2J6V | pdb_00002j6v

Crystal structure of the DNA repair enzyme UV Damage Endonuclease

PDB DOI: https://doi.org/10.2210/pdb2J6V/pdb

Classification: LYASE
Organism(s): Thermus thermophilus
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2006-10-04 Released: 2007-10-16
Deposition Author(s): Paspaleva, K., Thomassen, E.A.J., Pannu, N.S., Goossen, N., Abrahams, J.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.212 (Depositor), 0.214 (DCC)
R-Value Work:
0.182 (Depositor), 0.184 (DCC)
R-Value Observed:
0.184 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure of the DNA Repair Enzyme Ultraviolet Damage Endonuclease.

Paspaleva, K., Thomassen, E.A.J., Pannu, N.S., Iwai, S., Moolenaar, G.F., Goosen, N., Abrahams, J.P.

(2007) Structure 15: 1316

PubMed: 17937920 Search on PubMed
DOI: https://doi.org/10.1016/j.str.2007.05.010
Primary Citation Related Structures:
2J6V

PubMed Abstract:
The ultraviolet damage endonuclease (UVDE) performs the initial step in an alternative excision repair pathway of UV-induced DNA damage, nicking immediately adjacent to the 5' phosphate of the damaged nucleotides. Unique for a single-protein DNA repair endonuclease, it can detect different types of damage. Here we show that Thermus thermophilus UVDE shares some essential structural features with Endo IV, an enzyme from the base excision repair pathway that exclusively nicks at abasic sites. A comparison between the structures indicates how DNA is bound by UVDE, how UVDE may recognize damage, and which of its residues are involved in catalysis. Furthermore, the comparison suggests an elegant explanation of UVDE's potential to recognize different types of damage. Incision assays including point mutants of UVDE confirmed the relevance of these conclusions.

Organizational Affiliation

Laboratory of Molecular Genetics, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.

Macromolecule Content

Total Structure Weight: 68.94 kDa
Atom Count: 4,829
Modeled Residue Count: 561
Deposited Residue Count: 604
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UV ENDONUCLEASE	A, B	301	Thermus thermophilus	Mutation(s): 1
UniProt
Find proteins for Q746K1 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q746K1 Go to UniProtKB: Q746K1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q746K1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A]	F [auth A], J [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] G [auth B] H [auth B] C [auth A], D [auth A], E [auth A], G [auth B], H [auth B], I [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B]

Modified Residues 3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY Query on ALY	A, B	L-PEPTIDE LINKING	C₈ H₁₆ N₂ O₃		LYS
KCX Query on KCX	A, B	L-PEPTIDE LINKING	C₇ H₁₄ N₂ O₄		LYS
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.212 (Depositor), 0.214 (DCC)
R-Value Work: 0.182 (Depositor), 0.184 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.352	α = 106.14
b = 48.7	β = 94.36
c = 68.763	γ = 114.2

Software Package:

Software Name	Purpose
ARP/wARP	model building
MOSFLM	data reduction
SCALA	data scaling
AFRO	phasing
CRUNCH2	phasing
BP3	phasing
ARP/wARP	phasing
REFMAC	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-10-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-10-16
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-06-28
Changes: Refinement description
Version 1.4: 2024-10-23
Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary