DB code: T00231

RLCP classification 1.15.8230.362 : Hydrolysis
CATH domain 2.70.40.10 : Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A Catalytic domain
2.70.40.10 : Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A Catalytic domain
2.70.40.10 : Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A Catalytic domain
E.C. 3.6.1.23
CSA 1dup
M-CSA 1dup
MACiE

CATH domain Related DB codes (homologues)
2.70.40.10 : Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A M00206

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam RefSeq
A4GD96
DUTP pyrophosphatase
EC 3.6.1.23
PF00692 (dUTPase)
[Graphical View]
P06968 Deoxyuridine 5''-triphosphate nucleotidohydrolase
dUTPase
EC 3.6.1.23
dUTP pyrophosphatase
PF00692 (dUTPase)
[Graphical View] 		NP_418097.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_491793.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
P0A552 Deoxyuridine 5''-triphosphate nucleotidohydrolase
dUTPase
EC 3.6.1.23
dUTP pyrophosphatase
PF00692 (dUTPase)
[Graphical View] 		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)
O34919
YosS protein (DUTPase homolog)
PF00692 (dUTPase)
[Graphical View] 		NP_389883.1 (Protein)
NC_000964.3 (DNA/RNA sequence)
P33317 Deoxyuridine 5''-triphosphate nucleotidohydrolase
dUTPase
EC 3.6.1.23
dUTP pyrophosphatase
PF00692 (dUTPase)
[Graphical View] 		NP_009811.3 (Protein)
NM_001178600.3 (DNA/RNA sequence)

KEGG enzyme name
dUTP diphosphatase
Deoxyuridine-triphosphatase
dUTPase
dUTP pyrophosphatase
Deoxyuridine 5'-triphosphate nucleotidohydrolase
Deoxyuridine 5'-triphosphatase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
A4GD96 A4GD96_9POXV
P06968 DUT_ECOLI dUTP + H(2)O = dUMP + diphosphate. Homotrimer.
P0A552 DUT_MYCTU dUTP + H(2)O = dUMP + diphosphate.
O34919 O34919_BACSU
P33317 DUT_YEAST dUTP + H(2)O = dUMP + diphosphate.

KEGG Pathways
Map code Pathways E.C.
MAP00240 Pyrimidine metabolism

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00460 C00001 C00365 C00013
E.C.
Compound Magnesium dUTP H2O dUMP Pyrophosphate
Type divalent metal (Ca2+, Mg2+) amide group,nucleotide H2O amide group,nucleotide phosphate group/phosphate ion
ChEBI 18420
 18420
 		17625
 17625
 		15377
 15377
 		17622
 17622
 		29888
 29888
PubChem 888
 888
 		65070
 65070
 		22247451
 962
 22247451
 962
 		65063
 65063
 		1023
 21961011
 1023
 21961011
2okbA Unbound Unbound Unbound Analogue:SO4
2okbB Unbound Unbound Unbound Analogue:SO4
2okbC Unbound Unbound Unbound Analogue:SO4
2okdA Unbound Unbound Unbound Unbound
2okdB Unbound Unbound Unbound Unbound
2okdC Unbound Unbound Unbound Unbound
2okeA Unbound Analogue:DUP Unbound Unbound
2okeB Bound:_MG Analogue:DUP Unbound Unbound
2okeC Unbound Analogue:DUP Unbound Unbound
2ol0A Unbound Analogue:DUD Unbound Unbound
2ol0B Bound:_MG Analogue:DUD Unbound Unbound
2ol0C Unbound Analogue:DUD Unbound Unbound
2ol1A Unbound Unbound Bound:UMP Unbound
2ol1B Unbound Unbound Bound:UMP Unbound
2ol1C Unbound Unbound Bound:UMP Unbound
1dudA Unbound Analogue:DUD Bound:HOH 271 Unbound Unbound
1dupA Unbound Unbound Unbound Unbound
1eu5A Unbound Unbound Unbound Unbound
1euwA Unbound Unbound Unbound Unbound
1rn8A Bound:_MG Analogue:DUP Bound:HOH 5 Unbound Unbound
1rnjA Bound:_MG Analogue:DUP Unbound Unbound
1sehA Unbound Unbound Bound:UMP Unbound
1sylA Bound:_MG Bound:DUT Bound:HOH 107 Unbound Unbound
2hr6A Analogue:_MN Analogue:DUD Bound:HOH 1012 Unbound Unbound
2hrmA Unbound Analogue:UC5 Unbound Unbound
1mq7A Unbound Unbound Unbound Unbound
1sixA Bound:_MG Analogue:DUP Unbound Unbound
1sjnA Bound:_MG Analogue:DUP Bound:HOH 1202 Unbound Unbound
1sjnB Bound:_MG Analogue:DUP Bound:HOH 3214 Unbound Unbound
1sjnC Bound:_MG Analogue:DUP Bound:HOH 3178 Unbound Unbound
1slhA Bound:_MG Analogue:DUD Unbound Unbound
1slhB Bound:_MG Analogue:DUD Unbound Unbound
1slhC Bound:_MG Analogue:DUD Unbound Unbound
1sm8A Analogue:_CR Bound:DUT Unbound Unbound
1sm8B Analogue:_CR Bound:DUT Unbound Unbound
1sm8C Analogue:_CR Bound:DUT Unbound Unbound
1smcA Unbound Bound:DUT Bound:HOH 365 Unbound Unbound
1smcB Unbound Bound:DUT Unbound Unbound
1smcC Unbound Bound:DUT Bound:HOH 282 Unbound Unbound
1snfA Bound:_MG Unbound Bound:UMP Unbound
1snfB Bound:_MG Unbound Bound:UMP Unbound
1snfC Bound:_MG Unbound Bound:UMP Unbound
2py4A Bound:_MG Analogue:DUP Bound:HOH 813 Unbound Unbound
2bazA Unbound Unbound Unbound Unbound
2bazB Unbound Unbound Unbound Unbound
2bazC Unbound Unbound Unbound Unbound
3f4fA Unbound Unbound Bound:UMP Unbound
3f4fB Unbound Unbound Bound:UMP Unbound
3f4fC Unbound Unbound Bound:UMP Unbound

Reference for Active-site residues
resource references E.C.
literature [20]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
2okbA ARG 69;SER 70;ASP 85;GLN 114 SER 70;GLY 71;VAL 83
2okbB ARG 69;SER 70;ASP 85;GLN 114 SER 70;GLY 71;VAL 83
2okbC ARG 69;SER 70;ASP 85;GLN 114 SER 70;GLY 71;VAL 83
2okdA ARG 69;SER 70;ASP 85;GLN 114 SER 70;GLY 71;VAL 83
2okdB ARG 69;SER 70;ASP 85;GLN 114 SER 70;GLY 71;VAL 83
2okdC ARG 69;SER 70;ASP 85;GLN 114 SER 70;GLY 71;VAL 83
2okeA ARG 69;SER 70;ASP 85;GLN 114 SER 70;GLY 71;VAL 83
2okeB ARG 69;SER 70;ASP 85;GLN 114 SER 70;GLY 71;VAL 83
2okeC ARG 69;SER 70;ASP 85;GLN 114 SER 70;GLY 71;VAL 83
2ol0A ARG 69;SER 70;ASP 85;GLN 114 SER 70;GLY 71;VAL 83
2ol0B ARG 69;SER 70;ASP 85;GLN 114 SER 70;GLY 71;VAL 83
2ol0C ARG 69;SER 70;ASP 85;GLN 114 SER 70;GLY 71;VAL 83
2ol1A ARG 69;SER 70;ASP 85;GLN 114 SER 70;GLY 71;VAL 83
2ol1B ARG 69;SER 70;ASP 85;GLN 114 SER 70;GLY 71;VAL 83
2ol1C ARG 69;SER 70;ASP 85;GLN 114 SER 70;GLY 71;VAL 83
1dudA ARG 71;SER 72;ASP 90;GLN 119 SER 72;GLY 73;LEU 88
1dupA ARG 71;SER 72;ASP 90;GLN 119 SER 72;GLY 73;LEU 88
1eu5A ARG 71;SER 72;ASP 90;GLN 119 SER 72;GLY 73;LEU 88
1euwA ARG 71;SER 72;ASP 90;GLN 119 SER 72;GLY 73;LEU 88
1rn8A ARG 71;SER 72;ASP 90;GLN 119 SER 72;GLY 73;LEU 88
1rnjA ARG 71;SER 72; ;GLN 119 SER 72;GLY 73;LEU 88 mutant D90N
1sehA ARG 71;SER 72;ASP 90;GLN 119 SER 72;GLY 73;LEU 88
1sylA ARG 71;SER 72; ;GLN 119 SER 72;GLY 73;LEU 88 mutant D90N
2hr6A ARG 71;SER 72;ASP 90;GLN 119 SER 72;GLY 73;LEU 88
2hrmA ARG 71;SER 72;ASP 90;GLN 119 SER 72;GLY 73;LEU 88
1mq7A ARG 64;SER 65;ASP 83;GLN 113 SER 65;GLY 66;THR 81
1sixA ARG 64;SER 65;ASP 83;GLN 113 SER 65;GLY 66;THR 81
1sjnA ARG 64;SER 65;ASP 83;GLN 113 SER 65;GLY 66;THR 81
1sjnB ARG 64;SER 65;ASP 83;GLN 113 SER 65;GLY 66;THR 81
1sjnC ARG 64;SER 65;ASP 83;GLN 113 SER 65;GLY 66;THR 81
1slhA ARG 64;SER 65;ASP 83;GLN 113 SER 65;GLY 66;THR 81
1slhB ARG 64;SER 65;ASP 83;GLN 113 SER 65;GLY 66;THR 81
1slhC ARG 64;SER 65;ASP 83;GLN 113 SER 65;GLY 66;THR 81
1sm8A ARG 64;SER 65;ASP 83;GLN 113 SER 65;GLY 66;THR 81
1sm8B ARG 64;SER 65;ASP 83;GLN 113 SER 65;GLY 66;THR 81
1sm8C ARG 64;SER 65;ASP 83;GLN 113 SER 65;GLY 66;THR 81
1smcA ARG 64;SER 65;ASP 83;GLN 113 SER 65;GLY 66;THR 81
1smcB ARG 64;SER 65;ASP 83;GLN 113 SER 65;GLY 66;THR 81
1smcC ARG 64;SER 65;ASP 83;GLN 113 SER 65;GLY 66;THR 81
1snfA ARG 64;SER 65;ASP 83;GLN 113 SER 65;GLY 66;THR 81
1snfB ARG 64;SER 65;ASP 83;GLN 113 SER 65;GLY 66;THR 81
1snfC ARG 64;SER 65;ASP 83;GLN 113 SER 65;GLY 66;THR 81
2py4A ARG 64;SER 65;ASP 83;GLN 113 SER 65;GLY 66;THR 81
2bazA ARG 61;SER 62;ASP 80;GLN 110 SER 62;SER 63;VAL 78
2bazB ARG 61;SER 62;ASP 80;GLN 110 SER 62;SER 63;VAL 78
2bazC ARG 61;SER 62;ASP 80;GLN 110 SER 62;SER 63;VAL 78
3f4fA ARG 68;SER 69;ASP 85;GLN 114 SER 69;GLY 70;VAL 83
3f4fB ARG 68;SER 69;ASP 85;GLN 114 SER 69;GLY 70;VAL 83
3f4fC ARG 68;SER 69;ASP 85;GLN 114 SER 69;GLY 70;VAL 83

References for Catalytic Mechanism
References Sections No. 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]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
Medline ID 92158084
PubMed ID 1311056
Journal Nature
Year 1992
Volume 355
Pages 740-3
Authors Cedergren-Zeppezauer ES, Larsson G, Nyman PO, Dauter Z, Wilson KS
Title Crystal structure of a dUTPase.
Related PDB 1dup
Related UniProtKB P06968
[2]
Resource
Comments
Medline ID
PubMed ID 8393252
Journal Virology
Year 1993
Volume 195
Pages 863-5
Authors Broyles SS
Title Vaccinia virus encodes a functional dUTPase.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 7958294
Journal Biochem Soc Trans
Year 1994
Volume 22
Pages 233S
Authors Vertessy BG, Zeppezauer M
Title Identification of tyrosine as an active site residue involved in the catalytic mechanism of Escherichia coli dUTPase.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 8142479
Journal Biochim Biophys Acta
Year 1994
Volume 1205
Pages 146-50
Authors Vertessy BG, Zalud P, Nyman PO, Zeppezauer M
Title Identification of tyrosine as a functional residue in the active site of Escherichia coli dUTPase.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 8604980
Journal Biochem Biophys Res Commun
Year 1996
Volume 219
Pages 294-300
Authors Vertessy BG, Persson R, Rosengren AM, Zeppezauer M, Nyman PO
Title Specific derivatization of the active site tyrosine in dUTPase perturbs ligand binding to the active site.
Related PDB
Related UniProtKB
[6]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
Medline ID 96227973
PubMed ID 8646539
Journal Nat Struct Biol
Year 1996
Volume 3
Pages 532-8
Authors Larsson G, Svensson LA, Nyman PO
Title Crystal structure of the Escherichia coli dUTPase in complex with a substrate analogue (dUDP).
Related PDB 1dud
Related UniProtKB P06968
[7]
Resource
Comments
Medline ID
PubMed ID 8798636
Journal J Biol Chem
Year 1996
Volume 271
Pages 24010-6
Authors Larsson G, Nyman PO, Kvassman JO
Title Kinetic characterization of dUTPase from Escherichia coli.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 9261872
Journal Proteins
Year 1997
Volume 28
Pages 568-79
Authors Vertessy BG
Title Flexible glycine rich motif of Escherichia coli deoxyuridine triphosphate nucleotidohydrolase is important for functional but not for structural integrity of the enzyme.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 9462846
Journal FEBS Lett
Year 1998
Volume 421
Pages 83-8
Authors Vertessy BG, Larsson G, Persson T, Bergman AC, Persson R, Nyman PO
Title The complete triphosphate moiety of non-hydrolyzable substrate analogues is required for a conformational shift of the flexible C-terminus in E. coli dUTP pyrophosphatase.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 9465078
Journal Proc Natl Acad Sci U S A
Year 1998
Volume 95
Pages 1692-7
Authors Lazarevic V, Soldo B, Dusterhoft A, Hilbert H, Mauel C, Karamata D
Title Introns and intein coding sequence in the ribonucleotide reductase genes of Bacillus subtilis temperate bacteriophage SPbeta.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 9679200
Journal DNA Res
Year 1998
Volume 5
Pages 121-6
Authors Ghim SY, Choi SK, Shin BS, Park SH
Title An 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.
Related PDB
Related UniProtKB
[12]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
Medline ID 98437602
PubMed ID 9757088
Journal Acta Crystallogr D Biol Crystallogr
Year 1998
Volume 54
Pages 735-49
Authors Dauter Z, Wilson KS, Larsson G, Nyman PO, Cedergren-Zeppezauer ES
Title The refined structure of dUTPase from Escherichia coli.
Related PDB
Related UniProtKB P06968
[13]
Resource
Comments
Medline ID
PubMed ID 10438861
Journal J Virol
Year 1999
Volume 73
Pages 7710-21
Authors Baldo AM, McClure MA
Title Evolution and horizontal transfer of dUTPase-encoding genes in viruses and their hosts.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 11257499
Journal FEBS Lett
Year 2001
Volume 492
Pages 228-32
Authors Nord J, Nyman P, Larsson G, Drakenberg T
Title The C-terminus of dUTPase: observation on flexibility using NMR.
Related PDB
Related UniProtKB
[15]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.05 ANGSTROMS).
Medline ID 21268771
PubMed ID 11375495
Journal Acta Crystallogr D Biol Crystallogr
Year 2001
Volume 57
Pages 767-74
Authors Gonzalez A, Larsson G, Persson R, Cedergren-Zeppezauer E
Title Atomic resolution structure of Escherichia coli dUTPase determined ab initio.
Related PDB 1eu5 1euw
Related UniProtKB P06968
[16]
Resource
Comments
Medline ID
PubMed ID 12369925
Journal Curr Protein Pept Sci
Year 2001
Volume 2
Pages 277-85
Authors Nyman PO
Title Introduction. dUTPases.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 12369926
Journal Curr Protein Pept Sci
Year 2001
Volume 2
Pages 287-300
Authors Persson R, Cedergren-Zeppezauer ES, Wilson KS
Title Homotrimeric dUTPases; structural solutions for specific recognition and hydrolysis of dUTP.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 12369928
Journal Curr Protein Pept Sci
Year 2001
Volume 2
Pages 313-24
Authors McClure MA
Title Evolution of the DUT gene: horizontal transfer between host and pathogen in all three domains of life.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 12721364
Journal Proc Natl Acad Sci U S A
Year 2003
Volume 100
Pages 5670-5
Authors Mustafi D, Bekesi A, Vertessy BG, Makinen MW
Title Catalytic and structural role of the metal ion in dUTP pyrophosphatase.
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 15208312
Journal J Biol Chem
Year 2004
Volume 279
Pages 42907-15
Authors Barabas O, Pongracz V, Kovari J, Wilmanns M, Vertessy BG
Title Structural insights into the catalytic mechanism of phosphate ester hydrolysis by dUTPase.
Related PDB 1rn8 1rnj 1seh 1syl
Related UniProtKB
[21]
Resource
Comments
Medline ID
PubMed ID 15939294
Journal Protein Expr Purif
Year 2005
Volume 42
Pages 92-9
Authors Persson R, McGeehan J, Wilson KS
Title Cloning, expression, purification, and characterisation of the dUTPase encoded by the integrated Bacillus subtilis temperate bacteriophage SPbeta.
Related PDB 2baz
Related UniProtKB
[22]
Resource
Comments
Medline ID
PubMed ID 16359314
Journal Mol Microbiol
Year 2006
Volume 59
Pages 5-19
Authors Galperin MY, Moroz OV, Wilson KS, Murzin AG
Title House cleaning, a part of good housekeeping.
Related PDB
Related UniProtKB
[23]
Resource
Comments
Medline ID
PubMed ID 17452782
Journal Acta Crystallogr D Biol Crystallogr
Year 2007
Volume 63
Pages 571-80
Authors Samal A, Schormann N, Cook WJ, DeLucas LJ, Chattopadhyay D
Title Structures of vaccinia virus dUTPase and its nucleotide complexes.
Related PDB 2okb 2okd 2oke 2ol0 2ol1
Related UniProtKB
[24]
Resource
Comments
Medline ID
PubMed ID 17932923
Journal Proteins
Year 2008
Volume 71
Pages 308-19
Authors Kovari J, Barabas O, Varga B, Bekesi A, Tolgyesi F, Fidy J, Nagy J, Vertessy BG
Title Methylene substitution at the alpha-beta bridging position within the phosphate chain of dUDP profoundly perturbs ligand accommodation into the dUTPase active site.
Related PDB 2hr6 2hrm
Related UniProtKB
[25]
Resource
Comments
Medline ID
PubMed ID 18519027
Journal Biochem Biophys Res Commun
Year 2008
Volume 373
Pages 8-13
Authors Varga B, Barabas O, Takacs E, Nagy N, Nagy P, Vertessy BG
Title Active site of mycobacterial dUTPase: structural characteristics and a built-in sensor.
Related PDB 2py4
Related UniProtKB P0A552
[26]
Resource
Comments
Medline ID
PubMed ID 18597482
Journal Biochemistry
Year 2008
Volume 47
Pages 7863-74
Authors Palmen LG, Becker K, Bulow L, Kvassman JO
Title A double role for a strictly conserved serine: further insights into the dUTPase catalytic mechanism.
Related PDB
Related UniProtKB
[27]
Resource
Comments
Medline ID
PubMed ID 19342774
Journal Acta Crystallogr Sect F Struct Biol Cryst Commun
Year 2009
Volume 65
Pages 339-42
Authors Li GL, Wang J, Li LF, Su XD
Title Crystallization and preliminary X-ray analysis of three dUTPases from Gram-positive bacteria.
Related PDB 2baz
Related UniProtKB

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).

Created Updated
2002-09-10 2009-06-29