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 pyrophosphatase UDP-sugar diphosphatase 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 | UDP-sugar + H(2)O = UMP + alpha-D-aldose 1- phosphate. A 5''-ribonucleotide + H(2)O = a ribonucleoside + 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 29105 |
15377 15377 |
26078 26078 |
16695 16695 |
||||||||||||||
| PubChem |
32051 32051 |
22247451 962 22247451 962 |
1004 22486802 1004 22486802 |
6030 6030 |
||||||||||||||
| 1ho5A01 |
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Analogue:2x_MN | Unbound | Unbound | Unbound | Unbound | Unbound | Bound:PO4 | Unbound | Unbound | Unbound | Unbound | ||
| 1ho5B01 |
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|
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Analogue:2x_MN | Unbound | Unbound | Unbound | Unbound | Unbound | Bound:PO4 | Unbound | Unbound | Unbound | Unbound | ||
| 1hp1A01 |
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|
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Bound:2x_ZN | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1hpuA01 |
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Analogue:2x_MN | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1hpuB01 |
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|
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Analogue:2x_MN | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1hpuC01 |
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|
|
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Analogue:2x_MN | Bound:HOH_1137 | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1hpuD01 |
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Analogue:2x_MN | Bound:HOH_853 | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1oi8A01 |
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Analogue:2x_MN | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1oi8B01 |
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Analogue:2x_MN | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1oidA01 |
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Analogue:_NI | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1oidB01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1oieA01 |
|
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Analogue:_NI | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1ushA01 |
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Bound:2x_ZN | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 2ushA01 |
|
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Bound:2x_ZN | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 2ushB01 |
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Bound:2x_ZN | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1ho5A02 |
|
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Unbound | Unbound | Unbound | Unbound | Unbound | Bound:ADN | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1ho5B02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Bound:ADN | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1hp1A02 |
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Unbound | Unbound | Unbound | Bound:ATP | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1hpuA02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Analogue:A12 | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1hpuB02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Analogue:A12 | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1hpuC02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Analogue:A12 | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1hpuD02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Analogue:A12 | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1oi8A02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Analogue:SO4 | Unbound | Unbound | Unbound | Unbound | ||
| 1oi8B02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Analogue:SO4 | Unbound | Unbound | Unbound | Unbound | ||
| 1oidA02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1oidB02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1oieA02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1ushA02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Analogue:SO4_603 | Unbound | Unbound | Unbound | Unbound | ||
| 2ushA02 |
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Unbound | Unbound | Unbound | Unbound | Analogue:WO4_702-WO4_703 | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 2ushB02 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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|
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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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ARG 375;ARG 379;ARG 410 | ||||
| 1ho5B02 |
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ARG 375;ARG 379;ARG 410 | ||||
| 1hp1A02 |
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ARG 375;ARG 379;ARG 410 | ||||
| 1hpuA02 |
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ARG 375;ARG 379;ARG 410 | ||||
| 1hpuB02 |
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ARG 375;ARG 379;ARG 410 | ||||
| 1hpuC02 |
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ARG 375;ARG 379;ARG 410 | ||||
| 1hpuD02 |
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ARG 375;ARG 379;ARG 410 | ||||
| 1oi8A02 |
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ARG 375;ARG 379;ARG 410 | mutant L424C, disulfide bridge C90-C424 | |||
| 1oi8B02 |
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ARG 375;ARG 379;ARG 410 | mutant L424C, disulfide bridge C90-C424 | |||
| 1oidA02 |
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ARG 375;ARG 379;ARG 410 | mutant P513C, disulfide bridge C228-C513 | |||
| 1oidB02 |
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ARG 375;ARG 379;ARG 410 | mutant P513C, disulfide bridge C228-C513 | |||
| 1oieA02 |
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ARG 375;ARG 379;ARG 410 | mutant P513C, disulfide bridge C228-C513 | |||
| 1ushA02 |
|
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ARG 375;ARG 379;ARG 410 | ||||
| 2ushA02 |
|
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ARG 375;ARG 379;ARG 410 | ||||
| 2ushB02 |
|
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|
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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-, |
| 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. |
| 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], |
| Created | Updated |
|---|---|
| 2004-11-22 | 2009-02-26 |