EzCatDB: D00147
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DB codeD00147
CATH domainDomain 13.60.21.10 : Purple Acid Phosphatase; chain A, domain 2Catalytic domain
Domain 23.90.780.10 : 5'-nucleotidase; domain 2Catalytic domain
E.C.3.1.3.5,3.6.1.45
CSA1ush

CATH domainRelated DB codes (homologues)
3.60.21.10 : Purple Acid Phosphatase; chain A, domain 2D00146,D00151,S00435

Enzyme Name
UniProtKBKEGG

P07024
Protein nameProtein ushA5'-nucleotidase
   (EC 3.1.3.5)

uridine 5'-nucleotidase
   (EC 3.1.3.5)

5'-adenylic phosphatase
   (EC 3.1.3.5)

adenosine 5'-phosphatase
   (EC 3.1.3.5)

AMP phosphatase
   (EC 3.1.3.5)

adenosine monophosphatase
   (EC 3.1.3.5)

5'-mononucleotidase
   (EC 3.1.3.5)

AMPase
   (EC 3.1.3.5)

UMPase
   (EC 3.1.3.5)

snake venom 5'-nucleotidase
   (EC 3.1.3.5)

thimidine monophosphate nucleotidase
   (EC 3.1.3.5)

5'-AMPase
   (EC 3.1.3.5)

5'-AMP nucleotidase
   (EC 3.1.3.5)

AMP phosphohydrolase
   (EC 3.1.3.5)

IMP 5'-nucleotidase
   (EC 3.1.3.5)

UDP-sugar diphosphatase
   (EC 3.6.1.45)

nucleosidediphosphate-sugar pyrophosphatase
   (EC 3.6.1.45)

nucleosidediphosphate-sugar diphosphatase
   (EC 3.6.1.45)

UDP-sugar hydrolase
   (EC 3.6.1.45)

UDP-sugar pyrophosphatase
   (EC 3.6.1.45)

SynonymsNone
IncludesUDP-sugar hydrolase
   EC 3.6.1.45
UDP-sugar pyrophosphatase UDP-sugar diphosphatase
5''-nucleotidase
(5''-NT)
   EC 3.1.3.5
RefSeqNP_415013.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_488771.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PfamPF02872 (5_nucleotid_C)
PF00149 (Metallophos)
[Graphical view]

KEGG pathways
MAP codePathwaysE.C.
MAP00230Purine metabolism3.1.3.5
MAP00240Pyrimidine metabolism3.1.3.5
MAP00760Nicotinate and nicotinamide metabolism3.1.3.5

UniProtKB:Accession NumberP07024
Entry nameUSHA_ECOLI
ActivityUDP-sugar + H(2)O = UMP + alpha-D-aldose 1- phosphate.,A 5''-ribonucleotide + H(2)O = a ribonucleoside + phosphate.
SubunitMonomer.
Subcellular locationPeriplasm. Note=Exported from the cell, except a small proportion that is internally localized.
CofactorBinds 2 zinc ions per subunit.

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00038C00001C02520C05227C00201C00454C00911C00009C00105C00991C00454C02520
E.C.
3.1.3.5,3.6.1.453.1.3.53.6.1.45

3.1.3.53.1.3.53.6.1.453.6.1.45

CompoundZincH2O5'-RibonucleotideUDP-sugarNucleoside triphosphateNucleoside diphosphateRibonucleosidePhosphateUMPalpha-D-Aldose 1-phosphateNucleoside diphosphate5'-Ribonucleotide
Typeheavy metalH2Onucleotideamide group,carbohydrate,nucleotidenucleotidenucleotidenucleosidephosphate group/phosphate ionamide group,nucleotidecarbohydrate,phosphate group/phosphate ionnucleotidenucleotide
ChEBI29105
15377





26078
16695



PubChem32051
962
22247451





22486802
1004
6030



                    
1ho5A01Analogue:2x_MN UnboundUnboundUnboundUnboundUnboundBound:PO4UnboundUnboundUnboundUnbound
1ho5B01Analogue:2x_MN UnboundUnboundUnboundUnboundUnboundBound:PO4UnboundUnboundUnboundUnbound
1hp1A01Bound:2x_ZN UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1hpuA01Analogue:2x_MNUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1hpuB01Analogue:2x_MNUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1hpuC01Analogue:2x_MNBound:HOH 1137UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1hpuD01Analogue:2x_MNBound:HOH 853UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1oi8A01Analogue:2x_MN UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1oi8B01Analogue:2x_MN UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1oidA01Analogue:_NI UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1oidB01Unbound UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1oieA01Analogue:_NI UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1ushA01Bound:2x_ZN UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
2ushA01Bound:2x_ZN UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
2ushB01Bound:2x_ZN UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1ho5A02Unbound UnboundUnboundUnboundUnboundBound:ADNUnboundUnboundUnboundUnboundUnbound
1ho5B02Unbound UnboundUnboundUnboundUnboundBound:ADNUnboundUnboundUnboundUnboundUnbound
1hp1A02Unbound UnboundUnboundBound:ATPUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1hpuA02UnboundUnboundUnboundUnboundUnboundAnalogue:A12UnboundUnboundUnboundUnboundUnboundUnbound
1hpuB02UnboundUnboundUnboundUnboundUnboundAnalogue:A12UnboundUnboundUnboundUnboundUnboundUnbound
1hpuC02UnboundUnboundUnboundUnboundUnboundAnalogue:A12UnboundUnboundUnboundUnboundUnboundUnbound
1hpuD02UnboundUnboundUnboundUnboundUnboundAnalogue:A12UnboundUnboundUnboundUnboundUnboundUnbound
1oi8A02Unbound UnboundUnboundUnboundUnboundUnboundAnalogue:SO4UnboundUnboundUnboundUnbound
1oi8B02Unbound UnboundUnboundUnboundUnboundUnboundAnalogue:SO4UnboundUnboundUnboundUnbound
1oidA02Unbound UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1oidB02Unbound UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1oieA02Unbound UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1ushA02Unbound UnboundUnboundUnboundUnboundUnboundAnalogue:SO4 603UnboundUnboundUnboundUnbound
2ushA02Unbound UnboundUnboundUnboundAnalogue:WO4 702-WO4 703UnboundUnboundUnboundUnboundUnboundUnbound
2ushB02Unbound UnboundUnboundUnboundUnboundUnboundAnalogue:WO4 701UnboundUnboundUnboundAnalogue:WO4 704

Active-site residues
resource
literature [3], [5]
pdbCatalytic residuesCofactor-binding residuescomment
           
1ho5A01ASN 116;HIS 117;ASP 120
ASP 41;HIS 43;GLN 254(Zinc-1);ASP 84(Zinc-1 & 2);ASN 116;HIS 217;HIS 252(Zinc-2)
 
1ho5B01ASN 116;HIS 117;ASP 120
ASP 41;HIS 43;GLN 254(Zinc-1);ASP 84(Zinc-1 & 2);ASN 116;HIS 217;HIS 252(Zinc-2)
 
1hp1A01ASN 116;HIS 117;ASP 120
ASP 41;HIS 43;GLN 254(Zinc-1);ASP 84(Zinc-1 & 2);ASN 116;HIS 217;HIS 252(Zinc-2)
 
1hpuA01ASN 116;HIS 117;ASP 120
ASP 41;HIS 43;GLN 254(Zinc-1);ASP 84(Zinc-1 & 2);ASN 116;HIS 217;HIS 252(Zinc-2)
 
1hpuB01ASN 116;HIS 117;ASP 120
ASP 41;HIS 43;GLN 254(Zinc-1);ASP 84(Zinc-1 & 2);ASN 116;HIS 217;HIS 252(Zinc-2)
 
1hpuC01ASN 116;HIS 117;ASP 120
ASP 41;HIS 43;GLN 254(Zinc-1);ASP 84(Zinc-1 & 2);ASN 116;HIS 217;HIS 252(Zinc-2)
 
1hpuD01ASN 116;HIS 117;ASP 120
ASP 41;HIS 43;GLN 254(Zinc-1);ASP 84(Zinc-1 & 2);ASN 116;HIS 217;HIS 252(Zinc-2)
 
1oi8A01ASN 116;HIS 117;ASP 120
ASP 41;HIS 43;GLN 254(Zinc-1);ASP 84(Zinc-1 & 2);ASN 116;HIS 217;HIS 252(Zinc-2)
mutant P90C, disulfide bridge(C90-C424)
1oi8B01ASN 116;HIS 117;ASP 120
ASP 41;HIS 43;GLN 254(Zinc-1);ASP 84(Zinc-1 & 2);ASN 116;HIS 217;HIS 252(Zinc-2)
mutant P90C, disulfide bridge(C90-C424)
1oidA01ASN 116;HIS 117;ASP 120
ASP 41;HIS 43;GLN 254(Zinc-1);ASP 84(Zinc-1 & 2);ASN 116;HIS 217;HIS 252(Zinc-2)
mutant S228C, disulfide bridge(C228-C513)
1oidB01ASN 116;HIS 117;ASP 120
ASP 41;HIS 43;GLN 254(Zinc-1);ASP 84(Zinc-1 & 2);ASN 116;HIS 217;HIS 252(Zinc-2)
mutant S228C, disulfide bridge(C228-C513)
1oieA01ASN 116;HIS 117;ASP 120
ASP 41;HIS 43;GLN 254(Zinc-1);ASP 84(Zinc-1 & 2);ASN 116;HIS 217;HIS 252(Zinc-2)
mutant S228C, disulfide bridge(C228-C513)
1ushA01ASN 116;HIS 117;ASP 120
ASP 41;HIS 43;GLN 254(Zinc-1);ASP 84(Zinc-1 & 2);ASN 116;HIS 217;HIS 252(Zinc-2)
 
2ushA01ASN 116;HIS 117;ASP 120
ASP 41;HIS 43;GLN 254(Zinc-1);ASP 84(Zinc-1 & 2);ASN 116;HIS 217;HIS 252(Zinc-2)
 
2ushB01ASN 116;HIS 117;ASP 120
ASP 41;HIS 43;GLN 254(Zinc-1);ASP 84(Zinc-1 & 2);ASN 116;HIS 217;HIS 252(Zinc-2)
 
1ho5A02ARG 375;ARG 379;ARG 410
 
 
1ho5B02ARG 375;ARG 379;ARG 410
 
 
1hp1A02ARG 375;ARG 379;ARG 410
 
 
1hpuA02ARG 375;ARG 379;ARG 410
 
 
1hpuB02ARG 375;ARG 379;ARG 410
 
 
1hpuC02ARG 375;ARG 379;ARG 410
 
 
1hpuD02ARG 375;ARG 379;ARG 410
 
 
1oi8A02ARG 375;ARG 379;ARG 410
 
mutant L424C, disulfide bridge C90-C424
1oi8B02ARG 375;ARG 379;ARG 410
 
mutant L424C, disulfide bridge C90-C424
1oidA02ARG 375;ARG 379;ARG 410
 
mutant P513C, disulfide bridge C228-C513
1oidB02ARG 375;ARG 379;ARG 410
 
mutant P513C, disulfide bridge C228-C513
1oieA02ARG 375;ARG 379;ARG 410
 
mutant P513C, disulfide bridge C228-C513
1ushA02ARG 375;ARG 379;ARG 410
 
 
2ushA02ARG 375;ARG 379;ARG 410
 
 
2ushB02ARG 375;ARG 379;ARG 410
 
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]Fig.4, p.239-240
[3]p.449-450, p.451-452
[5]Fig.8, p.249-252
[10]Fig.22, p.3357-3358

references
[1]
PubMed ID6321242
JournalFEBS Lett
Year1984
Volume167
Pages235-40
AuthorsWorku Y, Luzio JP, Newby AC
TitleIdentification of histidyl and cysteinyl residues essential for catalysis by 5'-nucleotidase.
[2]
PubMed ID9180021
JournalComp Biochem Physiol B Biochem Mol Biol
Year1997
Volume117
Pages135-42
AuthorsGarcia L, Chayet L, Kettlun AM, Collados L, Chiong M, Traverso-Cori A, Mancilla M, Valenzuela MA
TitleKinetic characteristics of nucleoside mono-, di- and triphosphatase activities of the periplasmic 5'-nucleotidase of Escherichia coli.
[3]
CommentsX-RAY CRYSTALLOGRAPHY (1.73 ANGSTROMS) OF 26-550
Medline ID99260739
PubMed ID10331872
JournalNat Struct Biol
Year1999
Volume6
Pages448-53
AuthorsKnofel T, Strater N
TitleX-ray structure of the Escherichia coli periplasmic 5'-nucleotidase containing a dimetal catalytic site.
Related PDB1ush,2ush
Related UniProtKBP07024
[4]
CommentsX-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEX WITH SUBSTRATE.
PubMed ID11491294
JournalJ Mol Biol
Year2001
Volume309
Pages255-66
AuthorsKnofel T, Strater N
TitleE. coli 5'-nucleotidase undergoes a hinge-bending domain rotation resembling a ball-and-socket motion.
Related UniProtKBP07024
[5]
CommentsX-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEX WITH SUBSTRATE; PRODUCT AND INHIBITOR.
PubMed ID11491293
JournalJ Mol Biol
Year2001
Volume309
Pages239-54
AuthorsKnofel T, Strater N
TitleMechanism of hydrolysis of phosphate esters by the dimetal center of 5'-nucleotidase based on crystal structures.
Related PDB1ho5,1hp1,1hpu
Related UniProtKBP07024
[6]
PubMed ID12603203
JournalBiochem J
Year2003
Volume372
Pages625-30
AuthorsMcMillen L, Beacham IR, Burns DM
TitleCobalt activation of Escherichia coli 5'-nucleotidase is due to zinc ion displacement at only one of two metal-ion-binding sites.
[7]
PubMed ID12947102
JournalJ Biol Chem
Year2003
Volume278
Pages46195-8
AuthorsBianchi V, Spychala J
TitleMammalian 5'-nucleotidases.
[8]
CommentsX-ray crystallography
PubMed ID15215524
JournalProtein Sci
Year2004
Volume13
Pages1811-22
AuthorsSchultz-Heienbrok R, Maier T, Strater N
TitleTrapping a 96 degrees domain rotation in two distinct conformations by engineered disulfide bridges.
Related PDB1oi8,1oid,1oie
[9]
PubMed ID15709736
JournalBiochemistry
Year2005
Volume44
Pages2244-52
AuthorsSchultz-Heienbrok R, Maier T, Strater N
TitleA large hinge bending domain rotation is necessary for the catalytic function of Escherichia coli 5'-nucleotidase.
[10]
PubMed ID16895331
JournalChem Rev
Year2006
Volume106
Pages3338-63
AuthorsMitic N, Smith SJ, Neves A, Guddat LW, Gahan LR, Schenk G
TitleThe catalytic mechanisms of binuclear metallohydrolases.

comments
According to the literature [2], this enzyme can hydrolyze nucleoside triphosphate (C00201) and nucleoside diphosphate (C00454) in addition to 5'-ribonucleotides (activity of EC 3.1.3.5) and UDP-sugars (activity of EC 3.6.1.45).

createdupdated
2004-11-222009-02-26


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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