DB code: S00454
| CATH domain | 3.90.79.10 : Nucleoside Triphosphate Pyrophosphohydrolase | Catalytic domain |
|---|---|---|
| E.C. | 5.3.3.2 | |
| CSA | 1i9a | |
| M-CSA | 1i9a | |
| MACiE | ||
| CATH domain | Related DB codes (homologues) |
|---|---|
| 3.90.79.10 : Nucleoside Triphosphate Pyrophosphohydrolase | S00814 S00815 S00920 S00921 S00922 S00923 S00924 |
| Uniprot Enzyme Name | UniprotKB | Protein name | Synonyms | RefSeq | Pfam |
|---|---|---|---|---|
| Q46822 |
Isopentenyl-diphosphate Delta-isomerase
|
IPP isomerase
EC 5.3.3.2 Isopentenyl pyrophosphate isomerase IPP:DMAPP isomerase |
NP_417365.1
(Protein)
NC_000913.2 (DNA/RNA sequence) YP_491090.1 (Protein) NC_007779.1 (DNA/RNA sequence) |
PF00293
(NUDIX)
[Graphical View] |
| KEGG enzyme name |
|---|
|
isopentenyl-diphosphate Delta-isomerase
isopentenylpyrophosphate Delta-isomerase methylbutenylpyrophosphate isomerase isopentenylpyrophosphate isomerase |
| UniprotKB: Accession Number | Entry name | Activity | Subunit | Subcellular location | Cofactor |
|---|---|---|---|---|---|
| Q46822 | IDI_ECOLI | Isopentenyl diphosphate = dimethylallyl diphosphate. | Homodimer. | Cytoplasm. | Binds 1 magnesium ion per subunit. The magnesium ion binds only when substrate is bound. Binds 1 manganese ion per subunit. |
| KEGG Pathways | Map code | Pathways | E.C. |
|---|---|---|
| MAP00100 | Biosynthesis of steroids | |
| MAP00900 | Terpenoid biosynthesis |
| Compound table | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Cofactors | Substrates | Products | Intermediates | |||||||
| KEGG-id | C00034 | C00305 | C00129 | C00235 | ||||||
| E.C. | ||||||||||
| Compound | Manganese | Magnesium | Isopentenyl diphosphate | Dimethylallyl diphosphate | ||||||
| Type | heavy metal | divalent metal (Ca2+, Mg2+) | lipid,phosphate group/phosphate ion | lipid,phosphate group/phosphate ion | ||||||
| ChEBI |
18291 35154 18291 35154 |
18420 18420 |
16584 16584 |
16057 16057 |
||||||
| PubChem |
23930 23930 |
888 888 |
1195 1195 |
647 647 |
||||||
| 1i9aA |
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Bound:_MN | Unbound | Unbound | Unbound | |
| 1i9aB |
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Bound:_MN | Unbound | Unbound | Unbound | |
| Reference for Active-site residues | ||
|---|---|---|
| resource | references | E.C. |
| Swiss-prot;Q46822, PDB & literature [6] | ||
| Active-site residues | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| PDB | Catalytic residues | Cofactor-binding residues | Modified residues | Main-chain involved in catalysis | Comment | |||||
| 1i9aA |
|
|
|
|
|
CYS 67;TYR 104;GLU 116 | HIS 25;HIS 32;HIS 69;GLU 114;GLU 116(Manganese binding) | MSE 137;MSE 162;MSE 164(modified by Selenium) | ||
| 1i9aB |
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CYS 1067;TYR 1104;GLU 1116 | HIS 1025;HIS 1032;HIS 1069;GLU 1114;GLU 1116(Manganese binding) | MSE 1137;MSE 1162;MSE 1164(modified by Selenium) | ||
| References for Catalytic Mechanism | ||
|---|---|---|
| References | Sections | No. of steps in catalysis |
|
[3]
|
Fig.5B, p.1532-1535 | 2 |
|
[6]
|
Fig.3B, Fig.4 | 4 |
| References | |
|---|---|
| [1] | |
| Resource | |
| Comments | FUNCTION. |
| Medline ID | 98269038 |
| PubMed ID | 9603997 |
| Journal | J Biochem (Tokyo) |
| Year | 1998 |
| Volume | 123 |
| Pages | 1088-96 |
| Authors | Hemmi H, Ohnuma S, Nagaoka K, Nishino T |
| Title | Identification of genes affecting lycopene formation in Escherichia coli transformed with carotenoid biosynthetic genes: candidates for early genes in isoprenoid biosynthesis. |
| Related PDB | |
| Related UniProtKB | Q46822 |
| [2] | |
| Resource | |
| Comments | CHARACTERIZATION. |
| Medline ID | 99350411 |
| PubMed ID | 10419945 |
| Journal | J Bacteriol |
| Year | 1999 |
| Volume | 181 |
| Pages | 4499-504 |
| Authors | Hahn FM, Hurlburt AP, Poulter CD |
| Title |
Escherichia coli open reading frame 696 is idi, |
| Related PDB | |
| Related UniProtKB | Q46822 |
| [3] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 11285217 |
| Journal | EMBO J |
| Year | 2001 |
| Volume | 20 |
| Pages | 1530-7 |
| Authors | Durbecq V, Sainz G, Oudjama Y, Clantin B, Bompard-Gilles C, Tricot C, Caillet J, Stalon V, Droogmans L, Villeret V |
| Title | Crystal structure of isopentenyl diphosphate:dimethylallyl diphosphate isomerase. |
| Related PDB | |
| Related UniProtKB | |
| [4] | |
| Resource | |
| Comments | X-ray crystallography |
| Medline ID | |
| PubMed ID | 11698677 |
| Journal | Proc Natl Acad Sci U S A |
| Year | 2001 |
| Volume | 98 |
| Pages | 12896-901 |
| Authors | Bonanno JB, Edo C, Eswar N, Pieper U, Romanowski MJ, Ilyin V, Gerchman SE, Kycia H, Studier FW, Sali A, Burley SK |
| Title | Structural genomics of enzymes involved in sterol/isoprenoid biosynthesis. |
| Related PDB | 1i9a |
| Related UniProtKB | |
| [5] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 11158573 |
| Journal | Proc Natl Acad Sci U S A |
| Year | 2001 |
| Volume | 98 |
| Pages | 932-7 |
| Authors | Kaneda K, Kuzuyama T, Takagi M, Hayakawa Y, Seto H |
| Title |
An unusual isopentenyl diphosphate isomerase found in the mevalonate pathway gene cluster from Streptomyces sp. |
| Related PDB | |
| Related UniProtKB | |
| [6] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 12540835 |
| Journal | J Biol Chem |
| Year | 2003 |
| Volume | 278 |
| Pages | 11903-8 |
| Authors | Wouters J, Oudjama Y, Barkley SJ, Tricot C, Stalon V, Droogmans L, Poulter CD |
| Title |
Catalytic mechanism of Escherichia coli isopentenyl diphosphate isomerase involves Cys-67, |
| Related PDB | |
| Related UniProtKB | |
| Comments |
|---|
| Created | Updated |
|---|---|
| 2002-04-30 | 2009-02-26 |