1LAU

URACIL-DNA GLYCOSYLASE

PDB DOI: https://doi.org/10.2210/pdb1LAU/pdb
NAKB: 1LAU

Classification: HYDROLASE/DNA
Organism(s): Human alphaherpesvirus 1
Mutation(s): No

Deposited: 1996-01-03 Released: 1996-06-10
Deposition Author(s): Pearl, L.H., Savva, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.225
R-Value Work: 0.174
R-Value Observed: 0.174

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

The structural basis of specific base-excision repair by uracil-DNA glycosylase.

Savva, R., McAuley-Hecht, K., Brown, T., Pearl, L.

(1995) Nature 373: 487-493

PubMed: 7845459 Search on PubMed
DOI: https://doi.org/10.1038/373487a0
Primary Citation of Related Structures:
1LAU, 1UDG, 1UDH

PubMed Abstract:
The 1.75-A crystal structure of the uracil-DNA glycosylase from herpes simplex virus type-1 reveals a new fold, distantly related to dinucleotide-binding proteins. Complexes with a trideoxynucleotide, and with uracil, define the DNA-binding site and allow a detailed understanding of the exquisitely specific recognition of uracil in DNA. The overall structure suggests binding models for elongated single- and double-stranded DNA substrates. Conserved residues close to the uracil-binding site suggest a catalytic mechanism for hydrolytic base excision.

Organizational Affiliation

Department of Biochemistry and Molecular Biology, University College London, UK.

Macromolecule Content

Total Structure Weight: 28.23 kDa
Atom Count: 2,048
Modelled Residue Count: 231
Deposited Residue Count: 247
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (URACIL-DNA GLYCOSYLASE (E.C.3.2.2.-))	B [auth E]	244	Human alphaherpesvirus 1	Mutation(s): 0 EC: 3.2.2.27
UniProt
Find proteins for P10186 (Human herpesvirus 1 (strain 17)) Explore P10186 Go to UniProtKB: P10186
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P10186
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(TPTP*T)-3')	A [auth D]	3	N/A
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.225
R-Value Work: 0.174
R-Value Observed: 0.174
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.66	α = 90
b = 61.83	β = 90
c = 86.67	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
MOSFLM	data reduction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 1996-06-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1996-06-10
Type: Initial release
Version 1.1: 2008-05-22
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-02-14
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.