DB code: S00815

RLCP classification 1.15.8240.1166 : Hydrolysis
CATH domain 3.90.79.10 : Nucleoside Triphosphate Pyrophosphohydrolase Catalytic domain
E.C. 3.6.1.17
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
3.90.79.10 : Nucleoside Triphosphate Pyrophosphohydrolase S00814 S00920 S00921 S00922 S00923 S00924 S00454

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
Q9U2M7 Bis(5''-nucleosyl)-tetraphosphatase {asymmetrical}
EC 3.6.1.-
Diadenosine 5'',5''''''-P1,P4-tetraphosphate asymmetrical hydrolase
Diadenosine tetraphosphatase
Ap4A hydrolase
Ap4Aase
Nudix hydrolase 4
NP_493413.1 (Protein)
NM_061012.4 (DNA/RNA sequence)
PF00293 (NUDIX)
[Graphical View]
P50583 Bis(5''-nucleosyl)-tetraphosphatase {asymmetrical}
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
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)
PF00293 (NUDIX)
[Graphical View]

KEGG enzyme name
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

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
Q9U2M7 AP4A_CAEEL P1,P(4)-bis(5'-adenosyl) tetraphosphate + H2O = ATP + AMP. Monomer. Divalent ions. Magnesium, cobalt, manganese, zinc or calcium.
P50583 AP4A_HUMAN P1,P(4)-bis(5'-guanosyl) tetraphosphate + H2O = GTP + GMP. Divalent ions (By similarity).

KEGG Pathways
Map code Pathways E.C.
MAP00230 Purine metabolism
MAP00240 Pyrimidine metabolism

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C02148 C01260 C01261 C00001 C00002 C00020 C00044 C00144
E.C.
Compound Divalent metal P1,P4-Bis(5'-adenosyl) tetraphosphate P1,P4-bis(5'-guanosyl) tetraphosphate H2O ATP AMP GTP GMP
Type divalent metal (Ca2+, Mg2+) amide group,amine group,nucleotide amide group,amine group,nucleotide H2O amine group,nucleotide amine group,nucleotide amide group,amine group,nucleotide amide group,amine group,nucleotide
ChEBI 17422
 17422
 		15883
 15883
 		15377
 15377
 		15422
 15422
 		16027
 16027
 		15996
 15996
 		17345
 17345
PubChem 21706
 21706
 		165186
 165186
 		22247451
 962
 22247451
 962
 		5957
 5957
 		6083
 6083
 		6830
 6830
 		6804
 6804
1kt9A00 Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1ktgA00 Bound:4x_MG Unbound Unbound Bound:_OH Analogue:AMP Unbound Analogue:PO4 Unbound
1ktgB00 Bound:4x_MG Unbound Unbound Bound:_OH Unbound Unbound Unbound Unbound
1xsaA00 Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1xsbA00 Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1xscA00 Unbound Unbound Unbound Bound:ATP Unbound Unbound Unbound
3u53A00 Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3u53B00 Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3u53C00 Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3u53D00 Unbound Unbound Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
Literature [5], [7], [8], [9]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1kt9A00 GLU 52;LYS 36;LYS 83 LYS 36(Magnesium-2);GLU 52; (Magnesium-1);GLU 56(Magnesium-1,2) invisible 26, 103-105
1ktgA00 GLU 52;LYS 36;LYS 83 LYS 36(Magnesium-2);GLU 52;GLU 103(Magnesium-1);GLU 56(Magnesium-1,2)
1ktgB00 GLU 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
3u53A00 GLU 58;LYS 42;LYS 89 LYS 42(Magnesium-2);GLU 58;GLU 110(Magnesium-1);GLU 62(Magnesium-1,2)
3u53B00 GLU 58;LYS 42;LYS 89 LYS 42(Magnesium-2);GLU 58;GLU 110(Magnesium-1);GLU 62(Magnesium-1,2)
3u53C00 GLU 58;LYS 42;LYS 89 LYS 42(Magnesium-2);GLU 58;GLU 110(Magnesium-1);GLU 62(Magnesium-1,2)
3u53D00 GLU 58;LYS 42;LYS 89 LYS 42(Magnesium-2);GLU 58;GLU 110(Magnesium-1);GLU 62(Magnesium-1,2)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[5]
[7]
[8]
Fig. 6

References
[1]
Resource
Comments
Medline ID
PubMed ID 8286347
Journal Biochemistry
Year 1994
Volume 33
Pages 235-40
Authors Guranowski A, Brown P, Ashton PA, Blackburn GM
Title Regiospecificity of the hydrolysis of diadenosine polyphosphates catalyzed by three specific pyrophosphohydrolases.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 11183782
Journal J Mol Biol
Year 2000
Volume 302
Pages 1165-77
Authors Swarbrick JD, Bashtannyk T, Maksel D, Zhang XR, Blackburn GM, Gayler KR, Gooley PR
Title The three-dimensional structure of the Nudix enzyme diadenosine tetraphosphate hydrolase from Lupinus angustifolius L.
Related PDB 1f3y
Related UniProtKB O04841
[3]
Resource
Comments NUCLEOTIDE SEQUENCE [GENOMIC DNA], X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS), FUNCTION, COFACTOR.
Medline ID
PubMed ID 11738085
Journal Biochim Biophys Acta
Year 2001
Volume 1550
Pages 27-36
Authors Abdelghany HM, Gasmi L, Cartwright JL, Bailey S, Rafferty JB, McLennan AG
Title Cloning, characterisation and crystallisation of a diadenosine 5',5"'-P(1),P(4)-tetraphosphate pyrophosphohydrolase from Caenorhabditis elegans.
Related PDB
Related UniProtKB
[4]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
Medline ID
PubMed ID 11856844
Journal Acta Crystallogr D Biol Crystallogr
Year 2002
Volume 58
Pages 526-8
Authors Bailey S, Sedelnikova SE, Blackburn GM, Abdelghany HM, McLennan AG, Rafferty JB
Title Crystallization of a complex of Caenorhabditis elegans diadenosine tetraphosphate hydrolase and a non-hydrolysable substrate analogue, AppCH2ppA.
Related PDB
Related UniProtKB Q9U2M7
[5]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS), SUBUNIT.
Medline ID
PubMed ID 11937063
Journal Structure
Year 2002
Volume 10
Pages 589-600
Authors Bailey S, Sedelnikova SE, Blackburn GM, Abdelghany HM, Baker PJ, McLennan AG, Rafferty JB
Title The crystal structure of diadenosine tetraphosphate hydrolase from Caenorhabditis elegans in free and binary complex forms.
Related PDB 1kt9 1ktg
Related UniProtKB Q9U2M7
[6]
Resource
Comments
Medline ID
PubMed ID 11839306
Journal Structure
Year 2002
Volume 10
Pages 205-13
Authors Fletcher JI, Swarbrick JD, Maksel D, Gayler KR, Gooley PR
Title The structure of Ap(4)A hydrolase complexed with ATP-MgF(x) reveals the basis of substrate binding.
Related PDB 1jkn
Related UniProtKB O04841
[7]
Resource
Comments MUTAGENESIS.
Medline ID
PubMed ID 12475970
Journal J Biol Chem
Year 2003
Volume 278
Pages 4435-9
Authors Abdelghany HM, Bailey S, Blackburn GM, Rafferty JB, McLennan AG
Title Analysis of the catalytic and binding residues of the diadenosine tetraphosphate pyrophosphohydrolase from Caenorhabditis elegans by site-directed mutagenesis.
Related PDB
Related UniProtKB Q9U2M7
[8]
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
[9]
Resource
Comments STRUCTURE BY NMR.
Medline ID
PubMed ID 15596429
Journal J Biol Chem
Year 2005
Volume 280
Pages 8471-81
Authors Swarbrick JD, Buyya S, Gunawardana D, Gayler KR, McLennan AG, Gooley PR
Title Structure and substrate-binding mechanism of human Ap4A hydrolase.
Related PDB 1xsa 1xsb 1xsc
Related UniProtKB P50583
[10]
Resource
Comments
Medline ID
PubMed ID 15772762
Journal J Biomol NMR
Year 2005
Volume 31
Pages 181-2
Authors Swarbrick JD, Buyya S, Gunawardana D, Fletcher JI, Branson K, Smith B, Pepe S, McLennan AG, Gayler KR, Gooley PR
Title 1H, 13C, and 15N resonance assignments of the 17 kDa Ap4A hydrolase from Homo sapiens in the presence and absence of ATP.
Related PDB
Related UniProtKB

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.

Created Updated
2011-02-04 2013-02-27