DB code: S00920

RLCP classification	1.15.8240.1167 : 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 S00815 S00921 S00922 S00923 S00924 S00454

Uniprot Enzyme Name
UniprotKB	Protein name	Synonyms	Pfam
O04841		Diadenosine 5'',5''''''-P1,P4-tetraphosphate hydrolase EC 3.6.1.17	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
O04841	O04841_LUPAN

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

1f3yA00	Unbound	Unbound	Unbound		Unbound	Unbound	Unbound	Unbound
1jknA00	Unbound	Unbound	Unbound		Bound:ATP	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

1f3yA00	ARG 33;GLU 60;LYS 150	GLN 44(Magnesium-2);GLU 60;GLU 130(Magnesium-1);GLU 64(Magnesium-1,2)
1jknA00	ARG 33;GLU 60;LYS 150	GLN 44(Magnesium-2);GLU 60;GLU 130(Magnesium-1);GLU 64(Magnesium-1,2)

References for Catalytic Mechanism
References	Sections	No. of steps in catalysis
[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
(3) Mg-2 and Mg-3 stabilize the negative charge on the leaving phosphate groups of ATP. The sidechains of Arg33 and Lys150 also stabilize the negative charge as well. The nucleophilic substitution reaction seems to be SN2-like. 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 plant-type group. The animal-type enzymes correspond to the entry S00815 in EzCatDB. In comparison with the structure of the animal type enzymes (S00815 in EzCatDB), 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 Glu60, Glu64 and Glu130 (of 1f3y). Mg-2 is coordinated by mainchain carbonyl of Gln44, sidechain of Glu64, and phosphates-2 and -3. The reaction of this enzyme may proceed as follows (see [5], [7] and [8]). (1) Glu60 (of 1f3y) acts as a general base to deprotonate the water molecule, which is bound to Mg-1. Mg-1, which is bound to Glu60, Glu64 and Glu130, 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.

Comments

(3) Mg-2 and Mg-3 stabilize the negative charge on the leaving phosphate groups of ATP. The sidechains of Arg33 and Lys150 also stabilize the negative charge as well. The nucleophilic substitution reaction seems to be SN2-like.
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 plant-type group. The animal-type enzymes correspond to the entry S00815 in EzCatDB.
In comparison with the structure of the animal type enzymes (S00815 in EzCatDB), 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 Glu60, Glu64 and Glu130 (of 1f3y). Mg-2 is coordinated by mainchain carbonyl of Gln44, sidechain of Glu64, and phosphates-2 and -3.
The reaction of this enzyme may proceed as follows (see [5], [7] and [8]).
(1) Glu60 (of 1f3y) acts as a general base to deprotonate the water molecule, which is bound to Mg-1. Mg-1, which is bound to Glu60, Glu64 and Glu130, 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.

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