5GKF | pdb_00005gkf

Structure of EndoMS-dsDNA1' complex

• PDB DOI: https://doi.org/10.2210/pdb5GKF/pdb
• NAKB: 5GKF

• Classification: HYDROLASE/DNA
• Organism(s): Thermococcus kodakarensis KOD1, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-07-04 Released: 2016-11-02 
• Deposition Author(s): Nakae, S., Hijikata, A., Tsuji, T., Yonezawa, K., Kouyama, K., Mayanagi, K., Ishino, S., Ishino, Y., Shirai, T.
• Funding Organization(s): Japan Agency for Medical Research and Development, Ministry of Education, Culture, Sports, Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.247 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease

Nakae, S., Hijikata, A., Tsuji, T., Yonezawa, K., Kouyama, K.I., Mayanagi, K., Ishino, S., Ishino, Y., Shirai, T.

(2016) Structure 24: 1960-1971

• PubMed: 27773688 
• DOI: https://doi.org/10.1016/j.str.2016.09.005
• Primary Citation Related Structures: 
  5GKE, 5GKF, 5GKG, 5GKH, 5GKI, 5GKJ


• PubMed Abstract: 
  

  Archaeal NucS nuclease was thought to degrade the single-stranded region of branched DNA, which contains flapped and splayed DNA. However, recent findings indicated that EndoMS, the orthologous enzyme of NucS, specifically cleaves double-stranded DNA (dsDNA) containing mismatched bases. In this study, we determined the structure of the EndoMS-DNA complex. The complex structure of the EndoMS dimer with dsDNA unexpectedly revealed that the mismatched bases were flipped out into binding sites, and the overall architecture most resembled that of restriction enzymes. The structure of the apo form was similar to the reported structure of Pyrococcus abyssi NucS, indicating that movement of the C-terminal domain from the resting state was required for activity. In addition, a model of the EndoMS-PCNA-DNA complex was preliminarily verified with electron microscopy. The structures strongly support the idea that EndoMS acts in a mismatch repair pathway.

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Organizational Affiliation: 
• Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Tamura 1266, Nagahama, Shiga 526-0829, Japan.
Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan.
Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, Fukuoka 812-8581, Japan.
Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Tamura 1266, Nagahama, Shiga 526-0829, Japan. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 67.01 kDa 
• Atom Count: 5,093 
• Modeled Residue Count: 508 
• Deposited Residue Count: 534 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endonuclease EndoMS	A, B	252	Thermococcus kodakarensis KOD1	Mutation(s): 1  Gene Names: TK1898 EC: 3.1
UniProt
Find proteins for Q5JER9 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JER9  Go to UniProtKB:  Q5JER9

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*CP*TP*AP*CP*AP*TP*GP*TP*CP*GP*TP*CP*C)-3')	C	15	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*AP*CP*GP*AP*CP*TP*TP*GP*TP*AP*GP*CP*G)-3')	D	15	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	E [auth A], H [auth C], I [auth C], J [auth D], K [auth D]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
MG	F [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.247 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.44	α = 90
b = 92.44	β = 90
c = 404.32	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
MOSFLM	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-11-02 
Deposition Author(s): Nakae, S., Hijikata, A., Tsuji, T., Yonezawa, K., Kouyama, K., Mayanagi, K., Ishino, S., Ishino, Y., Shirai, T.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development	Japan	Drug Discovery and Life Science Research(Platform for Drug Discovery, Informatics and Structural Life Science)
Ministry of Education, Culture, Sports, Science and Technology	Japan	25280109
Ministry of Education, Culture, Sports, Science and Technology	Japan	26242075

Revision History  

• Version 1.0: 2016-11-02
  Type: Initial release
  
• Version 1.1: 2016-11-16
  Changes: Database references
• Version 1.2: 2020-02-26
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description