DB code: S00924

RLCP classification 1.15.8245.1168 : Hydrolysis
CATH domain 3.90.79.10 : Nucleoside Triphosphate Pyrophosphohydrolase Catalytic domain
E.C. 3.6.1.13 3.6.1.58
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
3.90.79.10 : Nucleoside Triphosphate Pyrophosphohydrolase S00814 S00815 S00920 S00921 S00922 S00923 S00454

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
Q9UKK9 ADP-sugar pyrophosphatase
EC 3.6.1.13
8-oxo-dGDP phosphatase
EC 3.6.1.58
Nucleoside diphosphate-linked moiety X motif 5
Nudix motif 5
YSA1H
NP_054861.2 (Protein)
NM_014142.2 (DNA/RNA sequence)
PF00293 (NUDIX)
[Graphical View]

KEGG enzyme name
ADP-ribose diphosphatase
(EC 3.6.1.13 )
ADPribose pyrophosphatase
(EC 3.6.1.13 )
Adenosine diphosphoribose pyrophosphatase
(EC 3.6.1.13 )
ADPR-PPase
(EC 3.6.1.13 )
8-oxo-dGDP phosphatase
(EC 3.6.1.58 )
NUDT5
(EC 3.6.1.58 )

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
Q9UKK9 NUDT5_HUMAN ADP-D-ribose + H(2)O = AMP + D-ribose 5-phosphate. ADP-sugar + H(2)O = AMP + alpha-D-aldose 5-phosphate. 8-oxo-dGDP + H(2)O = 8-oxo-dGMP + phosphate. Homodimer. Binds 3 magnesium ions per subunit.

KEGG Pathways
Map code Pathways E.C.
MAP00230 Purine metabolism 3.6.1.13

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00301 C20176 C00001 C00020 C00117 C19968 C00009
E.C. 3.6.1.13
3.6.1.58
3.6.1.13
3.6.1.58
3.6.1.13
3.6.1.58
3.6.1.13
3.6.1.13
3.6.1.58
3.6.1.58
Compound Magnesium ADP-ribose 8-Oxo-dGDP H2O AMP D-ribose 5-phosphate 8-Oxo-dGMP Orthophosphate
Type divalent metal (Ca2+, Mg2+) amine group,carbohydrate,nucleotide amide group,amine group,nucleotide H2O amine group,nucleotide carbohydrate,phosphate group/phosphate ion amide group,amine group,nucleotide phosphate group/phosphate ion
ChEBI 18420
63728
15377
16027
52742
63223
26078
PubChem 888
445794
49835950
22247451
962
6083
439167
447903
1004
22486802
2dsbA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2dsbB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2dsbC00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2dsbD00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2dscA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Bound:APR Unbound Unbound Unbound Unbound Unbound
2dscB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Bound:APR Unbound Unbound Unbound Unbound Unbound
2dsdA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:3x_MG Unbound Unbound Bound:AMP Unbound Unbound Unbound
2dsdB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:3x_MG Unbound Unbound Bound:AMP Unbound Unbound Unbound
3ac9A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Analogue:8GD Unbound Unbound Unbound Unbound
3ac9B00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:2x_MN Unbound Bound:8GD Unbound Unbound Unbound Unbound
3acaA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:3x_MN Unbound Analogue:8DD Unbound Unbound Unbound Unbound
3acaB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:2x_MN Unbound Analogue:8DD Unbound Unbound Unbound Unbound
3bm4A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:3x_MG Analogue:ADV Unbound Unbound Unbound Unbound Unbound
3bm4B00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:3x_MG Analogue:ADV Unbound Unbound Unbound Unbound Unbound
3l85A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Analogue:8OG Unbound
3l85B00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Bound:8OG Unbound

Reference for Active-site residues
resource references E.C.
literature [8], [10], [11]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
2dsbA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 84;GLU 166 ALA 96(Magnesium-1);GLU 112(Magnesium-2 & 3);GLU 116(Magnesium-1 & 2);GLU 166(Magnesium-2)
2dsbB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 84;GLU 166 ALA 96(Magnesium-1);GLU 112(Magnesium-2 & 3);GLU 116(Magnesium-1 & 2);GLU 166(Magnesium-2)
2dsbC00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 84;GLU 166 ALA 96(Magnesium-1);GLU 112(Magnesium-2 & 3);GLU 116(Magnesium-1 & 2);GLU 166(Magnesium-2)
2dsbD00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 84;GLU 166 ALA 96(Magnesium-1);GLU 112(Magnesium-2 & 3);GLU 116(Magnesium-1 & 2);GLU 166(Magnesium-2)
2dscA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 84;GLU 166 ALA 96(Magnesium-1);GLU 112(Magnesium-2 & 3);GLU 116(Magnesium-1 & 2);GLU 166(Magnesium-2)
2dscB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 84;GLU 166 ALA 96(Magnesium-1);GLU 112(Magnesium-2 & 3);GLU 116(Magnesium-1 & 2);GLU 166(Magnesium-2)
2dsdA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 84;GLU 166 ALA 96(Magnesium-1);GLU 112(Magnesium-2 & 3);GLU 116(Magnesium-1 & 2);GLU 166(Magnesium-2)
2dsdB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 84;GLU 166 ALA 96(Magnesium-1);GLU 112(Magnesium-2 & 3);GLU 116(Magnesium-1 & 2);GLU 166(Magnesium-2)
3ac9A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 84;GLU 166 ALA 96(Magnesium-1);GLU 112(Magnesium-2 & 3);GLU 116(Magnesium-1 & 2);GLU 166(Magnesium-2)
3ac9B00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 84;GLU 166 ALA 96(Magnesium-1);GLU 112(Magnesium-2 & 3);GLU 116(Magnesium-1 & 2);GLU 166(Magnesium-2)
3acaA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 84;GLU 166 ALA 96(Magnesium-1);GLU 112(Magnesium-2 & 3);GLU 116(Magnesium-1 & 2);GLU 166(Magnesium-2)
3acaB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 84;GLU 166 ALA 96(Magnesium-1);GLU 112(Magnesium-2 & 3);GLU 116(Magnesium-1 & 2);GLU 166(Magnesium-2)
3bm4A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 84;GLU 166 ALA 96(Magnesium-1);GLU 112(Magnesium-2 & 3);GLU 116(Magnesium-1 & 2);GLU 166(Magnesium-2)
3bm4B00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 84;GLU 166 ALA 96(Magnesium-1);GLU 112(Magnesium-2 & 3);GLU 116(Magnesium-1 & 2);GLU 166(Magnesium-2)
3l85A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 84;GLU 166 ALA 96(Magnesium-1);GLU 112(Magnesium-2 & 3);GLU 116(Magnesium-1 & 2);GLU 166(Magnesium-2)
3l85B00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 84;GLU 166 ALA 96(Magnesium-1);GLU 112(Magnesium-2 & 3);GLU 116(Magnesium-1 & 2);GLU 166(Magnesium-2)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[2]
FIGURE6
[6]
Table1, Fig.5
[8]
[10]
p.571-576, Fig.2
[11]
p.8978

References
[1]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF NATIVE ENZYME, COMPLEX WITH ADP-RIBOSE, COMPLEX WITH GADOLINIUM.
Medline ID
PubMed ID 11323725
Journal Nat Struct Biol
Year 2001
Volume 8
Pages 467-72
Authors Gabelli SB, Bianchet MA, Bessman MJ, Amzel LM
Title The structure of ADP-ribose pyrophosphatase reveals the structural basis for the versatility of the Nudix family.
Related PDB 1g0s 1g9q 1ga7
Related UniProtKB Q93K97
[2]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.07 ANGSTROMS), CATALYTIC MECHANISM.
Medline ID
PubMed ID 12135348
Journal Biochemistry
Year 2002
Volume 41
Pages 9279-85
Authors Gabelli SB, Bianchet MA, Ohnishi Y, Ichikawa Y, Bessman MJ, Amzel LM
Title Mechanism of the Escherichia coli ADP-ribose pyrophosphatase, a Nudix hydrolase.
Related PDB 1khz
Related UniProtKB Q93K97
[3]
Resource
Comments
Medline ID
PubMed ID 12948489
Journal J Mol Biol
Year 2003
Volume 332
Pages 385-98
Authors Shen BW, Perraud AL, Scharenberg A, Stoddard BL
Title The crystal structure and mutational analysis of human NUDT9.
Related PDB 1q33 1qvj
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 12906832
Journal Structure
Year 2003
Volume 11
Pages 1015-23
Authors Kang LW, Gabelli SB, Cunningham JE, O'Handley SF, Amzel LM
Title Structure and mechanism of MT-ADPRase, a nudix hydrolase from Mycobacterium tuberculosis.
Related PDB 1mk1 1mp2 1mqe 1mqw 1mr2
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 15210687
Journal J Biol Chem
Year 2004
Volume 279
Pages 37163-74
Authors Yoshiba S, Ooga T, Nakagawa N, Shibata T, Inoue Y, Yokoyama S, Kuramitsu S, Masui R
Title Structural insights into the Thermus thermophilus ADP-ribose pyrophosphatase mechanism via crystal structures with the bound substrate and metal.
Related PDB 1v8i 1v8l 1v8m 1v8n 1v8r 1v8s 1v8t 1v8u 1v8v 1v8w 1v8y
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 15581572
Journal Arch Biochem Biophys
Year 2005
Volume 433
Pages 129-43
Authors Mildvan AS, Xia Z, Azurmendi HF, Saraswat V, Legler PM, Massiah MA, Gabelli SB, Bianchet MA, Kang LW, Amzel LM
Title Structures and mechanisms of Nudix hydrolases.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 15981998
Journal Biochemistry
Year 2005
Volume 44
Pages 9320-9
Authors Ooga T, Yoshiba S, Nakagawa N, Kuramitsu S, Masui R
Title Molecular mechanism of the Thermus thermophilus ADP-ribose pyrophosphatase from mutational and kinetic studies.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 17052728
Journal J Mol Biol
Year 2006
Volume 364
Pages 1021-33
Authors Zha M, Zhong C, Peng Y, Hu H, Ding J
Title Crystal structures of human NUDT5 reveal insights into the structural basis of the substrate specificity.
Related PDB 2dsb 2dsc 2dsd
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 18039767
Journal J Bacteriol
Year 2008
Volume 190
Pages 1108-17
Authors Wakamatsu T, Nakagawa N, Kuramitsu S, Masui R
Title Structural basis for different substrate specificities of two ADP-ribose pyrophosphatases from Thermus thermophilus HB8.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 18462755
Journal J Mol Biol
Year 2008
Volume 379
Pages 568-78
Authors Zha M, Guo Q, Zhang Y, Yu B, Ou Y, Zhong C, Ding J
Title Molecular mechanism of ADP-ribose hydrolysis by human NUDT5 from structural and kinetic studies.
Related PDB 3bm4
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 21768126
Journal Nucleic Acids Res
Year 2011
Volume 39
Pages 8972-83
Authors Arimori T, Tamaoki H, Nakamura T, Kamiya H, Ikemizu S, Takagi Y, Ishibashi T, Harashima H, Sekiguchi M, Yamagata Y
Title Diverse substrate recognition and hydrolysis mechanisms of human NUDT5.
Related PDB 3ac9 3aca 3l85
Related UniProtKB

Comments
This enzyme belongs to Nudix (nucleoside diphosphate linked to x) hydrolase family.
There are several types of ADP-ribose pyrophosphatases from various organisms (EzCatDB; S00814, S00921, S00922, S00923, D00880), in terms of substrate specificities, metal binding, active sites and reaction mechanisms.
This enzyme also hydrolyzes 8-oxo-dGDP as well as ADP-ribose (see [11]).
The magnesium numbering is based on the literature [8], in contrast to those homologous enzymes (EzCatDB; S00814, S00921, S00922), whose numberings are opposite, based on literature [6]. Magnesium-3 is bound to Glu112 and alpha-phosphate of ADP-ribose, whereas Magnesium-2 is bound to Glu112, Glu116, Glu166 and alpha-phosphate. Magnesium-1 is bound to mainchain carbonyl of Ala96, Glu116 and both of the phosphate groups. The water that is bound to magnesium-2 and magnesium-3 is the nucleophile, which attacks on the alpha-phosphate of ADP-ribose(see [10]).
On the other hand, for the hydrolysis of 8-oxo-dGDP, the beta-phosphate is attacked by the activated water (see [11]). According to the literature [11], 8-oxo-dGDP adopts a Z-shaped conformation, whereas ADP-ribose adopts a horse-shoe conformation. The difference in the adopted conformations of the substrates leads to the different nucleophilic substitution sites (see [11]).
According to the literature [6] and [9], the reaction for ADP-ribose proceeds as follows:
(0) A water molecule is bound to Magnesium-2 and -3. These magnesium ions may lower the pKa of the water molecule so that the water molecule can be a better nucleophile, and also stabilize the negative charge on the alpha-phosphate group. On the other hand, magnesium-1 that bridges the two phosphate groups may stabilize the negative charge of the leaving group, beta-phosphate.
(1) Glu166 may act as a weak base to deprotonate the water molecule, forming a hydroxide ion. (The contribution of this general base is smaller than those acidic residues, Glu112 and Glu116, which bind magnesium-2 and -3, according to the literature [9].)
(2) The hydroxide ion makes a nucleophilic attack on the alpha-phosphate of ADP-ribose. (SN2-like reaction)
(3) Arg84 and magnesium-1 may stabilize the negative charge on the leaving beta-phosphate group.
For the hydrolysis of 8-oxo-dGDP, alpha-phosphate group is the leaving group, whereas beta-phosphate is the nucleophilic substitution site. Otherwise, the reaction mechanism must be similar to that for ADP-ribose.

Created Updated
2009-12-25 2013-03-29