1D02 | pdb_00001d02

CRYSTAL STRUCTURE OF MUNI RESTRICTION ENDONUCLEASE IN COMPLEX WITH COGNATE DNA

• PDB DOI: https://doi.org/10.2210/pdb1D02/pdb
• NAKB: 1D02

• Classification: HYDROLASE/DNA
• Organism(s): Mycoplasma
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1999-09-08 Released: 2000-03-08 
• Deposition Author(s): Deibert, M., Grazulis, S., Janulaitis, A., Siksnys, V., Huber, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.213 (Depositor) 
• R-Value Work: 
  0.180 (Depositor) 
• R-Value Observed: 
  0.180 (Depositor) 

Literature

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

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

(1999) EMBO J 18: 5805-5816

• PubMed: 10545092 
• DOI: https://doi.org/10.1093/emboj/18.21.5805
• Primary Citation Related Structures: 
  1D02


• PubMed 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.

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Organizational Affiliation: 
• Max-Planck-Institut für Biochemie, D-82152 Planegg-Martinsried, Germany. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 52.84 kDa 
• Atom Count: 4,312 
• Modeled Residue Count: 417 
• Deposited Residue Count: 424 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TYPE II RESTRICTION ENZYME MUNI	C [auth A], D [auth B]	202	Mycoplasma	Mutation(s): 1  EC: 3.1.21.4
UniProt
Find proteins for P43642 (Mycoplasma sp) Explore P43642  Go to UniProtKB:  P43642

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*CP*AP*AP*TP*TP*GP*GP*C)-3')	A [auth C], B [auth D]	10	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.213 (Depositor) 
• R-Value Work:  0.180 (Depositor) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.4	α = 90
b = 72.47	β = 90
c = 121.67	γ = 90

Software Package:

Software Name	Purpose
MLPHARE	phasing
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-03-08 
Deposition Author(s): Deibert, M., Grazulis, S., Janulaitis, A., Siksnys, V., Huber, R.

Revision History  

• Version 1.0: 2000-03-08
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-03-14
  Changes: Database references
• Version 1.4: 2024-02-07
  Changes: Data collection, Database references