5ZCW | pdb_00005zcw

Structure of the Methanosarcina mazei class II CPD-photolyase in complex with intact, phosphodiester linked, CPD-lesion

• PDB DOI: https://doi.org/10.2210/pdb5ZCW/pdb
• NAKB: 5ZCW

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Methanosarcina mazei, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-02-21 Released: 2018-08-22 
• Deposition Author(s): Maestre-Reyna, M., Bessho, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.257 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

Twist and turn: a revised structural view on the unpaired bubble of class II CPD photolyase in complex with damaged DNA.

Maestre-Reyna, M., Yamamoto, J., Huang, W.C., Tsai, M.D., Essen, L.O., Bessho, Y.

(2018) IUCrJ 5: 608-618

• PubMed: 30224964 
• DOI: https://doi.org/10.1107/S205225251800996X
• Primary Citation Related Structures: 
  5ZCW


• PubMed Abstract: 
  

  Cyclobutane pyrimidine dimer (CPD) photolyases harness the energy of blue light to repair UV-induced DNA CPDs. Upon binding, CPD photolyases cause the photodamage to flip out of the duplex DNA and into the catalytic site of the enzyme. This process, called base-flipping, induces a kink in the DNA, as well as an unpaired bubble, which are stabilized by a network of protein-nucleic acid interactions. Previously, several co-crystal structures have been reported in which the binding mode of CPD photolyases has been studied in detail. However, in all cases the internucleoside linkage of the photodamage site was a chemically synthesized formacetal analogue and not the natural phosphodiester. Here, the first crystal structure and conformational analysis via molecular-dynamics simulations of a class II CPD photolyase in complex with photodamaged DNA that contains a natural cyclobutane pyrimidine dimer with an intra-lesion phosphodiester linkage are presented. It is concluded that a highly conserved bubble-intruding region (BIR) mediates stabilization of the open form of CPD DNA when complexed with class II CPD photolyases.

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Organizational Affiliation: 
• Institute of Biological Chemistry, Academia Sinica, 128, Academia Road, Sec. 2, Nankang, Taipei 115, Taiwan.
Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.
Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany.
LOEWE Center for Synthetic Microbiology, Philipps University Marburg, Hans-Meerwein Strasse 6, Marburg 35032, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 129.72 kDa 
• Atom Count: 8,319 
• Modeled Residue Count: 935 
• Deposited Residue Count: 1,020 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyribodipyrimidine photolyase	A, B	482	Methanosarcina mazei	Mutation(s): 1  EC: 4.1.99.3
UniProt
Find proteins for Q8PYK9 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)) Explore Q8PYK9  Go to UniProtKB:  Q8PYK9

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*AP*TP*CP*GP*GP*CP*(TTD)P*CP*GP*CP*GP*CP*AP*A)-3'	C, E	14	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*TP*GP*CP*GP*CP*GP*AP*AP*GP*CP*CP*GP*AP*T)-3'	D, F	14	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	H [auth A], J [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
SO4	G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	I [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.257 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.1	α = 90
b = 114.42	β = 90
c = 166.42	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-22 
Deposition Author(s): Maestre-Reyna, M., Bessho, Y.

Revision History  

• Version 1.0: 2018-08-22
  Type: Initial release
  
• Version 1.1: 2018-10-03
  Changes: Data collection, Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description, Structure summary