EzCatDB: T00231
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DB codeT00231
RLCP classification1.15.8230.362 : Hydrolysis
CATH domainDomain 12.70.40.10 : Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain ACatalytic domain
Domain 22.70.40.10 : Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain ACatalytic domain
Domain 32.70.40.10 : Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain ACatalytic domain
E.C.3.6.1.23
CSA1dup

CATH domainRelated DB codes (homologues)
2.70.40.10 : Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain AM00206

Enzyme Name
UniProtKBKEGG

A4GD96P06968P0A552O34919P33317
Protein name
Deoxyuridine 5''-triphosphate nucleotidohydrolaseDeoxyuridine 5''-triphosphate nucleotidohydrolase
Deoxyuridine 5''-triphosphate nucleotidohydrolasedUTP diphosphatase
Deoxyuridine-triphosphatase
dUTPase
dUTP pyrophosphatase
Deoxyuridine 5'-triphosphate nucleotidohydrolase
Deoxyuridine 5'-triphosphatase
SynonymsDUTP pyrophosphatase
EC 3.6.1.23
dUTPase
EC 3.6.1.23
dUTP pyrophosphatase
dUTPase
EC 3.6.1.23
dUTP pyrophosphatase
YosS protein (DUTPase homolog)
dUTPase
EC 3.6.1.23
dUTP pyrophosphatase
RefSeq
NP_418097.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_491793.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
NP_217213.1 (Protein)
NC_000962.3 (DNA/RNA sequence)
NP_337272.1 (Protein)
NC_002755.2 (DNA/RNA sequence)
YP_006516141.1 (Protein)
NC_018143.1 (DNA/RNA sequence)
NP_389883.1 (Protein)
NC_000964.3 (DNA/RNA sequence)
NP_009811.3 (Protein)
NM_001178600.3 (DNA/RNA sequence)
PfamPF00692 (dUTPase)
[Graphical view]
PF00692 (dUTPase)
[Graphical view]
PF00692 (dUTPase)
[Graphical view]
PF00692 (dUTPase)
[Graphical view]
PF00692 (dUTPase)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00240Pyrimidine metabolism

UniProtKB:Accession NumberA4GD96P06968P0A552O34919P33317
Entry nameA4GD96_9POXVDUT_ECOLIDUT_MYCTUO34919_BACSUDUT_YEAST
Activity
dUTP + H(2)O = dUMP + diphosphate.dUTP + H(2)O = dUMP + diphosphate.
dUTP + H(2)O = dUMP + diphosphate.
Subunit
Homotrimer.


Subcellular location




Cofactor





Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00305C00460C00001C00365C00013
CompoundMagnesiumdUTPH2OdUMPPyrophosphate
Typedivalent metal (Ca2+, Mg2+)amide group,nucleotideH2Oamide group,nucleotidephosphate group/phosphate ion
ChEBI18420
17625
15377
17622
29888
PubChem888
65070
962
22247451
65063
21961011
1023
             
2okbAUnboundUnbound UnboundAnalogue:SO4
2okbBUnboundUnbound UnboundAnalogue:SO4
2okbCUnboundUnbound UnboundAnalogue:SO4
2okdAUnboundUnbound UnboundUnbound
2okdBUnboundUnbound UnboundUnbound
2okdCUnboundUnbound UnboundUnbound
2okeAUnboundAnalogue:DUP UnboundUnbound
2okeBBound:_MGAnalogue:DUP UnboundUnbound
2okeCUnboundAnalogue:DUP UnboundUnbound
2ol0AUnboundAnalogue:DUD UnboundUnbound
2ol0BBound:_MGAnalogue:DUD UnboundUnbound
2ol0CUnboundAnalogue:DUD UnboundUnbound
2ol1AUnboundUnbound Bound:UMPUnbound
2ol1BUnboundUnbound Bound:UMPUnbound
2ol1CUnboundUnbound Bound:UMPUnbound
1dudAUnboundAnalogue:DUDBound:HOH 271UnboundUnbound
1dupAUnboundUnbound UnboundUnbound
1eu5AUnboundUnbound UnboundUnbound
1euwAUnboundUnbound UnboundUnbound
1rn8ABound:_MGAnalogue:DUPBound:HOH 5UnboundUnbound
1rnjABound:_MGAnalogue:DUP UnboundUnbound
1sehAUnboundUnbound Bound:UMPUnbound
1sylABound:_MGBound:DUTBound:HOH 107UnboundUnbound
2hr6AAnalogue:_MNAnalogue:DUDBound:HOH 1012UnboundUnbound
2hrmAUnboundAnalogue:UC5 UnboundUnbound
1mq7AUnboundUnbound UnboundUnbound
1sixABound:_MGAnalogue:DUP UnboundUnbound
1sjnABound:_MGAnalogue:DUPBound:HOH 1202UnboundUnbound
1sjnBBound:_MGAnalogue:DUPBound:HOH 3214UnboundUnbound
1sjnCBound:_MGAnalogue:DUPBound:HOH 3178UnboundUnbound
1slhABound:_MGAnalogue:DUD UnboundUnbound
1slhBBound:_MGAnalogue:DUD UnboundUnbound
1slhCBound:_MGAnalogue:DUD UnboundUnbound
1sm8AAnalogue:_CRBound:DUT UnboundUnbound
1sm8BAnalogue:_CRBound:DUT UnboundUnbound
1sm8CAnalogue:_CRBound:DUT UnboundUnbound
1smcAUnboundBound:DUTBound:HOH 365UnboundUnbound
1smcBUnboundBound:DUT UnboundUnbound
1smcCUnboundBound:DUTBound:HOH 282UnboundUnbound
1snfABound:_MGUnbound Bound:UMPUnbound
1snfBBound:_MGUnbound Bound:UMPUnbound
1snfCBound:_MGUnbound Bound:UMPUnbound
2py4ABound:_MGAnalogue:DUPBound:HOH 813UnboundUnbound
2bazAUnboundUnbound UnboundUnbound
2bazBUnboundUnbound UnboundUnbound
2bazCUnboundUnbound UnboundUnbound
3f4fAUnboundUnbound Bound:UMPUnbound
3f4fBUnboundUnbound Bound:UMPUnbound
3f4fCUnboundUnbound Bound:UMPUnbound

Active-site residues
resource
literature [20]
pdbCatalytic residuesMain-chain involved in catalysiscomment
           
2okbAARG 69;SER 70;ASP 85;GLN 114
SER 70;GLY 71;VAL 83
 
2okbBARG 69;SER 70;ASP 85;GLN 114
SER 70;GLY 71;VAL 83
 
2okbCARG 69;SER 70;ASP 85;GLN 114
SER 70;GLY 71;VAL 83
 
2okdAARG 69;SER 70;ASP 85;GLN 114
SER 70;GLY 71;VAL 83
 
2okdBARG 69;SER 70;ASP 85;GLN 114
SER 70;GLY 71;VAL 83
 
2okdCARG 69;SER 70;ASP 85;GLN 114
SER 70;GLY 71;VAL 83
 
2okeAARG 69;SER 70;ASP 85;GLN 114
SER 70;GLY 71;VAL 83
 
2okeBARG 69;SER 70;ASP 85;GLN 114
SER 70;GLY 71;VAL 83
 
2okeCARG 69;SER 70;ASP 85;GLN 114
SER 70;GLY 71;VAL 83
 
2ol0AARG 69;SER 70;ASP 85;GLN 114
SER 70;GLY 71;VAL 83
 
2ol0BARG 69;SER 70;ASP 85;GLN 114
SER 70;GLY 71;VAL 83
 
2ol0CARG 69;SER 70;ASP 85;GLN 114
SER 70;GLY 71;VAL 83
 
2ol1AARG 69;SER 70;ASP 85;GLN 114
SER 70;GLY 71;VAL 83
 
2ol1BARG 69;SER 70;ASP 85;GLN 114
SER 70;GLY 71;VAL 83
 
2ol1CARG 69;SER 70;ASP 85;GLN 114
SER 70;GLY 71;VAL 83
 
1dudAARG 71;SER 72;ASP 90;GLN 119
SER 72;GLY 73;LEU 88
 
1dupAARG 71;SER 72;ASP 90;GLN 119
SER 72;GLY 73;LEU 88
 
1eu5AARG 71;SER 72;ASP 90;GLN 119
SER 72;GLY 73;LEU 88
 
1euwAARG 71;SER 72;ASP 90;GLN 119
SER 72;GLY 73;LEU 88
 
1rn8AARG 71;SER 72;ASP 90;GLN 119
SER 72;GLY 73;LEU 88
 
1rnjAARG 71;SER 72;      ;GLN 119
SER 72;GLY 73;LEU 88
mutant D90N
1sehAARG 71;SER 72;ASP 90;GLN 119
SER 72;GLY 73;LEU 88
 
1sylAARG 71;SER 72;      ;GLN 119
SER 72;GLY 73;LEU 88
mutant D90N
2hr6AARG 71;SER 72;ASP 90;GLN 119
SER 72;GLY 73;LEU 88
 
2hrmAARG 71;SER 72;ASP 90;GLN 119
SER 72;GLY 73;LEU 88
 
1mq7AARG 64;SER 65;ASP 83;GLN 113
SER 65;GLY 66;THR 81
 
1sixAARG 64;SER 65;ASP 83;GLN 113
SER 65;GLY 66;THR 81
 
1sjnAARG 64;SER 65;ASP 83;GLN 113
SER 65;GLY 66;THR 81
 
1sjnBARG 64;SER 65;ASP 83;GLN 113
SER 65;GLY 66;THR 81
 
1sjnCARG 64;SER 65;ASP 83;GLN 113
SER 65;GLY 66;THR 81
 
1slhAARG 64;SER 65;ASP 83;GLN 113
SER 65;GLY 66;THR 81
 
1slhBARG 64;SER 65;ASP 83;GLN 113
SER 65;GLY 66;THR 81
 
1slhCARG 64;SER 65;ASP 83;GLN 113
SER 65;GLY 66;THR 81
 
1sm8AARG 64;SER 65;ASP 83;GLN 113
SER 65;GLY 66;THR 81
 
1sm8BARG 64;SER 65;ASP 83;GLN 113
SER 65;GLY 66;THR 81
 
1sm8CARG 64;SER 65;ASP 83;GLN 113
SER 65;GLY 66;THR 81
 
1smcAARG 64;SER 65;ASP 83;GLN 113
SER 65;GLY 66;THR 81
 
1smcBARG 64;SER 65;ASP 83;GLN 113
SER 65;GLY 66;THR 81
 
1smcCARG 64;SER 65;ASP 83;GLN 113
SER 65;GLY 66;THR 81
 
1snfAARG 64;SER 65;ASP 83;GLN 113
SER 65;GLY 66;THR 81
 
1snfBARG 64;SER 65;ASP 83;GLN 113
SER 65;GLY 66;THR 81
 
1snfCARG 64;SER 65;ASP 83;GLN 113
SER 65;GLY 66;THR 81
 
2py4AARG 64;SER 65;ASP 83;GLN 113
SER 65;GLY 66;THR 81
 
2bazAARG 61;SER 62;ASP 80;GLN 110
SER 62;SER 63;VAL 78
 
2bazBARG 61;SER 62;ASP 80;GLN 110
SER 62;SER 63;VAL 78
 
2bazCARG 61;SER 62;ASP 80;GLN 110
SER 62;SER 63;VAL 78
 
3f4fAARG 68;SER 69;ASP 85;GLN 114
SER 69;GLY 70;VAL 83
 
3f4fBARG 68;SER 69;ASP 85;GLN 114
SER 69;GLY 70;VAL 83
 
3f4fCARG 68;SER 69;ASP 85;GLN 114
SER 69;GLY 70;VAL 83
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[6]p. 537-538
[20]Fig.1, p. 42909, 42912-42915
[23]p.577
[24]Fig.1 A, p. 315-316
[26]Fig.1 (c), p. 7864

references
[1]
CommentsX-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
Medline ID92158084
PubMed ID1311056
JournalNature
Year1992
Volume355
Pages740-3
AuthorsCedergren-Zeppezauer ES, Larsson G, Nyman PO, Dauter Z, Wilson KS
TitleCrystal structure of a dUTPase.
Related PDB1dup
Related UniProtKBP06968
[2]
PubMed ID8393252
JournalVirology
Year1993
Volume195
Pages863-5
AuthorsBroyles SS
TitleVaccinia virus encodes a functional dUTPase.
[3]
PubMed ID7958294
JournalBiochem Soc Trans
Year1994
Volume22
Pages233S
AuthorsVertessy BG, Zeppezauer M
TitleIdentification of tyrosine as an active site residue involved in the catalytic mechanism of Escherichia coli dUTPase.
[4]
PubMed ID8142479
JournalBiochim Biophys Acta
Year1994
Volume1205
Pages146-50
AuthorsVertessy BG, Zalud P, Nyman PO, Zeppezauer M
TitleIdentification of tyrosine as a functional residue in the active site of Escherichia coli dUTPase.
[5]
PubMed ID8604980
JournalBiochem Biophys Res Commun
Year1996
Volume219
Pages294-300
AuthorsVertessy BG, Persson R, Rosengren AM, Zeppezauer M, Nyman PO
TitleSpecific derivatization of the active site tyrosine in dUTPase perturbs ligand binding to the active site.
[6]
CommentsX-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
Medline ID96227973
PubMed ID8646539
JournalNat Struct Biol
Year1996
Volume3
Pages532-8
AuthorsLarsson G, Svensson LA, Nyman PO
TitleCrystal structure of the Escherichia coli dUTPase in complex with a substrate analogue (dUDP).
Related PDB1dud
Related UniProtKBP06968
[7]
PubMed ID8798636
JournalJ Biol Chem
Year1996
Volume271
Pages24010-6
AuthorsLarsson G, Nyman PO, Kvassman JO
TitleKinetic characterization of dUTPase from Escherichia coli.
[8]
PubMed ID9261872
JournalProteins
Year1997
Volume28
Pages568-79
AuthorsVertessy BG
TitleFlexible glycine rich motif of Escherichia coli deoxyuridine triphosphate nucleotidohydrolase is important for functional but not for structural integrity of the enzyme.
[9]
PubMed ID9462846
JournalFEBS Lett
Year1998
Volume421
Pages83-8
AuthorsVertessy BG, Larsson G, Persson T, Bergman AC, Persson R, Nyman PO
TitleThe complete triphosphate moiety of non-hydrolyzable substrate analogues is required for a conformational shift of the flexible C-terminus in E. coli dUTP pyrophosphatase.
[10]
PubMed ID9465078
JournalProc Natl Acad Sci U S A
Year1998
Volume95
Pages1692-7
AuthorsLazarevic V, Soldo B, Dusterhoft A, Hilbert H, Mauel C, Karamata D
TitleIntrons and intein coding sequence in the ribonucleotide reductase genes of Bacillus subtilis temperate bacteriophage SPbeta.
[11]
PubMed ID9679200
JournalDNA Res
Year1998
Volume5
Pages121-6
AuthorsGhim SY, Choi SK, Shin BS, Park SH
TitleAn 8 kb nucleotide sequence at the 3' flanking region of the sspC gene (184 degrees) on the Bacillus subtilis 168 chromosome containing an intein and an intron.
[12]
CommentsX-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
Medline ID98437602
PubMed ID9757088
JournalActa Crystallogr D Biol Crystallogr
Year1998
Volume54
Pages735-49
AuthorsDauter Z, Wilson KS, Larsson G, Nyman PO, Cedergren-Zeppezauer ES
TitleThe refined structure of dUTPase from Escherichia coli.
Related UniProtKBP06968
[13]
PubMed ID10438861
JournalJ Virol
Year1999
Volume73
Pages7710-21
AuthorsBaldo AM, McClure MA
TitleEvolution and horizontal transfer of dUTPase-encoding genes in viruses and their hosts.
[14]
PubMed ID11257499
JournalFEBS Lett
Year2001
Volume492
Pages228-32
AuthorsNord J, Nyman P, Larsson G, Drakenberg T
TitleThe C-terminus of dUTPase: observation on flexibility using NMR.
[15]
CommentsX-RAY CRYSTALLOGRAPHY (1.05 ANGSTROMS).
Medline ID21268771
PubMed ID11375495
JournalActa Crystallogr D Biol Crystallogr
Year2001
Volume57
Pages767-74
AuthorsGonzalez A, Larsson G, Persson R, Cedergren-Zeppezauer E
TitleAtomic resolution structure of Escherichia coli dUTPase determined ab initio.
Related PDB1eu5,1euw
Related UniProtKBP06968
[16]
PubMed ID12369925
JournalCurr Protein Pept Sci
Year2001
Volume2
Pages277-85
AuthorsNyman PO
TitleIntroduction. dUTPases.
[17]
PubMed ID12369926
JournalCurr Protein Pept Sci
Year2001
Volume2
Pages287-300
AuthorsPersson R, Cedergren-Zeppezauer ES, Wilson KS
TitleHomotrimeric dUTPases; structural solutions for specific recognition and hydrolysis of dUTP.
[18]
PubMed ID12369928
JournalCurr Protein Pept Sci
Year2001
Volume2
Pages313-24
AuthorsMcClure MA
TitleEvolution of the DUT gene: horizontal transfer between host and pathogen in all three domains of life.
[19]
PubMed ID12721364
JournalProc Natl Acad Sci U S A
Year2003
Volume100
Pages5670-5
AuthorsMustafi D, Bekesi A, Vertessy BG, Makinen MW
TitleCatalytic and structural role of the metal ion in dUTP pyrophosphatase.
[20]
PubMed ID15208312
JournalJ Biol Chem
Year2004
Volume279
Pages42907-15
AuthorsBarabas O, Pongracz V, Kovari J, Wilmanns M, Vertessy BG
TitleStructural insights into the catalytic mechanism of phosphate ester hydrolysis by dUTPase.
Related PDB1rn8,1rnj,1seh,1syl
[21]
PubMed ID15939294
JournalProtein Expr Purif
Year2005
Volume42
Pages92-9
AuthorsPersson R, McGeehan J, Wilson KS
TitleCloning, expression, purification, and characterisation of the dUTPase encoded by the integrated Bacillus subtilis temperate bacteriophage SPbeta.
Related PDB2baz
[22]
PubMed ID16359314
JournalMol Microbiol
Year2006
Volume59
Pages5-19
AuthorsGalperin MY, Moroz OV, Wilson KS, Murzin AG
TitleHouse cleaning, a part of good housekeeping.
[23]
PubMed ID17452782
JournalActa Crystallogr D Biol Crystallogr
Year2007
Volume63
Pages571-80
AuthorsSamal A, Schormann N, Cook WJ, DeLucas LJ, Chattopadhyay D
TitleStructures of vaccinia virus dUTPase and its nucleotide complexes.
Related PDB2okb,2okd,2oke,2ol0,2ol1
[24]
PubMed ID17932923
JournalProteins
Year2008
Volume71
Pages308-19
AuthorsKovari J, Barabas O, Varga B, Bekesi A, Tolgyesi F, Fidy J, Nagy J, Vertessy BG
TitleMethylene substitution at the alpha-beta bridging position within the phosphate chain of dUDP profoundly perturbs ligand accommodation into the dUTPase active site.
Related PDB2hr6,2hrm
[25]
PubMed ID18519027
JournalBiochem Biophys Res Commun
Year2008
Volume373
Pages8-13
AuthorsVarga B, Barabas O, Takacs E, Nagy N, Nagy P, Vertessy BG
TitleActive site of mycobacterial dUTPase: structural characteristics and a built-in sensor.
Related PDB2py4
Related UniProtKBP0A552
[26]
PubMed ID18597482
JournalBiochemistry
Year2008
Volume47
Pages7863-74
AuthorsPalmen LG, Becker K, Bulow L, Kvassman JO
TitleA double role for a strictly conserved serine: further insights into the dUTPase catalytic mechanism.
[27]
PubMed ID19342774
JournalActa Crystallogr Sect F Struct Biol Cryst Commun
Year2009
Volume65
Pages339-42
AuthorsLi GL, Wang J, Li LF, Su XD
TitleCrystallization and preliminary X-ray analysis of three dUTPases from Gram-positive bacteria.
Related PDB2baz

comments
According to the literature [16] & [22], there are at least two types of dUTPases, a homotrimeric enzyme and a homodimeric enzyme. The homotrimeric enzyme has mainly beta-structure, whereas the dimeric enzyme has mainly alpha-structure (see PDB;1ogk, 1w2y & 2cje).
This enzyme is a homotrimer with three active sites located at the interfaces between the two subunits (see [20]). This enzyme catalyzes Mg-dependent hydrolysis of dUTP into dUMP and pyrophosphate.
According to the literature [20], the reaction of this enzyme may proceed as follows:
(0) Mg2+ ion is bound to alpha-, beta- and gamma-phosphate oxygens, stabilizing the negative charges on the target group for nucleophilic water (or group adjacent to scissile bond; alpha-phosphate) and the leaving group (beta- and gamma-phosphate), which may stabilize the transition state. Here, the magnesium ion is not directly bound to the enzyme. Moreover, the target group, alpha-phosphate, is stabilized by Gln119' and mainchain amide group of Ser72' from adjacent subunit(of 1rn8). On the other hand, the leaving beta-phosphate is stabilized by the sidechain of Ser72' and Arg71', and the mainchain amide of Gly73' from the adjacent subunit.
(1) The catalytic water is bound to Asp90 (of 1rn8) and mainchain carbonyl of Leu88. Asp90 might play a role as a general base to activate the catalytic water, which acts as a nucleophilic water to performe a direct in-line attack on the alpha-phosphorous atom.
(2) The reaction proceeds by an associative reaction mechanism (or SN2-like mechanism).

createdupdated
2002-09-102009-06-29


Copyright: Nozomi Nagano, JST & CBRC-AIST
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Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
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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)
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