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
18420
16584
16057
PubChem 23930
888
1195
647
1i9aA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MN Unbound Unbound Unbound
1i9aB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain 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 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain 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 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain 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, a nonessential gene encoding isopentenyl diphosphate isomerase.
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. strain CL190.
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, Glu-116, and Tyr-104 as suggested by crystal structures of complexes with transition state analogues and irreversible inhibitors.
Related PDB
Related UniProtKB

Comments

Created Updated
2002-04-30 2009-02-26