DB code: S00401

RLCP classification 1.40.4930.61 : Hydrolysis
CATH domain 3.40.470.10 : Uracil-DNA Glycosylase, subunit E Catalytic domain
E.C. 3.2.2.-
CSA 1eug
M-CSA 1eug
MACiE M0071

CATH domain Related DB codes (homologues)

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P13051 Uracil-DNA glycosylase
UDG
EC 3.2.2.-
NP_003353.1 (Protein)
NM_003362.3 (DNA/RNA sequence)
NP_550433.1 (Protein)
NM_080911.2 (DNA/RNA sequence)
PF03167 (UDG)
[Graphical View]
P12295 Uracil-DNA glycosylase
UDG
EC 3.2.2.-
NP_417075.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_490808.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF03167 (UDG)
[Graphical View]
P10186 Uracil-DNA glycosylase
UDG
EC 3.2.2.-
NP_044603.1 (Protein)
NC_001806.1 (DNA/RNA sequence)
PF03167 (UDG)
[Graphical View]

KEGG enzyme name

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P13051 UNG_HUMAN Monomer. Interacts with HIV-1 Vpr. Isoform 1: Mitochondrion. Isoform 2: Nucleus.
P12295 UNG_ECOLI Monomer. Cytoplasm.
P10186 UNG_HHV11

KEGG Pathways
Map code Pathways E.C.

Compound table
Substrates Products Intermediates
KEGG-id L00033 C00001 C00106 C02270
E.C.
Compound DNA uracil H2O Uracil Base-removed DNA
Type amide group,nucleic acids H2O amide group,aromatic ring (with nitrogen atoms) carbohydrate,nucleic acids,phosphate group/phosphate ion
ChEBI 15377
17568
PubChem 22247451
962
1174
1emhA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:T-G-T-P2U-A-T-C-T-T (chain B:double stranded DNA) Unbound Unbound
1emjA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:URA Bound:T-G-T-ASU-A-T-C-T-T (chain B:double stranded DNA)
1eugA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1flzA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:URA Unbound
1sspE Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:URA Bound:C-T-G-T-ORP-A-T-C-T-T (chain A:double stranded DNA)
1ughE Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1uugA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1uugC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
2eugA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:URA Unbound
2sspE Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:C-T-G-T-AAB-A-T-C-T-T (chain A:double stranded DNA)
2uugA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
2uugB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
3eugA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
4eugA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
4sknE Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:URA Bound:T-G-G-G-ORP-G-G-C-T-T (chain A:double stranded DNA)
5eugA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:URA Unbound
1lauE Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:T-T-T (chain D:single stranded DNA) Unbound Unbound
1udgA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1udhA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:URA Unbound

Reference for Active-site residues
resource references E.C.
literature [18],[19]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1emhA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 145;TYR 147;ASN 204;HIS 268
1emjA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 145;TYR 147;ASN 204;HIS 268
1eugA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 64;TYR 66;ASN 123;HIS 187
1flzA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 64;TYR 66;ASN 123;HIS 187
1sspE Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 145;TYR 147;ASN 204;HIS 268
1ughE Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 145;TYR 147;ASN 204;HIS 268
1uugA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 64;TYR 66;ASN 123;HIS 187
1uugC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 64;TYR 66;ASN 123;HIS 187
2eugA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 64;TYR 66;ASN 123;HIS 187
2sspE Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 145;TYR 147;ASN 204;HIS 268
2uugA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 64;TYR 66;ASN 123; mutant H187D
2uugB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 64;TYR 66;ASN 123; mutant H187D
3eugA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 64;TYR 66;ASN 123;HIS 187
4eugA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 64;TYR 66;ASN 123; mutant H187Q
4sknE Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;TYR 147;ASN 204;HIS 268 mutant D145N
5eugA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 64;TYR 66;ASN 123; mutant H187Q
1lauE Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 88;TYR 90;ASN 147;HIS 210
1udgA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 88;TYR 90;ASN 147;HIS 210
1udhA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 88;TYR 90;ASN 147;HIS 210

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
p.873-875, Fig.5 2
[3]
p.491-493, Fig.5 2
[6]
p.5220-5221
[7]
p.4884-4885
[10]
p.22-23
[12]
Fig.5
[13]
Fig.6, Fig.7
[14]
p.190-194, Fig.5
[15]
p.7718
[16]
p.754
[17]
p.6-9, Fig.5 2
[18]
p.15391
[19]
Scheme 1
[20]
p.1928

References
[1]
Resource
Comments X-ray crystallography (2.0 Angstroms)
Medline ID 95211838
PubMed ID 7697717
Journal Cell
Year 1995
Volume 80
Pages 869-78
Authors Mol CD, Arvai AS, Slupphaug G, Kavli B, Alseth I, Krokan HE, Tainer JA
Title Crystal structure and mutational analysis of human uracil-DNA glycosylase: structural basis for specificity and catalysis.
Related PDB
Related UniProtKB P13051
[2]
Resource
Comments X-ray crystallography (1.9 Angstroms)
Medline ID 95401260
PubMed ID 7671300
Journal Cell
Year 1995
Volume 82
Pages 701-8
Authors Mol CD, Arvai AS, Sanderson RJ, Slupphaug G, Kavli B, Krokan HE, Mosbaugh DW, Tainer JA
Title Crystal structure of human uracil-DNA glycosylase in complex with a protein inhibitor: protein mimicry of DNA.
Related PDB 1ugh
Related UniProtKB P13051
[3]
Resource
Comments
Medline ID
PubMed ID 7845459
Journal Nature
Year 1995
Volume 373
Pages 487-93
Authors Savva R, McAuley-Hecht K, Brown T, Pearl L
Title The structural basis of specific base-excision repair by uracil-DNA glycosylase.
Related PDB 1lau 1udg 1udh
Related UniProtKB
[4]
Resource
Comments X-ray crystallography
Medline ID 97055940
PubMed ID 8900285
Journal Nature
Year 1996
Volume 384
Pages 87-92
Authors Slupphaug G, Mol CD, Kavli B, Arvai AS, Krokan HE, Tainer JA
Title A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA.
Related PDB 4skn
Related UniProtKB P13051
[5]
Resource
Comments NMR
Medline ID 97407932
PubMed ID 9261156
Journal J Biol Chem
Year 1997
Volume 272
Pages 21408-19
Authors Lundquist AJ, Beger RD, Bennett SE, Bolton PH, Mosbaugh DW
Title Site-directed mutagenesis and characterization of uracil-DNA glycosylase inhibitor protein. Role of specific carboxylic amino acids in complex formation with Escherichia coli uracil-DNA glycosylase.
Related PDB
Related UniProtKB P12295
[6]
Resource
Comments X-ray crystallography
Medline ID 98393562
PubMed ID 9724657
Journal EMBO J
Year 1998
Volume 17
Pages 5214-26
Authors Parikh SS, Mol CD, Slupphaug G, Bharati S, Krokan HE, Tainer JA
Title Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylase with DNA.
Related PDB 1ssp 2ssp
Related UniProtKB P13051
[7]
Resource
Comments X-ray crystallography
Medline ID 98451580
PubMed ID 9776748
Journal Nucleic Acids Res
Year 1998
Volume 26
Pages 4880-4887
Authors Ravishankar R, Bidya Sagar M, Roy S, Purnapatre K, Handa P, Varshney U, Vijayan M
Title X-ray analysis of a complex of Escherichia coli uracil DNA glycosylase (EcUDG) with a proteinaceous inhibitor. The structure elucidation of a prokaryotic UDG.
Related PDB P12295
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 9417045
Journal J Biol Chem
Year 1998
Volume 273
Pages 45-50
Authors Panayotou G, Brown T, Barlow T, Pearl LH, Savva R
Title Direct measurement of the substrate preference of uracil-DNA glycosylase.
Related PDB
Related UniProtKB
[9]
Resource
Comments X-ray crystallography
Medline ID 99182421
PubMed ID 10080896
Journal J Mol Biol
Year 1999
Volume 287
Pages 331-346
Authors Putnam CD, Shroyer MJ, Lundquist AJ, Mol CD, Arvai AS, Mosbaugh DW, Tainer JA
Title Protein mimicry of DNA from crystal structures of the uracil-DNA glycosylase inhibitor protein and its complex with Escherichia coli uracil-DNA glycosylase.
Related PDB 1uug 2uug
Related UniProtKB P12295
[10]
Resource
Comments X-ray crystallography (1.43-1.60 Angstroms)
Medline ID 99188668
PubMed ID 10090282
Journal Proteins
Year 1999
Volume 35
Pages 13-24
Authors Xiao G, Tordova M, Jagadeesh J, Drohat AC, Stivers JT, Gilliland GL
Title Crystal structure of Escherichia coli uracil DNA glycosylase and its complexes with uracil and glycerol: structure and glycosylase mechanism revisited.
Related PDB 1eug 2eug 3eug 4eug 5eug
Related UniProtKB P12295
[11]
Resource
Comments X-ray crystallography
Medline ID 20480086
PubMed ID 11027138
Journal Biochemistry
Year 2000
Volume 39
Pages 12585-12594
Authors Werner RM, Jiang YL, Gordley RG, Jagadeesh GJ, Ladner JE, Xiao G, Tordova M, Gilliland GL, Stivers JT
Title Stressing-out DNA? The contribution of serine-phosphodiester interactions in catalysis by uracil DNA glycosylase.
Related PDB 1flz
Related UniProtKB P12295
[12]
Resource
Comments X-ray crystallography (1.8-2.0 Angstroms)
Medline ID
PubMed ID 10805771
Journal Proc Natl Acad Sci U S A
Year 2000
Volume 97
Pages 5083-5088
Authors Parikh SS, Walcher G, Jones GD, Slupphaug G, Krokan HE, Blackburn GM, Tainer JA
Title Uracil-DNA glycosylase-DNA substrate and product structures: conformational strain promotes catalytic efficiency by coupled stereoelectronic effects.
Related PDB 1emh 1emj
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 10946228
Journal Mutat Res
Year 2000
Volume 460
Pages 183-99
Authors Parikh SS, Putnam CD, Tainer JA
Title Lessons learned from structural results on uracil-DNA glycosylase.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 11087352
Journal Biochemistry
Year 2000
Volume 39
Pages 14054-64
Authors Werner RM, Stivers JT
Title Kinetic isotope effect studies of the reaction catalyzed by uracil DNA glycosylase: evidence for an oxocarbenium ion-uracil anion intermediate.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 11412125
Journal Biochemistry
Year 2001
Volume 40
Pages 7710-9
Authors Jiang YL, Stivers JT
Title Reconstructing the substrate for uracil DNA glycosylase: tracking the transmission of binding energy in catalysis.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 11607036
Journal Nature
Year 2001
Volume 413
Pages 752-5
Authors Dinner AR, Blackburn GM, Karplus M
Title Uracil-DNA glycosylase acts by substrate autocatalysis.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 11716455
Journal Arch Biochem Biophys
Year 2001
Volume 396
Pages 1-9
Authors Stivers JT, Drohat AC
Title Uracil DNA glycosylase: insights from a master catalyst.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 11859082
Journal J Biol Chem
Year 2002
Volume 277
Pages 15385-92
Authors Jiang YL, Drohat AC, Ichikawa Y, Stivers JT
Title Probing the limits of electrostatic catalysis by uracil DNA glycosylase using transition state mimicry and mutagenesis.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 12136091
Journal Nucleic Acids Res
Year 2002
Volume 30
Pages 3086-95
Authors Handa P, Acharya N, Varshney U
Title Effects of mutations at tyrosine 66 and asparagine 123 in the active site pocket of Escherichia coli uracil DNA glycosylase on uracil excision from synthetic DNA oligomers: evidence for the occurrence of long-range interactions between the enzyme and substrate.
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 12590578
Journal Biochemistry
Year 2003
Volume 42
Pages 1922-9
Authors Jiang YL, Ichikawa Y, Song F, Stivers JT
Title Powering DNA repair through substrate electrostatic interactions.
Related PDB
Related UniProtKB

Comments
Many catalytic mechanisms of this enzyme, UDG, have been proposed to date. This enzyme exists ubiquitously, and its active sites are conserved throughout those from viral, eukaryotic, and mammalian sources [7].
Initially, the catalysis of UDG was considered to be SN2-like reaction mechanism, in which Asp88 and His210 (of 1lau; UDG from herpes simplex virus type-1) acts as base and acid, respectively [1], [3] & [7].
In recent years, however, an alternative mechanism, SN1-like dissociative mechanism, in which oxocarbenium-ion transition-state would be stablised, was proposed [10], [13]. The catalysis is supported by the following factors;
(a) the active site residues (see [17], [18], [19])
(b) the DNA backbone phosphodiester (especially, from +1, -1, & -2 subsite nucleotides) (see [11], [15], [16], [17])
(c) the normally trigonal planar 1-position of uracil strained to an almost tetrahedral geometry (see [12], [14], [17], [20])
Taken together, the reaction proceeds as follows:
(1) An oxocarbenium-ion transition-state is formed (SN1-like dissociative mechanism), where negative charge and positive charge are developed on uracil group and O4' (or C1') atom of deoxyribose, respectively. Here, Asp88 and His210 stabilize the negative charge and positive charge, respectively. Moreover, the stabilization of the positive charge must be assisted by nearby DNA backbone phosphodiester groups.
(2) Asp88 acts as a general base to activate a water.
(3) The activated water makes a nucleophilic attack on the C1' atom.
(4) His210 acts as a general acid to protonate the N1 atom of the leaving uracil.

Created Updated
2002-09-27 2009-02-26