Any feedback?
Information on EC 3.1.3.5 - 5'-nucleotidase and Organism(s) Escherichia coli and UniProt Accession P07024
for references in articles please use BRENDA:EC3.1.3.5Please wait a moment until all data is loaded. This message will disappear when all data is loaded.
EC Tree
3.1.3.5 5'-nucleotidaseIUBMB Comments
Wide specificity for 5'-nucleotides.
Specify your search results
Word Map
- 3.1.3.5
- nucleoside
- adp
- deaminase
- triphosphate
-
purinergic
-
ecto-5\'-nucleotidase
- lymphocyte
- endothelial
- phosphodiesterase
- ntpdases
- agonist
-
diphosphohydrolase
- erythrocyte
- adenylate
- inosine
- platelet
- phosphorylase
- na+
-
cytochemical
- glucose-6-phosphatase
- 5'-monophosphate
- hypoxanthine
-
histochemistry
-
concanavalin
- acetylcholinesterase
- apyrase
-
ecto-enzymes
-
synaptosomes
- 5'-diphosphate
- adpase
- ecto-atpase
- suramin
- mg2+-atpase
- deoxycytidine
-
k+-atpase
- dpcpx
- dipyridamole
-
ouabain-sensitive
-
purinoceptors
- phosphomonoesterase
- sarcolemma
-
plasma-membrane
-
neuromodulator
- antivenoms
-
ppads
- ehna
- 8-cyclopentyl-1,3-dipropylxanthine
-
ectonucleotide
-
8-phenyltheophylline
- nutrition
- hgprt
- medicine
- pharmacology
The taxonomic range for the selected organisms is: Escherichia coli
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Synonyms
5'-nucleotidase, ecto-5'-nucleotidase, ectonucleotidase, 5'nucleotidase, 5'-nt, cn-ii, ecto-nucleotidase, pyrimidine 5'-nucleotidase, cytosolic 5'-nucleotidase, ampase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
5'-adenylic phosphatase
-
-
-
-
5'-AMP nucleotidase
-
-
-
-
5'-AMPase
-
-
-
-
5'-mononucleotidase
-
-
-
-
5'nucleotidase
-
-
-
-
adenosine 5'-monophosphatase
-
-
-
-
adenosine 5'-phosphatase
-
-
-
-
adenosine monophosphatase
-
-
-
-
AMP phosphatase
-
-
-
-
AMP phosphohydrolase
-
-
-
-
AMPase
-
-
-
-
CD73 antigen
-
-
-
-
ecto-5'-nucleotidase
-
-
-
-
IMP 5'-nucleotidase
-
-
-
-
snake venom 5'-nucleotidase
-
-
-
-
thymidine monophosphate nucleotidase
-
-
-
-
UMPase
-
-
-
-
uridine 5'-nucleotidase
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
hydrolysis of phosphoric ester
hydrolysis of phosphoric ester
-
-
-
-
PATHWAY SOURCE
PATHWAYS
BRENDA
KEGG
-
-, -, -, -, -, -, -, -, -, -
SYSTEMATIC NAME
IUBMB Comments
5'-ribonucleotide phosphohydrolase
Wide specificity for 5'-nucleotides.
CAS REGISTRY NUMBER
COMMENTARY
9027-73-0
-
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
(polyphosphate)n + H2O
(polyphosphate)(n-1) + phosphate
-
-
-
?
5'-AMP + H2O
?
-
enzyme in the system for the hydrolysis of extracellular nucleotides so that product nucleosides are readily transported into the cell
-
-
?
p-nitrophenyl phosphate + H2O
p-nitrophenol + phosphate
-
-
-
?
additional information
?
-
-
bifunctional enzyme with UDP-sugar hydrolase and 5'-nucleotidase activities
-
?
4-nitrophenyl phosphate + H2O
4-nitrophenol + phosphate
-
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
5'-AMP + H2O
?
-
enzyme in the system for the hydrolysis of extracellular nucleotides so that product nucleosides are readily transported into the cell
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Co2+
Mg2+
KD: 224.7 +/- 35.1 microM Mg2+ with p-nitrophenyl phosphate, KD: 140.0 +/- 9.99 microM Mg2+ with 5'-AMP
Mn2+
KD: 7.24 +/- 0.71 microM Mn2+ with p-nitrophenyl phosphate, KD: 2.23 +/- 0.14 micorM Mn2+ with 5'-AMP
Ni2+
KD: 72.3 +/- 7.61 microM Ni2+ with p-nitrophenyl phosphate, KD: 29.4 +/- 3.69 microM Ni2+ with 5'-AMP
Co2+
-
activation is due to zinc ion displacement at only one of two metal-ion-binding sites, displacement occurs at the metal-ion bionding site consisting of the residues Asp84, Asn116, His217 and His252. Km for wild-type enzyme: 0.0925 mM
Co2+
activates with p-nitrophenyl phosphate, KD: 537.7 +/- 19.7 microM
Co2+
KD: 46.9 +/- 5.66 microM Co2+ with p-nitrophenyl phosphate, KD: 10.7 +/- 1.07 microM Co2+ with 5'-AMP
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
Specific protein inhibitor
-
the periplasmic enzyme has a specific protein inhibitor located in the cytoplasm. The physiological role of the inhibitor is to protect the intracellular nucleotide pool from any cytoplasmic 5'-nucleotidase activity
-
additional information
no substrate inhibition by p-nitrophenyl phosphate
-
additional information
-
no substrate inhibition by p-nitrophenyl phosphate
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
dithiothreitol
mutant P90C/L424C, 2fold activation, mutant S228C/P513C, 250fold activation
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
-
the two domains can be expressed individually in Escherichia coli and fold independently. The C-terminal domain, which contains the substrate-binding pocket, is completely inactive while the N-terminal domain with the two-metal-ion-centers and the core catalytic residues exhibits significant activity, especially towards substrates with activated phosphate bonds such as ATP, ADP, 4-nitrophenyl phosphate. The two domains do not reconstitute the full-length protein from the two folded individual domains
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
monomer
oligomer
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
four different crystal forms: analysis of the structure of ATP bound to the enzyme in crystal form I, which contains one molecule in the asymmetric unit, the structure of an enzyme/adenosine/phosphate complex in crystal form III, which contains two independent molecules and the structure of alpha,beta-methylene-ADP in complex with the enzyme in crystal form IV, containing four complexes in the asymmetric unit
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
P90C/L424C
enzyme variant that can adopt a closed and a half open conformation, active in oxidized state
S228C/P513C
enzyme variant trapped in open conformation, almost inactive, but up to 250fold activation by reduction of disulfide bridge
D41N
-
specific activity of the mutant enzyme is 9.1% of the wild-type enzyme, activation by Co2+ is less than 2fold the level of activation of the wild-type enzyme
D84N
-
mutant enzyme exhibits 900fold decreased specific activity and increased level of activation by Co2+, 2700fold compared with approximately 40fold for the wild-type enzyme
E118Q
-
specific activity of the mutant enzyme is 6.1% of the wild-type enzyme, activation by Co2+ is 2.5fold the level of activation of the wild-type enzyme
H117N
-
specific activity of the mutant enzyme is 0.037% of the wild-type activity in presence of Co2+ and 0.042% of the wild-type activity in absence of Co2+
H217N
-
specific activity of the mutant enzyme is 0.23% of the wild-type enzyme. Activation by Co2+ is approximately 6fold the level of activation of the wild-type enzyme
H43N
-
specific activity of the mutant enzyme is 0.76% of the wild-type enzyme, activation by Co2+ is 4fold less than the activation of the wild-type enzyme
additional information
-
individual expression of the N-terminal domain, amino acid residues Y26-V362, and the C-terminal domain, amino acid residues K363-Q550. The domains fold independently and properly. The C-terminal domain, which contains the substrate-binding pocket, is completely inactive while the N-terminal domain with the two-metal-ion-centers and the core catalytic residues exhibits significant activity, especially towards substrates with activated phosphate bonds such as ATP, ADP, 4-nitrophenyl phosphate
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
4°C, 5% glycerol, 0.5 M NaCl, pH 7.5, no loss in activity after several months
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Broad, D.F.; Smith, J.T.
Escherichia coli 5'-nucleotidase: purification, properties and its release by osmotic shock
J. Gen. Microbiol.
123
241-247
1981
Escherichia coli
Drummond, G.I.; Yamamoto, M.
Nucleotide phosphomonoesterases
The Enzymes, 3rd Ed. (Boyer, P. D. , ed. )
4
337-354
1971
Bothrops atrox, Saccharomyces cerevisiae, Crotalus adamanteus, Escherichia coli, Hemachatus haemachatus, Ovis aries, Naja naja, Proteus vulgaris, Daboia russelii, Salmonella enterica subsp. enterica serovar Heidelberg, Shigella sonnei, Solanum tuberosum
-
Garcia, L.; Chayet, L.; Kettlun, A.M.; Collados, L.; Chiong, M.; Traverso-Cori, A.; Mancilla, M.; Valenzuela, M.A.
Kinetic characteristics of nucleoside mono-, di- and triphosphate activities of the periplasmic 5'-nucleotidase of Escherichia coli
Comp. Biochem. Physiol. B
117
135-142
1997
Escherichia coli
McMillen, L.; Beacham, I.R.; Burns, D.M.
Cobalt activation of Escherichia coli 5'-nucleotidase is due to zinc ion displacement at only one of two metal-ion-binding sites
Biochem. J.
372
625-630
2003
Escherichia coli
Innes, D.; Beacham, I.R.; Burns, D.M.
The role of the intracellular inhibitor of periplasmic UDP-sugar hydrolase (5'-nucleotidase) in Escherichia coli: cytoplasmic localisation of 5'-nucleotidase is conditionally lethal
J. Basic Microbiol.
41
329-337
2001
Escherichia coli
Knofel, T.; Strater, N.
Mechanism of hydrolysis of phosphate esters by the dimetal center of 5'-nucleotidase based on crystal structures
J. Mol. Biol.
309
239-254
2001
Escherichia coli (P07024)
Knfel, T.; Strter, N.
E. coli 5'-nucleotidase undergoes a hinge-bending domain rotation resembling a ball-and-socket motion
J. Mol. Biol.
309
255-266
2001
Escherichia coli
Proudfoot, M.; Kuznetsova, E.; Brown, G.; Rao, N.N.; Kitagawa, M.; Mori, H.; Savchenko, A.; Yakunin, A.F.
General Enzymatic Screens Identify Three New Nucleotidases in Escherichia coli. Biochemical Characterization of SurE, YfbR, and Yjjg
J. Biol. Chem.
279
54687-54694
2004
Escherichia coli (P0A840), Escherichia coli (P76491)
Schultz-Heienbrok, R.; Maier, T.; Strater, N.
A large hinge bending domain rotation is necessary for the catalytic function of Escherichia coli 5'-nucleotidase
Biochemistry
44
2244-2252
2005
Escherichia coli (P07024), Escherichia coli
Krug, U.; Patzschke, R.; Zebisch, M.; Balbach, J.; Straeter, N.
Contribution of the two domains of E. coli 5'-nucleotidase to substrate specificity and catalysis
FEBS Lett.
587
460-466
2013
Escherichia coli
Krug, U.; Alexander, N.S.; Stein, R.A.; Keim, A.; Mchaourab, H.S.; Straeter, N.; Meiler, J.
Characterization of the domain orientations of E. coli 5'-nucleotidase by fitting an ensemble of conformers to DEER distance distributions
Structure
24
43-56
2016
Escherichia coli (P07024), Escherichia coli
EXTERNAL LINKS (specific for EC-Number 3.1.3.5)
Use of this online version of BRENDA is free under the CC BY 4.0 license. See terms of use for full details.
Release 2023.1 (January 2023)
Legal
Curated at
Member of
