EzCatDB: S00401
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DB codeS00401
RLCP classification1.40.4930.61 : Hydrolysis
CATH domainDomain 13.40.470.10 : Uracil-DNA Glycosylase, subunit ECatalytic domain
E.C.3.2.2.-
CSA1eug
MACiEM0071


Enzyme Name
UniProtKB

P13051P12295P10186
Protein nameUracil-DNA glycosylaseUracil-DNA glycosylaseUracil-DNA glycosylase
SynonymsUDG
EC 3.2.2.-
UDG
EC 3.2.2.-
UDG
EC 3.2.2.-
RefSeqNP_003353.1 (Protein)
NM_003362.3 (DNA/RNA sequence)
NP_550433.1 (Protein)
NM_080911.2 (DNA/RNA sequence)
NP_417075.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_490808.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
NP_044603.1 (Protein)
NC_001806.1 (DNA/RNA sequence)
PfamPF03167 (UDG)
[Graphical view]
PF03167 (UDG)
[Graphical view]
PF03167 (UDG)
[Graphical view]


UniProtKB:Accession NumberP13051P12295P10186
Entry nameUNG_HUMANUNG_ECOLIUNG_HHV11
Activity


SubunitMonomer. Interacts with HIV-1 Vpr.Monomer.
Subcellular locationIsoform 1: Mitochondrion.,Isoform 2: Nucleus.Cytoplasm.
Cofactor



Compound table: links to PDB-related databases & PoSSuM

SubstratesProducts
KEGG-idL00033C00001C00106C02270
CompoundDNA uracilH2OUracilBase-removed DNA
Typeamide group,nucleic acidsH2Oamide group,aromatic ring (with nitrogen atoms)carbohydrate,nucleic acids,phosphate group/phosphate ion
ChEBI
15377
17568

PubChem
22247451
962
1174

            
1emhAAnalogue:T-G-T-P2U-A-T-C-T-T(chain B:double stranded DNA) UnboundUnbound
1emjAUnbound Bound:URABound:T-G-T-ASU-A-T-C-T-T(chain B:double stranded DNA)
1eugAUnbound UnboundUnbound
1flzAUnbound Bound:URAUnbound
1sspEUnbound Bound:URABound:C-T-G-T-ORP-A-T-C-T-T(chain A:double stranded DNA)
1ughEUnbound UnboundUnbound
1uugAUnbound UnboundUnbound
1uugCUnbound UnboundUnbound
2eugAUnbound Bound:URAUnbound
2sspEUnbound UnboundBound:C-T-G-T-AAB-A-T-C-T-T(chain A:double stranded DNA)
2uugAUnbound UnboundUnbound
2uugBUnbound UnboundUnbound
3eugAUnbound UnboundUnbound
4eugAUnbound UnboundUnbound
4sknEUnbound Bound:URABound:T-G-G-G-ORP-G-G-C-T-T(chain A:double stranded DNA)
5eugAUnbound Bound:URAUnbound
1lauEAnalogue:T-T-T(chain D:single stranded DNA) UnboundUnbound
1udgAUnbound UnboundUnbound
1udhAUnbound Bound:URAUnbound

Active-site residues
resource
literature [18],[19]
pdbCatalytic residuescomment
          
1emhAASP 145;TYR 147;ASN 204;HIS 268
 
1emjAASP 145;TYR 147;ASN 204;HIS 268
 
1eugAASP  64;TYR  66;ASN 123;HIS 187
 
1flzAASP  64;TYR  66;ASN 123;HIS 187
 
1sspEASP 145;TYR 147;ASN 204;HIS 268
 
1ughEASP 145;TYR 147;ASN 204;HIS 268
 
1uugAASP  64;TYR  66;ASN 123;HIS 187
 
1uugCASP  64;TYR  66;ASN 123;HIS 187
 
2eugAASP  64;TYR  66;ASN 123;HIS 187
 
2sspEASP 145;TYR 147;ASN 204;HIS 268
 
2uugAASP  64;TYR  66;ASN 123;       
mutant H187D
2uugBASP  64;TYR  66;ASN 123;       
mutant H187D
3eugAASP  64;TYR  66;ASN 123;HIS 187
 
4eugAASP  64;TYR  66;ASN 123;       
mutant H187Q
4sknE       ;TYR 147;ASN 204;HIS 268
mutant D145N
5eugAASP  64;TYR  66;ASN 123;       
mutant H187Q
1lauEASP  88;TYR  90;ASN 147;HIS 210
 
1udgAASP  88;TYR  90;ASN 147;HIS 210
 
1udhAASP  88;TYR  90;ASN 147;HIS 210
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]p.873-875, Fig.52
[3]p.491-493, Fig.52
[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.52
[18]p.15391
[19]Scheme 1
[20]p.1928

references
[1]
CommentsX-ray crystallography (2.0 Angstroms)
Medline ID95211838
PubMed ID7697717
JournalCell
Year1995
Volume80
Pages869-78
AuthorsMol CD, Arvai AS, Slupphaug G, Kavli B, Alseth I, Krokan HE, Tainer JA
TitleCrystal structure and mutational analysis of human uracil-DNA glycosylase: structural basis for specificity and catalysis.
Related UniProtKBP13051
[2]
CommentsX-ray crystallography (1.9 Angstroms)
Medline ID95401260
PubMed ID7671300
JournalCell
Year1995
Volume82
Pages701-8
AuthorsMol CD, Arvai AS, Sanderson RJ, Slupphaug G, Kavli B, Krokan HE, Mosbaugh DW, Tainer JA
TitleCrystal structure of human uracil-DNA glycosylase in complex with a protein inhibitor: protein mimicry of DNA.
Related PDB1ugh
Related UniProtKBP13051
[3]
PubMed ID7845459
JournalNature
Year1995
Volume373
Pages487-93
AuthorsSavva R, McAuley-Hecht K, Brown T, Pearl L
TitleThe structural basis of specific base-excision repair by uracil-DNA glycosylase.
Related PDB1lau,1udg,1udh
[4]
CommentsX-ray crystallography
Medline ID97055940
PubMed ID8900285
JournalNature
Year1996
Volume384
Pages87-92
AuthorsSlupphaug G, Mol CD, Kavli B, Arvai AS, Krokan HE, Tainer JA
TitleA nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA.
Related PDB4skn
Related UniProtKBP13051
[5]
CommentsNMR
Medline ID97407932
PubMed ID9261156
JournalJ Biol Chem
Year1997
Volume272
Pages21408-19
AuthorsLundquist AJ, Beger RD, Bennett SE, Bolton PH, Mosbaugh DW
TitleSite-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 UniProtKBP12295
[6]
CommentsX-ray crystallography
Medline ID98393562
PubMed ID9724657
JournalEMBO J
Year1998
Volume17
Pages5214-26
AuthorsParikh SS, Mol CD, Slupphaug G, Bharati S, Krokan HE, Tainer JA
TitleBase excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylase with DNA.
Related PDB1ssp,2ssp
Related UniProtKBP13051
[7]
CommentsX-ray crystallography
Medline ID98451580
PubMed ID9776748
JournalNucleic Acids Res
Year1998
Volume26
Pages4880-4887
AuthorsRavishankar R, Bidya Sagar M, Roy S, Purnapatre K, Handa P, Varshney U, Vijayan M
TitleX-ray analysis of a complex of Escherichia coli uracil DNA glycosylase (EcUDG) with a proteinaceous inhibitor. The structure elucidation of a prokaryotic UDG.
Related PDBP12295
[8]
PubMed ID9417045
JournalJ Biol Chem
Year1998
Volume273
Pages45-50
AuthorsPanayotou G, Brown T, Barlow T, Pearl LH, Savva R
TitleDirect measurement of the substrate preference of uracil-DNA glycosylase.
[9]
CommentsX-ray crystallography
Medline ID99182421
PubMed ID10080896
JournalJ Mol Biol
Year1999
Volume287
Pages331-346
AuthorsPutnam CD, Shroyer MJ, Lundquist AJ, Mol CD, Arvai AS, Mosbaugh DW, Tainer JA
TitleProtein mimicry of DNA from crystal structures of the uracil-DNA glycosylase inhibitor protein and its complex with Escherichia coli uracil-DNA glycosylase.
Related PDB1uug,2uug
Related UniProtKBP12295
[10]
CommentsX-ray crystallography (1.43-1.60 Angstroms)
Medline ID99188668
PubMed ID10090282
JournalProteins
Year1999
Volume35
Pages13-24
AuthorsXiao G, Tordova M, Jagadeesh J, Drohat AC, Stivers JT, Gilliland GL
TitleCrystal structure of Escherichia coli uracil DNA glycosylase and its complexes with uracil and glycerol: structure and glycosylase mechanism revisited.
Related PDB1eug,2eug,3eug,4eug,5eug
Related UniProtKBP12295
[11]
CommentsX-ray crystallography
Medline ID20480086
PubMed ID11027138
JournalBiochemistry
Year2000
Volume39
Pages12585-12594
AuthorsWerner RM, Jiang YL, Gordley RG, Jagadeesh GJ, Ladner JE, Xiao G, Tordova M, Gilliland GL, Stivers JT
TitleStressing-out DNA? The contribution of serine-phosphodiester interactions in catalysis by uracil DNA glycosylase.
Related PDB1flz
Related UniProtKBP12295
[12]
CommentsX-ray crystallography (1.8-2.0 Angstroms)
PubMed ID10805771
JournalProc Natl Acad Sci U S A
Year2000
Volume97
Pages5083-5088
AuthorsParikh SS, Walcher G, Jones GD, Slupphaug G, Krokan HE, Blackburn GM, Tainer JA
TitleUracil-DNA glycosylase-DNA substrate and product structures: conformational strain promotes catalytic efficiency by coupled stereoelectronic effects.
Related PDB1emh,1emj
[13]
PubMed ID10946228
JournalMutat Res
Year2000
Volume460
Pages183-99
AuthorsParikh SS, Putnam CD, Tainer JA
TitleLessons learned from structural results on uracil-DNA glycosylase.
[14]
PubMed ID11087352
JournalBiochemistry
Year2000
Volume39
Pages14054-64
AuthorsWerner RM, Stivers JT
TitleKinetic isotope effect studies of the reaction catalyzed by uracil DNA glycosylase: evidence for an oxocarbenium ion-uracil anion intermediate.
[15]
PubMed ID11412125
JournalBiochemistry
Year2001
Volume40
Pages7710-9
AuthorsJiang YL, Stivers JT
TitleReconstructing the substrate for uracil DNA glycosylase: tracking the transmission of binding energy in catalysis.
[16]
PubMed ID11607036
JournalNature
Year2001
Volume413
Pages752-5
AuthorsDinner AR, Blackburn GM, Karplus M
TitleUracil-DNA glycosylase acts by substrate autocatalysis.
[17]
PubMed ID11716455
JournalArch Biochem Biophys
Year2001
Volume396
Pages1-9
AuthorsStivers JT, Drohat AC
TitleUracil DNA glycosylase: insights from a master catalyst.
[18]
PubMed ID11859082
JournalJ Biol Chem
Year2002
Volume277
Pages15385-92
AuthorsJiang YL, Drohat AC, Ichikawa Y, Stivers JT
TitleProbing the limits of electrostatic catalysis by uracil DNA glycosylase using transition state mimicry and mutagenesis.
[19]
PubMed ID12136091
JournalNucleic Acids Res
Year2002
Volume30
Pages3086-95
AuthorsHanda P, Acharya N, Varshney U
TitleEffects 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.
[20]
PubMed ID12590578
JournalBiochemistry
Year2003
Volume42
Pages1922-9
AuthorsJiang YL, Ichikawa Y, Song F, Stivers JT
TitlePowering DNA repair through substrate electrostatic interactions.

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.

createdupdated
2002-09-272009-02-26
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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