structure of MunI restriction endonuclease in complex with cognate DNA at 1.7 A resolution. EMBO J, 18, 5805-5816. PubMed id: 10545092 DOI: 10.1093/emboj/18.21.5805

Date:

08-Sep-99 Release date: 08-Mar-00

Protein chains

P43642  (T2MU_MYCSP) -  Type-2 restriction enzyme MunI

Seq: 202 a.a.

Struc: 197 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

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: Magnesium

 Gene Ontology (GO) functional annotation 

• Biological process: DNA restriction-modification system (1 term)
• Biochemical function: hydrolase activity (5 terms)

DOI no: 10.1093/emboj/18.21.5805

EMBO J 18:5805-5816 (1999)

PubMed id: 10545092

Crystal structure of MunI restriction endonuclease in complex with cognate DNA at 1.7 A resolution.

M.Deibert, S.Grazulis, A.Janulaitis, V.Siksnys, R.Huber.

ABSTRACT

The MunI restriction enzyme recognizes the palindromic hexanucleotide sequence C/AATTG (the '/' indicates the cleavage site). The crystal structure of its active site mutant D83A bound to cognate DNA has been determined at 1.7 A resolution. Base-specific contacts between MunI and DNA occur exclusively in the major groove. While DNA-binding sites of most other restriction enzymes are comprised of discontinuous sequence segments, MunI combines all residues involved in the base-specific contacts within one short stretch (residues R115-R121) located at the N-terminal region of the 3(10)4 helix. The outer CG base pair of the recognition sequence is recognized solely by R115 through hydrogen bonds made by backbone and side chain atoms to both bases. The mechanism of recognition of the central AATT nucleotides by MunI is similar to that of EcoRI, which recognizes the G/AATTC sequence. The local conformation of AATT deviates from the typical B-DNA form and is remarkably similar to EcoRI-DNA. It appears to be essential for specific hydrogen bonding and recognition by MunI and EcoRI.

Selected figure(s)

Figure 1.
Figure 1 DNA sequence of the decameric oligonucleotide used in the MunI D83A -DNA complex. The recognition sequence is boxed. The cleavage sites are indicated by arrows. The position of the crystallographic 2-fold axis is shown.

Figure 6.
Figure 6 Stereo view of MunI active site arrangement. Active site residues are labelled. Water molecules are depicted as blue spheres, with hydrogen bonds shown as dashed black lines. One DNA strand is shown in stick representation, with the scissile phosphate shown as purple and O1P and O2P as red spheres.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (1999, 18, 5805-5816) copyright 1999.

Figures were selected by an automated process.