DB code: D00147

CATH domain 3.60.21.10 : Purple Acid Phosphatase; chain A, domain 2 Catalytic domain
3.90.780.10 : 5'-nucleotidase; domain 2 Catalytic domain
E.C. 3.1.3.5 3.6.1.45
CSA 1ush
M-CSA 1ush
MACiE

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

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Includes RefSeq Pfam
P07024 Protein UshA
None UDP-sugar hydrolase
EC 3.6.1.45
UDP-sugar diphosphatase UDP-sugar pyrophosphatase
5''-nucleotidase
(5''-NT)
EC 3.1.3.5
NP_415013.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_488771.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF02872 (5_nucleotid_C)
PF00149 (Metallophos)
[Graphical View]

KEGG enzyme name
5'-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 )

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P07024 USHA_ECOLI A 5''-ribonucleotide + H(2)O = a ribonucleoside + phosphate. UDP-sugar + H(2)O = UMP + alpha-D-aldose 1- phosphate. Monomer. Periplasm. Note=Exported from the cell, except a small proportion that is internally localized. Binds 2 zinc ions per subunit.

KEGG Pathways
Map code Pathways E.C.
MAP00230 Purine metabolism 3.1.3.5
MAP00240 Pyrimidine metabolism 3.1.3.5
MAP00760 Nicotinate and nicotinamide metabolism 3.1.3.5

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00038 C00001 C02520 C05227 C00201 C00454 C00911 C00009 C00105 C00991 C00454 C02520
E.C. 3.1.3.5
3.6.1.45
3.1.3.5
3.6.1.45
3.1.3.5
3.1.3.5
3.6.1.45
3.6.1.45
Compound Zinc H2O 5'-Ribonucleotide UDP-sugar Nucleoside triphosphate Nucleoside diphosphate Ribonucleoside Phosphate UMP alpha-D-Aldose 1-phosphate Nucleoside diphosphate 5'-Ribonucleotide
Type heavy metal H2O nucleotide amide group,carbohydrate,nucleotide nucleotide nucleotide nucleoside phosphate group/phosphate ion amide group,nucleotide carbohydrate,phosphate group/phosphate ion nucleotide nucleotide
ChEBI 29105
15377
26078
16695
PubChem 32051
22247451
962
1004
22486802
6030
1ho5A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:2x_MN Unbound Unbound Unbound Unbound Unbound Bound:PO4 Unbound Unbound Unbound Unbound
1ho5B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:2x_MN Unbound Unbound Unbound Unbound Unbound Bound:PO4 Unbound Unbound Unbound Unbound
1hp1A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_ZN Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1hpuA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:2x_MN Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1hpuB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:2x_MN Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1hpuC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:2x_MN Bound:HOH_1137 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1hpuD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:2x_MN Bound:HOH_853 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1oi8A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:2x_MN Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1oi8B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:2x_MN Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1oidA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:_NI Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1oidB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1oieA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:_NI Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1ushA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_ZN Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2ushA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_ZN Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2ushB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_ZN Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1ho5A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Bound:ADN Unbound Unbound Unbound Unbound Unbound
1ho5B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Bound:ADN Unbound Unbound Unbound Unbound Unbound
1hp1A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:ATP Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1hpuA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Analogue:A12 Unbound Unbound Unbound Unbound Unbound Unbound
1hpuB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Analogue:A12 Unbound Unbound Unbound Unbound Unbound Unbound
1hpuC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Analogue:A12 Unbound Unbound Unbound Unbound Unbound Unbound
1hpuD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Analogue:A12 Unbound Unbound Unbound Unbound Unbound Unbound
1oi8A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Analogue:SO4 Unbound Unbound Unbound Unbound
1oi8B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Analogue:SO4 Unbound Unbound Unbound Unbound
1oidA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1oidB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1oieA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1ushA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Analogue:SO4_603 Unbound Unbound Unbound Unbound
2ushA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Analogue:WO4_702-WO4_703 Unbound Unbound Unbound Unbound Unbound Unbound
2ushB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Analogue:WO4_701 Unbound Unbound Unbound Analogue:WO4_704

Reference for Active-site residues
resource references E.C.
literature [3], [5]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1ho5A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 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)
1ho5B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 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)
1hp1A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 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)
1hpuA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 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)
1hpuB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 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)
1hpuC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 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)
1hpuD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 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)
1oi8A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 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)
1oi8B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 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)
1oidA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 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)
1oidB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 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)
1oieA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 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)
1ushA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 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)
2ushA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 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)
2ushB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 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)
1ho5A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 375;ARG 379;ARG 410
1ho5B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 375;ARG 379;ARG 410
1hp1A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 375;ARG 379;ARG 410
1hpuA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 375;ARG 379;ARG 410
1hpuB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 375;ARG 379;ARG 410
1hpuC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 375;ARG 379;ARG 410
1hpuD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 375;ARG 379;ARG 410
1oi8A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 375;ARG 379;ARG 410 mutant L424C, disulfide bridge C90-C424
1oi8B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 375;ARG 379;ARG 410 mutant L424C, disulfide bridge C90-C424
1oidA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 375;ARG 379;ARG 410 mutant P513C, disulfide bridge C228-C513
1oidB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 375;ARG 379;ARG 410 mutant P513C, disulfide bridge C228-C513
1oieA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 375;ARG 379;ARG 410 mutant P513C, disulfide bridge C228-C513
1ushA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 375;ARG 379;ARG 410
2ushA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 375;ARG 379;ARG 410
2ushB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 375;ARG 379;ARG 410

References for Catalytic Mechanism
References Sections No. 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]
Resource
Comments
Medline ID
PubMed ID 6321242
Journal FEBS Lett
Year 1984
Volume 167
Pages 235-40
Authors Worku Y, Luzio JP, Newby AC
Title Identification of histidyl and cysteinyl residues essential for catalysis by 5'-nucleotidase.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 9180021
Journal Comp Biochem Physiol B Biochem Mol Biol
Year 1997
Volume 117
Pages 135-42
Authors Garcia L, Chayet L, Kettlun AM, Collados L, Chiong M, Traverso-Cori A, Mancilla M, Valenzuela MA
Title Kinetic characteristics of nucleoside mono-, di- and triphosphatase activities of the periplasmic 5'-nucleotidase of Escherichia coli.
Related PDB
Related UniProtKB
[3]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.73 ANGSTROMS) OF 26-550
Medline ID 99260739
PubMed ID 10331872
Journal Nat Struct Biol
Year 1999
Volume 6
Pages 448-53
Authors Knofel T, Strater N
Title X-ray structure of the Escherichia coli periplasmic 5'-nucleotidase containing a dimetal catalytic site.
Related PDB 1ush 2ush
Related UniProtKB P07024
[4]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEX WITH SUBSTRATE.
Medline ID
PubMed ID 11491294
Journal J Mol Biol
Year 2001
Volume 309
Pages 255-66
Authors Knofel T, Strater N
Title E. coli 5'-nucleotidase undergoes a hinge-bending domain rotation resembling a ball-and-socket motion.
Related PDB
Related UniProtKB P07024
[5]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEX WITH SUBSTRATE; PRODUCT AND INHIBITOR.
Medline ID
PubMed ID 11491293
Journal J Mol Biol
Year 2001
Volume 309
Pages 239-54
Authors Knofel T, Strater N
Title Mechanism of hydrolysis of phosphate esters by the dimetal center of 5'-nucleotidase based on crystal structures.
Related PDB 1ho5 1hp1 1hpu
Related UniProtKB P07024
[6]
Resource
Comments
Medline ID
PubMed ID 12603203
Journal Biochem J
Year 2003
Volume 372
Pages 625-30
Authors McMillen L, Beacham IR, Burns DM
Title Cobalt activation of Escherichia coli 5'-nucleotidase is due to zinc ion displacement at only one of two metal-ion-binding sites.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 12947102
Journal J Biol Chem
Year 2003
Volume 278
Pages 46195-8
Authors Bianchi V, Spychala J
Title Mammalian 5'-nucleotidases.
Related PDB
Related UniProtKB
[8]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 15215524
Journal Protein Sci
Year 2004
Volume 13
Pages 1811-22
Authors Schultz-Heienbrok R, Maier T, Strater N
Title Trapping a 96 degrees domain rotation in two distinct conformations by engineered disulfide bridges.
Related PDB 1oi8 1oid 1oie
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 15709736
Journal Biochemistry
Year 2005
Volume 44
Pages 2244-52
Authors Schultz-Heienbrok R, Maier T, Strater N
Title A large hinge bending domain rotation is necessary for the catalytic function of Escherichia coli 5'-nucleotidase.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 16895331
Journal Chem Rev
Year 2006
Volume 106
Pages 3338-63
Authors Mitic N, Smith SJ, Neves A, Guddat LW, Gahan LR, Schenk G
Title The catalytic mechanisms of binuclear metallohydrolases.
Related PDB
Related UniProtKB

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).

Created Updated
2004-11-22 2009-02-26