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Protein

Isopentenyl-diphosphate Delta-isomerase

Gene

idi

Organism
Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its highly electrophilic allylic isomer, dimethylallyl diphosphate (DMAPP).UniRule annotation

Catalytic activityi

Isopentenyl diphosphate = dimethylallyl diphosphate.UniRule annotation

Cofactori

Protein has several cofactor binding sites:
  • Mg2+UniRule annotationNote: Binds 1 Mg2+ ion per subunit. The magnesium ion binds only when substrate is bound.UniRule annotation
  • Mn2+UniRule annotationNote: Binds 1 Mn2+ ion per subunit.UniRule annotation

Pathwayi: dimethylallyl diphosphate biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes dimethylallyl diphosphate from isopentenyl diphosphate.UniRule annotation
Proteins known to be involved in this subpathway in this organism are:
  1. Isopentenyl-diphosphate Delta-isomerase (idi)
This subpathway is part of the pathway dimethylallyl diphosphate biosynthesis, which is itself part of Isoprenoid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes dimethylallyl diphosphate from isopentenyl diphosphate, the pathway dimethylallyl diphosphate biosynthesis and in Isoprenoid biosynthesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi27 – 271ManganeseUniRule annotation
Metal bindingi34 – 341ManganeseUniRule annotation
Active sitei69 – 691UniRule annotation
Metal bindingi69 – 691Magnesium; via carbonyl oxygenUniRule annotation
Metal bindingi71 – 711ManganeseUniRule annotation
Metal bindingi89 – 891MagnesiumUniRule annotation
Metal bindingi119 – 1191ManganeseUniRule annotation
Active sitei121 – 1211UniRule annotation
Metal bindingi121 – 1211ManganeseUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

Isoprene biosynthesis

Keywords - Ligandi

Magnesium, Manganese, Metal-binding

Enzyme and pathway databases

UniPathwayiUPA00059; UER00104.

Names & Taxonomyi

Protein namesi
Recommended name:
Isopentenyl-diphosphate Delta-isomeraseUniRule annotation (EC:5.3.3.2UniRule annotation)
Short name:
IPP isomeraseUniRule annotation
Alternative name(s):
IPP:DMAPP isomeraseUniRule annotation
Isopentenyl pyrophosphate isomeraseUniRule annotation
Gene namesi
Name:idiUniRule annotation
Ordered Locus Names:Cgl2305, cg2531
OrganismiCorynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)
Taxonomic identifieri196627 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesCorynebacteriaceaeCorynebacterium
Proteomesi
  • UP000000582 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 189189Isopentenyl-diphosphate Delta-isomerasePRO_0000205247Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi196627.cg2531.

Structurei

3D structure databases

ProteinModelPortaliQ8NN99.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini32 – 171140Nudix hydrolaseAdd
BLAST

Sequence similaritiesi

Belongs to the IPP isomerase type 1 family.UniRule annotation
Contains 1 nudix hydrolase domain.Curated

Phylogenomic databases

eggNOGiENOG4108ZEY. Bacteria.
COG1443. LUCA.
HOGENOMiHOG000274107.
KOiK01823.
OMAiSPWMVLQ.
OrthoDBiEOG6MSS4M.

Family and domain databases

Gene3Di3.90.79.10. 1 hit.
HAMAPiMF_00202. Idi.
InterProiIPR011876. IsopentenylPP_isomerase_typ1.
IPR000086. NUDIX_hydrolase_dom.
IPR015797. NUDIX_hydrolase_dom-like.
[Graphical view]
PANTHERiPTHR10885. PTHR10885. 1 hit.
PfamiPF00293. NUDIX. 1 hit.
[Graphical view]
PIRSFiPIRSF018427. Isopntndiph_ism. 1 hit.
SUPFAMiSSF55811. SSF55811. 1 hit.
TIGRFAMsiTIGR02150. IPP_isom_1. 1 hit.
PROSITEiPS51462. NUDIX. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q8NN99-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTTEVELVVL ADSEGNPIGT APKATVHTKD TPLHFAFSTY ILNPRGELLV
60 70 80 90 100
TRRALSKKTW PGVWTNSMCG HPGPDETNAD AIRRRGVDEL GLEVDSFLDI
110 120 130 140 150
QEILPDYQYR AVDASGIVEW ELCPVHLVRL AVGEFVEPLD DEVEEFEWAE
160 170 180
PQKLFDAVDA TPFVFSPWLV DQLSAPELRQ AILEAFDAE
Length:189
Mass (Da):21,121
Last modified:October 10, 2002 - v1
Checksum:iC9AA9F41E55755F8
GO

Sequence cautioni

The sequence BAB99698.1 differs from that shown. Reason: Erroneous initiation. Curated
The sequence CAF20647.1 differs from that shown. Reason: Erroneous initiation. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000036 Genomic DNA. Translation: BAB99698.1. Different initiation.
BX927154 Genomic DNA. Translation: CAF20647.1. Different initiation.
RefSeqiNP_601504.2. NC_003450.3.
WP_011015025.1. NC_003450.3.
WP_020948619.1. NC_006958.1.

Genome annotation databases

EnsemblBacteriaiBAB99698; BAB99698; BAB99698.
CAF20647; CAF20647; cg2531.
GeneIDi1020256.
KEGGicgb:cg2531.
cgl:NCgl2223.
PATRICi21496614. VBICorGlu203724_2239.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000036 Genomic DNA. Translation: BAB99698.1. Different initiation.
BX927154 Genomic DNA. Translation: CAF20647.1. Different initiation.
RefSeqiNP_601504.2. NC_003450.3.
WP_011015025.1. NC_003450.3.
WP_020948619.1. NC_006958.1.

3D structure databases

ProteinModelPortaliQ8NN99.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi196627.cg2531.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAB99698; BAB99698; BAB99698.
CAF20647; CAF20647; cg2531.
GeneIDi1020256.
KEGGicgb:cg2531.
cgl:NCgl2223.
PATRICi21496614. VBICorGlu203724_2239.

Phylogenomic databases

eggNOGiENOG4108ZEY. Bacteria.
COG1443. LUCA.
HOGENOMiHOG000274107.
KOiK01823.
OMAiSPWMVLQ.
OrthoDBiEOG6MSS4M.

Enzyme and pathway databases

UniPathwayiUPA00059; UER00104.

Family and domain databases

Gene3Di3.90.79.10. 1 hit.
HAMAPiMF_00202. Idi.
InterProiIPR011876. IsopentenylPP_isomerase_typ1.
IPR000086. NUDIX_hydrolase_dom.
IPR015797. NUDIX_hydrolase_dom-like.
[Graphical view]
PANTHERiPTHR10885. PTHR10885. 1 hit.
PfamiPF00293. NUDIX. 1 hit.
[Graphical view]
PIRSFiPIRSF018427. Isopntndiph_ism. 1 hit.
SUPFAMiSSF55811. SSF55811. 1 hit.
TIGRFAMsiTIGR02150. IPP_isom_1. 1 hit.
PROSITEiPS51462. NUDIX. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "The Corynebacterium glutamicum genome: features and impacts on biotechnological processes."
    Ikeda M., Nakagawa S.
    Appl. Microbiol. Biotechnol. 62:99-109(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025.

Entry informationi

Entry nameiIDI_CORGL
AccessioniPrimary (citable) accession number: Q8NN99
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 10, 2002
Last sequence update: October 10, 2002
Last modified: June 8, 2016
This is version 95 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.