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Protein

Isopentenyl-diphosphate Delta-isomerase 2

Gene

idi2

Organism
Photorhabdus luminescens subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01)
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 1 (idi1), Isopentenyl-diphosphate Delta-isomerase 2 (idi2)
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 bindingi24 – 241ManganeseUniRule annotation
Metal bindingi30 – 301ManganeseUniRule annotation
Active sitei65 – 651UniRule annotation
Metal bindingi65 – 651Magnesium; via carbonyl oxygenUniRule annotation
Metal bindingi67 – 671ManganeseUniRule annotation
Metal bindingi85 – 851MagnesiumUniRule annotation
Metal bindingi110 – 1101ManganeseUniRule annotation
Active sitei112 – 1121UniRule annotation
Metal bindingi112 – 1121ManganeseUniRule 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-isomerase 2UniRule annotation (EC:5.3.3.2UniRule annotation)
Short name:
IPP isomerase 2UniRule annotation
Alternative name(s):
IPP:DMAPP isomerase 2UniRule annotation
Isopentenyl pyrophosphate isomerase 2UniRule annotation
Gene namesi
Name:idi2UniRule annotation
Ordered Locus Names:plu3987
OrganismiPhotorhabdus luminescens subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01)
Taxonomic identifieri243265 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaePhotorhabdus
Proteomesi
  • UP000002514 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 – 177177Isopentenyl-diphosphate Delta-isomerase 2PRO_0000205258Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi243265.plu3987.

Structurei

3D structure databases

ProteinModelPortaliQ7N0A6.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini28 – 160133Nudix 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.
OMAiTPWLRIY.
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.

Q7N0A6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDEILVLVDK HDNPIGSAGK ADIHQKGMLH RAFSIFVFDN KGNLLLQKRA
60 70 80 90 100
ATKYHSAGLW TNSCCGHPRV GEALEAAAHR RLGEEMGFDC PLKKVSSFIY
110 120 130 140 150
HAILPNNLIE YEYDHVFIGR FDKEPIINLD EVSDYKWVNL LKLRALINNA
160 170
PDVYTVWFKK IINGLSYQDI EEWQRLI
Length:177
Mass (Da):20,340
Last modified:December 15, 2003 - v1
Checksum:i43BE9A99A0EEE46A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BX571872 Genomic DNA. Translation: CAE16359.1.
RefSeqiWP_011148119.1. NC_005126.1.

Genome annotation databases

EnsemblBacteriaiCAE16359; CAE16359; plu3987.
KEGGiplu:plu3987.
PATRICi20512542. VBIPhoLum48522_4513.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BX571872 Genomic DNA. Translation: CAE16359.1.
RefSeqiWP_011148119.1. NC_005126.1.

3D structure databases

ProteinModelPortaliQ7N0A6.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243265.plu3987.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAE16359; CAE16359; plu3987.
KEGGiplu:plu3987.
PATRICi20512542. VBIPhoLum48522_4513.

Phylogenomic databases

eggNOGiENOG4108ZEY. Bacteria.
COG1443. LUCA.
HOGENOMiHOG000274107.
KOiK01823.
OMAiTPWLRIY.
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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: DSM 15139 / CIP 105565 / TT01.

Entry informationi

Entry nameiIDI2_PHOLL
AccessioniPrimary (citable) accession number: Q7N0A6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 8, 2005
Last sequence update: December 15, 2003
Last modified: March 16, 2016
This is version 94 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.