6KII | pdb_00006kii

photolyase from Arthrospira platensis

PDB DOI: https://doi.org/10.2210/pdb6KII/pdb

Classification: DNA BINDING PROTEIN, LYASE
Organism(s): Limnospira platensis
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2019-07-18 Released: 2020-07-22
Deposition Author(s): Yan, H., Zhu, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.174 (Depositor), 0.170 (DCC)
R-Value Work:
0.155 (Depositor), 0.160 (DCC)
R-Value Observed:
0.156 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

A newly identified photolyase from Arthrospira platensis possesses a unique methenyltetrahydrofolate chromophore-binding pattern.

Yan, H., Zhu, K., Teng, M., Li, X.

(2020) FEBS Lett 594: 740-750

PubMed: 31675429 Search on PubMed
DOI: https://doi.org/10.1002/1873-3468.13657
Primary Citation of Related Structures:
6KII

PubMed Abstract:
Cyclobutane pyrimidine dimers (CPD), as a common DNA damage caused by UV radiation, often lead to skin cancer. Here, we identified a photolyase from the alga Arthrospira platensis (designated as Ap-phr), which has been regarded as a safe organism for humans for centuries, that can efficiently repair CPD lesions in ssDNA and dsDNA in vitro. The 1.6 Å resolution crystal structure of Ap-phr revealed that it possesses a unique methenyltetrahydrofolate chromophore-binding pattern with high energy transfer efficiency. Our study of Ap-phr highlights its potential use in cosmetic, industrial and aesthetic medicine applications.

Organizational Affiliation

Hefei National Laboratory for Physical Sciences at Microscale, National Synchrotron Radiation Laboratory, School of Life Sciences, University of Science and Technology of China, Hefei, China.

Macromolecule Content

Total Structure Weight: 58.52 kDa
Atom Count: 4,675
Modeled Residue Count: 485
Deposited Residue Count: 490
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyribopyrimidine photolyase	A	490	Limnospira platensis	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MHF (Subject of Investigation/LOI) Query on MHF Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	5,10-METHENYL-6,7,8-TRIHYDROFOLIC ACID C₂₀ H₂₃ N₇ O₆ QYNUQALWYRSVHF-OLZOCXBDSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	D [auth A], E [auth A], F [auth A], G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]