EzCatDB: S00454

DB codeS00454
CATH domainDomain 13.90.79.10Catalytic domain
E.C.5.3.3.2
CSA1i9a

CATH domainRelated DB codes (homologues)
3.90.79.10S00814,S00815,S00920,S00921,S00922,S00923,S00924

Enzyme Name
Swiss-protKEGG

Q46822
Protein nameIsopentenyl-diphosphate Delta-isomeraseisopentenyl-diphosphate Delta-isomerase
isopentenylpyrophosphate Delta-isomerase
methylbutenylpyrophosphate isomerase
isopentenylpyrophosphate isomerase
SynonymsIPP isomerase
EC 5.3.3.2
Isopentenyl pyrophosphate isomerase
IPP:DMAPP isomerase

KEGG pathways
MAP codePathways
MAP00100Biosynthesis of steroids
MAP00900Terpenoid biosynthesis

Swiss-prot:Accession NumberQ46822
Entry nameIDI_ECOLI
ActivityIsopentenyl diphosphate = dimethylallyl diphosphate.
SubunitHomodimer.
Subcellular locationCytoplasm.
CofactorBinds 1 magnesium ion per subunit. The magnesium ion binds only when substrate is bound.,Binds 1 manganese ion per subunit.


CofactorsSubstratesProducts
KEGG-idC00034C00305C00129C00235
CompoundManganeseMagnesiumIsopentenyl diphosphateDimethylallyl diphosphate
Typeheavy metaldivalent metal (Ca2+, Mg2+)lipid,phosphate group/phosphate ionlipid,phosphate group/phosphate ion
1i9aABound:_MNUnboundUnboundUnbound
1i9aBBound:_MNUnboundUnboundUnbound

Active-site residues
resource
Swiss-prot;Q46822, PDB & literature [6]
pdbCatalytic residuesCofactor-binding residuesModified residues
1i9aACYS   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)
1i9aBCYS 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
ReferencesSectionsNo. of steps in catalysis
[3]Fig.5B, p.1532-15352
[6]Fig.3B, Fig.44

references
[1]
CommentsFUNCTION.
Medline ID98269038
PubMed ID9603997
JournalJ Biochem (Tokyo)
Year1998
Volume123
Pages1088-96
AuthorsHemmi H, Ohnuma S, Nagaoka K, Nishino T
TitleIdentification of genes affecting lycopene formation in Escherichia coli transformed with carotenoid biosynthetic genes: candidates for early genes in isoprenoid biosynthesis.
Related Swiss-protQ46822
[2]
CommentsCHARACTERIZATION.
Medline ID99350411
PubMed ID10419945
JournalJ Bacteriol
Year1999
Volume181
Pages4499-504
AuthorsHahn FM, Hurlburt AP, Poulter CD
TitleEscherichia coli open reading frame 696 is idi, a nonessential gene encoding isopentenyl diphosphate isomerase.
Related Swiss-protQ46822
[3]
PubMed ID11285217
JournalEMBO J
Year2001
Volume20
Pages1530-7
AuthorsDurbecq V, Sainz G, Oudjama Y, Clantin B, Bompard-Gilles C, Tricot C, Caillet J, Stalon V, Droogmans L, Villeret V
TitleCrystal structure of isopentenyl diphosphate:dimethylallyl diphosphate isomerase.
[4]
CommentsX-ray crystallography
PubMed ID11698677
JournalProc Natl Acad Sci U S A
Year2001
Volume98
Pages12896-901
AuthorsBonanno JB, Edo C, Eswar N, Pieper U, Romanowski MJ, Ilyin V, Gerchman SE, Kycia H, Studier FW, Sali A, Burley SK
TitleStructural genomics of enzymes involved in sterol/isoprenoid biosynthesis.
Related PDB1i9a
[5]
PubMed ID11158573
JournalProc Natl Acad Sci U S A
Year2001
Volume98
Pages932-7
AuthorsKaneda K, Kuzuyama T, Takagi M, Hayakawa Y, Seto H
TitleAn unusual isopentenyl diphosphate isomerase found in the mevalonate pathway gene cluster from Streptomyces sp. strain CL190.
[6]
PubMed ID12540835
JournalJ Biol Chem
Year2003
Volume278
Pages11903-8
AuthorsWouters J, Oudjama Y, Barkley SJ, Tricot C, Stalon V, Droogmans L, Poulter CD
TitleCatalytic 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.


createdupdated
2002-04-302009-02-26


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 2010)
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)

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