EzCatDB: S00924
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DB codeS00924
RLCP classification1.15.8245.1168 : Hydrolysis
CATH domainDomain 13.90.79.10 : Nucleoside Triphosphate PyrophosphohydrolaseCatalytic domain
E.C.3.6.1.13,3.6.1.58

CATH domainRelated DB codes (homologues)
3.90.79.10 : Nucleoside Triphosphate PyrophosphohydrolaseS00814,S00815,S00920,S00921,S00922,S00923,S00454

Enzyme Name
UniProtKBKEGG

Q9UKK9
Protein nameADP-sugar pyrophosphataseADP-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)

SynonymsEC 3.6.1.13
EC 3.6.1.-
Nucleoside diphosphate-linked moiety X motif 5
Nudix motif 5
YSA1H
RefSeqNP_054861.2 (Protein)
NM_014142.2 (DNA/RNA sequence)
PfamPF00293 (NUDIX)
[Graphical view]

KEGG pathways
MAP codePathwaysE.C.
MAP00230Purine metabolism3.6.1.13

UniProtKB:Accession NumberQ9UKK9
Entry nameNUDT5_HUMAN
ActivityADP-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.
SubunitHomodimer.
Subcellular location
CofactorBinds 3 magnesium ions per subunit.

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00305C00301C20176C00001C00020C00117C19968C00009
E.C.3.6.1.13,3.6.1.583.6.1.133.6.1.583.6.1.13,3.6.1.583.6.1.133.6.1.133.6.1.583.6.1.58
CompoundMagnesiumADP-ribose8-Oxo-dGDPH2OAMPD-ribose 5-phosphate8-Oxo-dGMPOrthophosphate
Typedivalent metal (Ca2+, Mg2+)amine group,carbohydrate,nucleotideamide group,amine group,nucleotideH2Oamine group,nucleotidecarbohydrate,phosphate group/phosphate ionamide group,amine group,nucleotidephosphate group/phosphate ion
ChEBI18420

63728
15377
16027
52742
63223
26078
PubChem888
445794
49835950
962
22247451
6083
439167
447903
22486802
1004
                
2dsbA00UnboundUnboundUnbound UnboundUnboundUnboundUnbound
2dsbB00UnboundUnboundUnbound UnboundUnboundUnboundUnbound
2dsbC00UnboundUnboundUnbound UnboundUnboundUnboundUnbound
2dsbD00UnboundUnboundUnbound UnboundUnboundUnboundUnbound
2dscA00Bound:_MGBound:APRUnbound UnboundUnboundUnboundUnbound
2dscB00Bound:_MGBound:APRUnbound UnboundUnboundUnboundUnbound
2dsdA00Bound:3x_MGUnboundUnbound Bound:AMPUnboundUnboundUnbound
2dsdB00Bound:3x_MGUnboundUnbound Bound:AMPUnboundUnboundUnbound
3ac9A00UnboundUnboundAnalogue:8GD UnboundUnboundUnboundUnbound
3ac9B00Analogue:2x_MNUnboundBound:8GD UnboundUnboundUnboundUnbound
3acaA00Analogue:3x_MNUnboundAnalogue:8DD UnboundUnboundUnboundUnbound
3acaB00Analogue:2x_MNUnboundAnalogue:8DD UnboundUnboundUnboundUnbound
3bm4A00Bound:3x_MGAnalogue:ADVUnbound UnboundUnboundUnboundUnbound
3bm4B00Bound:3x_MGAnalogue:ADVUnbound UnboundUnboundUnboundUnbound
3l85A00UnboundUnboundUnbound UnboundUnboundAnalogue:8OGUnbound
3l85B00UnboundUnboundUnbound UnboundUnboundBound:8OGUnbound

Active-site residues
resource
literature [8], [10], [11]
pdbCatalytic residuesCofactor-binding residues
          
2dsbA00ARG 84;GLU 166
ALA 96(Magnesium-1);GLU 112(Magnesium-2 & 3);GLU 116(Magnesium-1 & 2);GLU 166(Magnesium-2)
2dsbB00ARG 84;GLU 166
ALA 96(Magnesium-1);GLU 112(Magnesium-2 & 3);GLU 116(Magnesium-1 & 2);GLU 166(Magnesium-2)
2dsbC00ARG 84;GLU 166
ALA 96(Magnesium-1);GLU 112(Magnesium-2 & 3);GLU 116(Magnesium-1 & 2);GLU 166(Magnesium-2)
2dsbD00ARG 84;GLU 166
ALA 96(Magnesium-1);GLU 112(Magnesium-2 & 3);GLU 116(Magnesium-1 & 2);GLU 166(Magnesium-2)
2dscA00ARG 84;GLU 166
ALA 96(Magnesium-1);GLU 112(Magnesium-2 & 3);GLU 116(Magnesium-1 & 2);GLU 166(Magnesium-2)
2dscB00ARG 84;GLU 166
ALA 96(Magnesium-1);GLU 112(Magnesium-2 & 3);GLU 116(Magnesium-1 & 2);GLU 166(Magnesium-2)
2dsdA00ARG 84;GLU 166
ALA 96(Magnesium-1);GLU 112(Magnesium-2 & 3);GLU 116(Magnesium-1 & 2);GLU 166(Magnesium-2)
2dsdB00ARG 84;GLU 166
ALA 96(Magnesium-1);GLU 112(Magnesium-2 & 3);GLU 116(Magnesium-1 & 2);GLU 166(Magnesium-2)
3ac9A00ARG 84;GLU 166
ALA 96(Magnesium-1);GLU 112(Magnesium-2 & 3);GLU 116(Magnesium-1 & 2);GLU 166(Magnesium-2)
3ac9B00ARG 84;GLU 166
ALA 96(Magnesium-1);GLU 112(Magnesium-2 & 3);GLU 116(Magnesium-1 & 2);GLU 166(Magnesium-2)
3acaA00ARG 84;GLU 166
ALA 96(Magnesium-1);GLU 112(Magnesium-2 & 3);GLU 116(Magnesium-1 & 2);GLU 166(Magnesium-2)
3acaB00ARG 84;GLU 166
ALA 96(Magnesium-1);GLU 112(Magnesium-2 & 3);GLU 116(Magnesium-1 & 2);GLU 166(Magnesium-2)
3bm4A00ARG 84;GLU 166
ALA 96(Magnesium-1);GLU 112(Magnesium-2 & 3);GLU 116(Magnesium-1 & 2);GLU 166(Magnesium-2)
3bm4B00ARG 84;GLU 166
ALA 96(Magnesium-1);GLU 112(Magnesium-2 & 3);GLU 116(Magnesium-1 & 2);GLU 166(Magnesium-2)
3l85A00ARG 84;GLU 166
ALA 96(Magnesium-1);GLU 112(Magnesium-2 & 3);GLU 116(Magnesium-1 & 2);GLU 166(Magnesium-2)
3l85B00ARG 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
ReferencesSectionsNo. of steps in catalysis
[2]FIGURE6
[6]Table1, Fig.5
[8]

[10]p.571-576, Fig.2
[11]p.8978

references
[1]
CommentsX-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF NATIVE ENZYME, COMPLEX WITH ADP-RIBOSE, COMPLEX WITH GADOLINIUM.
PubMed ID11323725
JournalNat Struct Biol
Year2001
Volume8
Pages467-72
AuthorsGabelli SB, Bianchet MA, Bessman MJ, Amzel LM
TitleThe structure of ADP-ribose pyrophosphatase reveals the structural basis for the versatility of the Nudix family.
Related PDB1g0s,1g9q,1ga7
Related UniProtKBQ93K97
[2]
CommentsX-RAY CRYSTALLOGRAPHY (2.07 ANGSTROMS), CATALYTIC MECHANISM.
PubMed ID12135348
JournalBiochemistry
Year2002
Volume41
Pages9279-85
AuthorsGabelli SB, Bianchet MA, Ohnishi Y, Ichikawa Y, Bessman MJ, Amzel LM
TitleMechanism of the Escherichia coli ADP-ribose pyrophosphatase, a Nudix hydrolase.
Related PDB1khz
Related UniProtKBQ93K97
[3]
PubMed ID12948489
JournalJ Mol Biol
Year2003
Volume332
Pages385-98
AuthorsShen BW, Perraud AL, Scharenberg A, Stoddard BL
TitleThe crystal structure and mutational analysis of human NUDT9.
Related PDB1q33,1qvj
[4]
PubMed ID12906832
JournalStructure
Year2003
Volume11
Pages1015-23
AuthorsKang LW, Gabelli SB, Cunningham JE, O'Handley SF, Amzel LM
TitleStructure and mechanism of MT-ADPRase, a nudix hydrolase from Mycobacterium tuberculosis.
Related PDB1mk1,1mp2,1mqe,1mqw,1mr2
[5]
PubMed ID15210687
JournalJ Biol Chem
Year2004
Volume279
Pages37163-74
AuthorsYoshiba S, Ooga T, Nakagawa N, Shibata T, Inoue Y, Yokoyama S, Kuramitsu S, Masui R
TitleStructural insights into the Thermus thermophilus ADP-ribose pyrophosphatase mechanism via crystal structures with the bound substrate and metal.
Related PDB1v8i,1v8l,1v8m,1v8n,1v8r,1v8s,1v8t,1v8u,1v8v,1v8w,1v8y
[6]
PubMed ID15581572
JournalArch Biochem Biophys
Year2005
Volume433
Pages129-43
AuthorsMildvan AS, Xia Z, Azurmendi HF, Saraswat V, Legler PM, Massiah MA, Gabelli SB, Bianchet MA, Kang LW, Amzel LM
TitleStructures and mechanisms of Nudix hydrolases.
[7]
PubMed ID15981998
JournalBiochemistry
Year2005
Volume44
Pages9320-9
AuthorsOoga T, Yoshiba S, Nakagawa N, Kuramitsu S, Masui R
TitleMolecular mechanism of the Thermus thermophilus ADP-ribose pyrophosphatase from mutational and kinetic studies.
[8]
PubMed ID17052728
JournalJ Mol Biol
Year2006
Volume364
Pages1021-33
AuthorsZha M, Zhong C, Peng Y, Hu H, Ding J
TitleCrystal structures of human NUDT5 reveal insights into the structural basis of the substrate specificity.
Related PDB2dsb,2dsc,2dsd
[9]
PubMed ID18039767
JournalJ Bacteriol
Year2008
Volume190
Pages1108-17
AuthorsWakamatsu T, Nakagawa N, Kuramitsu S, Masui R
TitleStructural basis for different substrate specificities of two ADP-ribose pyrophosphatases from Thermus thermophilus HB8.
[10]
PubMed ID18462755
JournalJ Mol Biol
Year2008
Volume379
Pages568-78
AuthorsZha M, Guo Q, Zhang Y, Yu B, Ou Y, Zhong C, Ding J
TitleMolecular mechanism of ADP-ribose hydrolysis by human NUDT5 from structural and kinetic studies.
Related PDB3bm4
[11]
PubMed ID21768126
JournalNucleic Acids Res
Year2011
Volume39
Pages8972-83
AuthorsArimori T, Tamaoki H, Nakamura T, Kamiya H, Ikemizu S, Takagi Y, Ishibashi T, Harashima H, Sekiguchi M, Yamagata Y
TitleDiverse substrate recognition and hydrolysis mechanisms of human NUDT5.
Related PDB3ac9,3aca,3l85

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.

createdupdated
2009-12-252013-03-29


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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