1UGH

CRYSTAL STRUCTURE OF HUMAN URACIL-DNA GLYCOSYLASE IN COMPLEX WITH A PROTEIN INHIBITOR: PROTEIN MIMICRY OF DNA

PDB DOI: 10.2210/pdb1UGH/pdb

Classification: GLYCOSYLASE
Organism(s): Homo sapiens, Bacillus phage PBS2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 1999-02-05 Released: 1999-02-16
Deposition Author(s): Mol, C.D., Arvai, A.S., Sanderson, R.J., Slupphaug, G., Kavli, B., Krokan, H.E., Mosbaugh, D.W., Tainer, J.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.255
R-Value Work: 0.198

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of human uracil-DNA glycosylase in complex with a protein inhibitor: protein mimicry of DNA.

Mol, C.D., Arvai, A.S., Sanderson, R.J., Slupphaug, G., Kavli, B., Krokan, H.E., Mosbaugh, D.W., Tainer, J.A.

(1995) Cell 82: 701-708

PubMed: 7671300 Search on PubMed
DOI: 10.1016/0092-8674(95)90467-0
Primary Citation of Related Structures:
1UGH

PubMed Abstract:

Uracil-DNA glycosylase inhibitor (Ugi) is a B. subtilis bacteriophage protein that protects the uracil-containing phage DNA by irreversibly inhibiting the key DNA repair enzyme uracil-DNA glycosylase (UDG). The 1.9 A crystal structure of Ugi complexed to human UDG reveals that the Ugi structure, consisting of a twisted five-stranded antiparallel beta sheet and two alpha helices, binds by inserting a beta strand into the conserved DNA-binding groove of the enzyme without contacting the uracil specificity pocket. The resulting interface, which buries over 1200 A2 on Ugi and involves the entire beta sheet and an alpha helix, is polar and contains 22 water molecules. Ugi binds the sequence-conserved DNA-binding groove of UDG via shape and electrostatic complementarity, specific charged hydrogen bonds, and hydrophobic packing enveloping Leu-272 from a protruding UDG loop. The apparent mimicry by Ugi of DNA interactions with UDG provides both a structural mechanism for UDG binding to DNA, including the enzyme-assisted expulsion of uracil from the DNA helix, and a crystallographic basis for the design of inhibitors with scientific and therapeutic applications.

Related Citations:

Protein mimicry of DNA from crystal structures of the uracil-DNA glycosylase inhibitor protein and its complex with Escherichia coli uracil-DNA glycosylase.
Putnam, C.D., Shroyer, M.J., Lundquist, A.J., Mol, C.D., Arvai, A.S., Mosbaugh, D.W., Tainer, J.A.
(1999) J Mol Biol 287: 331

Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylase with DNA.
Parikh, S.S., Mol, C.D., Slupphaug, G., Bharati, S., Krokan, H.E., Tainer, J.A.
(1998) EMBO J 17: 5214

A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA.
Slupphaug, G., Mol, C.D., Kavli, B., Arvai, A.S., Krokan, H.E., Tainer, J.A.
(1996) Nature 384: 87

Crystal structure and mutational analysis of human uracil-DNA glycosylase: structural basis for specificity and catalysis.
Mol, C.D., Arvai, A.S., Slupphaug, G., Kavli, B., Alseth, I., Krokan, H.E., Tainer, J.A.
(1995) Cell 80: 869

Organizational Affiliation:

Department of Molecular Biology, Scripps Research Institute, La Jolla, California 92037, USA.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (URACIL-DNA GLYCOSYLASE)	A [auth E]	223	Homo sapiens	Mutation(s): 0 Gene Names: UNG, DGU, UNG1, UNG15 EC: 3.2.2.3 (PDB Primary Data), 3.2.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P13051 (Homo sapiens) Explore P13051 Go to UniProtKB: P13051
PHAROS: P13051 GTEx: ENSG00000076248
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13051
Protein Feature View Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (URACIL-DNA GLYCOSYLASE INHIBITOR)	B [auth I]	82	Bacillus phage PBS2	Mutation(s): 0 Gene Names: UGI
UniProt
Find proteins for P14739 (Bacillus phage PBS2) Explore P14739 Go to UniProtKB: P14739
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14739
Protein Feature View Expand
Reference Sequence