EzCatDB: S00815
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DB codeS00815
RLCP classification1.15.8240.1166 : Hydrolysis
CATH domainDomain 13.90.79.10 : Nucleoside Triphosphate PyrophosphohydrolaseCatalytic domain
E.C.3.6.1.17

CATH domainRelated DB codes (homologues)
3.90.79.10 : Nucleoside Triphosphate PyrophosphohydrolaseS00814,S00920,S00921,S00922,S00923,S00924,S00454

Enzyme Name
UniProtKBKEGG

Q9U2M7P50583
Protein nameBis(5''-nucleosyl)-tetraphosphatase {asymmetrical}Bis(5''-nucleosyl)-tetraphosphatase {asymmetrical}Bis(5'-nucleosyl)-tetraphosphatase (asymmetrical)
Bis(5'-guanosyl)-tetraphosphatase
Bis(5'-adenosyl)-tetraphosphatase
Diguanosinetetraphosphatase (asymmetrical)
Dinucleosidetetraphosphatase (asymmetrical)
Diadenosine P1,P4-tetraphosphatase
Dinucleoside tetraphosphatase
1-P,4-P-bis(5'-nucleosyl)-tetraphosphate nucleotidohydrolase
SynonymsEC 3.6.1.-
Diadenosine 5'',5''''''-P1,P4-tetraphosphate asymmetrical hydrolase
Diadenosine tetraphosphatase
Ap4A hydrolase
Ap4Aase
Nudix hydrolase 4
EC 3.6.1.17
Diadenosine 5'',5''''''-P1,P4-tetraphosphate asymmetrical hydrolase
Diadenosine tetraphosphatase
Ap4A hydrolase
Ap4Aase
Nucleoside diphosphate-linked moiety X motif 2
Nudix motif 2
RefSeqNP_493413.1 (Protein)
NM_061012.4 (DNA/RNA sequence)
NP_001152.1 (Protein)
NM_001161.4 (DNA/RNA sequence)
NP_001231319.1 (Protein)
NM_001244390.1 (DNA/RNA sequence)
NP_671701.1 (Protein)
NM_147172.2 (DNA/RNA sequence)
NP_671702.1 (Protein)
NM_147173.2 (DNA/RNA sequence)
PfamPF00293 (NUDIX)
[Graphical view]
PF00293 (NUDIX)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00230Purine metabolism
MAP00240Pyrimidine metabolism

UniProtKB:Accession NumberQ9U2M7P50583
Entry nameAP4A_CAEELAP4A_HUMAN
ActivityP1,P(4)-bis(5'-adenosyl) tetraphosphate + H2O = ATP + AMP.P1,P(4)-bis(5'-guanosyl) tetraphosphate + H2O = GTP + GMP.
SubunitMonomer.
Subcellular location

CofactorDivalent ions. Magnesium, cobalt, manganese, zinc or calcium.Divalent ions (By similarity).

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC02148C01260C01261C00001C00002C00020C00044C00144
CompoundDivalent metalP1,P4-Bis(5'-adenosyl) tetraphosphateP1,P4-bis(5'-guanosyl) tetraphosphateH2OATPAMPGTPGMP
Typedivalent metal (Ca2+, Mg2+)amide group,amine group,nucleotideamide group,amine group,nucleotideH2Oamine group,nucleotideamine group,nucleotideamide group,amine group,nucleotideamide group,amine group,nucleotide
ChEBI
17422
15883
15377
15422
16027
15996
17345
PubChem
21706
165186
962
22247451
5957
6083
6830
6804
                
1kt9A00UnboundUnboundUnbound UnboundUnboundUnboundUnbound
1ktgA00Bound:4x_MGUnboundUnboundBound:_OHAnalogue:AMPUnboundAnalogue:PO4Unbound
1ktgB00Bound:4x_MGUnboundUnboundBound:_OHUnboundUnboundUnboundUnbound
1xsaA00UnboundUnboundUnbound UnboundUnboundUnboundUnbound
1xsbA00UnboundUnboundUnbound UnboundUnboundUnboundUnbound
1xscA00UnboundUnboundUnbound Bound:ATPUnboundUnboundUnbound
3u53A00UnboundUnboundUnbound UnboundUnboundUnboundUnbound
3u53B00UnboundUnboundUnbound UnboundUnboundUnboundUnbound
3u53C00UnboundUnboundUnbound UnboundUnboundUnboundUnbound
3u53D00UnboundUnboundUnbound UnboundUnboundUnboundUnbound

Active-site residues
resource
Literature [5], [7], [8], [9]
pdbCatalytic residuesCofactor-binding residuescomment
           
1kt9A00GLU 52;LYS 36;LYS 83
LYS 36(Magnesium-2);GLU 52;       (Magnesium-1);GLU 56(Magnesium-1,2)
invisible 26, 103-105
1ktgA00GLU 52;LYS 36;LYS 83
LYS 36(Magnesium-2);GLU 52;GLU 103(Magnesium-1);GLU 56(Magnesium-1,2)
 
1ktgB00GLU 52;LYS 36;LYS 83
LYS 36(Magnesium-2);GLU 52;GLU 103(Magnesium-1);GLU 56(Magnesium-1,2)
invisible 79-81
1xsaA00      ;LYS 47;LYS 94
LYS 47(Magnesium-2);      ;GLU 115(Magnesium-1);GLU 67(Magnesium-1,2)
mutant E63A
1xsbA00      ;LYS 47;LYS 94
LYS 47(Magnesium-2);      ;GLU 115(Magnesium-1);GLU 67(Magnesium-1,2)
mutant E63A
1xscA00      ;LYS 47;LYS 94
LYS 47(Magnesium-2);      ;GLU 115(Magnesium-1);GLU 67(Magnesium-1,2)
mutant E63A
3u53A00GLU 58;LYS 42;LYS 89
LYS 42(Magnesium-2);GLU 58;GLU 110(Magnesium-1);GLU 62(Magnesium-1,2)
 
3u53B00GLU 58;LYS 42;LYS 89
LYS 42(Magnesium-2);GLU 58;GLU 110(Magnesium-1);GLU 62(Magnesium-1,2)
 
3u53C00GLU 58;LYS 42;LYS 89
LYS 42(Magnesium-2);GLU 58;GLU 110(Magnesium-1);GLU 62(Magnesium-1,2)
 
3u53D00GLU 58;LYS 42;LYS 89
LYS 42(Magnesium-2);GLU 58;GLU 110(Magnesium-1);GLU 62(Magnesium-1,2)
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[5]

[7]

[8]Fig. 6

references
[1]
PubMed ID8286347
JournalBiochemistry
Year1994
Volume33
Pages235-40
AuthorsGuranowski A, Brown P, Ashton PA, Blackburn GM
TitleRegiospecificity of the hydrolysis of diadenosine polyphosphates catalyzed by three specific pyrophosphohydrolases.
[2]
PubMed ID11183782
JournalJ Mol Biol
Year2000
Volume302
Pages1165-77
AuthorsSwarbrick JD, Bashtannyk T, Maksel D, Zhang XR, Blackburn GM, Gayler KR, Gooley PR
TitleThe three-dimensional structure of the Nudix enzyme diadenosine tetraphosphate hydrolase from Lupinus angustifolius L.
Related PDB1f3y
Related UniProtKBO04841
[3]
CommentsNUCLEOTIDE SEQUENCE [GENOMIC DNA], X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS), FUNCTION, COFACTOR.
PubMed ID11738085
JournalBiochim Biophys Acta
Year2001
Volume1550
Pages27-36
AuthorsAbdelghany HM, Gasmi L, Cartwright JL, Bailey S, Rafferty JB, McLennan AG
TitleCloning, characterisation and crystallisation of a diadenosine 5',5"'-P(1),P(4)-tetraphosphate pyrophosphohydrolase from Caenorhabditis elegans.
[4]
CommentsX-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
PubMed ID11856844
JournalActa Crystallogr D Biol Crystallogr
Year2002
Volume58
Pages526-8
AuthorsBailey S, Sedelnikova SE, Blackburn GM, Abdelghany HM, McLennan AG, Rafferty JB
TitleCrystallization of a complex of Caenorhabditis elegans diadenosine tetraphosphate hydrolase and a non-hydrolysable substrate analogue, AppCH2ppA.
Related UniProtKBQ9U2M7
[5]
CommentsX-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS), SUBUNIT.
PubMed ID11937063
JournalStructure
Year2002
Volume10
Pages589-600
AuthorsBailey S, Sedelnikova SE, Blackburn GM, Abdelghany HM, Baker PJ, McLennan AG, Rafferty JB
TitleThe crystal structure of diadenosine tetraphosphate hydrolase from Caenorhabditis elegans in free and binary complex forms.
Related PDB1kt9,1ktg
Related UniProtKBQ9U2M7
[6]
PubMed ID11839306
JournalStructure
Year2002
Volume10
Pages205-13
AuthorsFletcher JI, Swarbrick JD, Maksel D, Gayler KR, Gooley PR
TitleThe structure of Ap(4)A hydrolase complexed with ATP-MgF(x) reveals the basis of substrate binding.
Related PDB1jkn
Related UniProtKBO04841
[7]
CommentsMUTAGENESIS.
PubMed ID12475970
JournalJ Biol Chem
Year2003
Volume278
Pages4435-9
AuthorsAbdelghany HM, Bailey S, Blackburn GM, Rafferty JB, McLennan AG
TitleAnalysis of the catalytic and binding residues of the diadenosine tetraphosphate pyrophosphohydrolase from Caenorhabditis elegans by site-directed mutagenesis.
Related UniProtKBQ9U2M7
[8]
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.
[9]
CommentsSTRUCTURE BY NMR.
PubMed ID15596429
JournalJ Biol Chem
Year2005
Volume280
Pages8471-81
AuthorsSwarbrick JD, Buyya S, Gunawardana D, Gayler KR, McLennan AG, Gooley PR
TitleStructure and substrate-binding mechanism of human Ap4A hydrolase.
Related PDB1xsa,1xsb,1xsc
Related UniProtKBP50583
[10]
PubMed ID15772762
JournalJ Biomol NMR
Year2005
Volume31
Pages181-2
AuthorsSwarbrick JD, Buyya S, Gunawardana D, Fletcher JI, Branson K, Smith B, Pepe S, McLennan AG, Gayler KR, Gooley PR
Title1H, 13C, and 15N resonance assignments of the 17 kDa Ap4A hydrolase from Homo sapiens in the presence and absence of ATP.

comments
This enzyme belongs to Nudix (nucleoside diphosphate linked to X) hydrolase superfamily.
The family of this enzyme (asymmetrical Ap4A hydrolase) can be subdivided into two groups: the "animal-type" group that includes the enzymes from animal and archaea, and the "plant-type" one that includes ones from plant and bacteria (see [5]). This enzyme belongs to the animal-type group. The plant-type enzymes correspond to the entry S00920 in EzCatDB.
According to the literature [8], Mg-3 is bound to the three phosphates of the leaving ATP, which are phosphates-1, -2 and -3 of substrate Ap4A. The catalytic water is bound to Mg-1, which is coordinated by Glu52, Glu56 and Glu103 (of 1ktg). Mg-2 is coordinated by mainchain carbonyl of Lys36, sidechain of Glu56, and phosphates-2 and -3.
The reaction of this enzyme may proceed as follows (see [5], [7] and [8]).
(1) Glu52 (of 1ktg) acts as a general base to deprotonate the water molecule, which is bound to Mg-1. Mg-1, which is bound to Glu52, Glu56 and Glu103, may lower the pKa of the catalytic water, so that it can be deprotonated easily.
(2) The activated water makes a nucleophilic attack on phosphate-4 of Ap4P.
(3) Mg-2 and Mg-3 stabilize the negative charge on the leaving phosphate groups of ATP. The sidechains of Lys36 and Lys83 also stabilize the negative charge as well. The nucleophilic substitution reaction seems to be SN2-like.

createdupdated
2011-02-042013-02-27


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)
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)
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