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Protein

Isopentenyl-diphosphate Delta-isomerase

Gene

idi

Organism
Kocuria rhizophila (strain ATCC 9341 / DSM 348 / NBRC 103217 / DC2201)
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 bindingi29 – 291ManganeseUniRule annotation
Metal bindingi36 – 361ManganeseUniRule annotation
Active sitei71 – 711UniRule annotation
Metal bindingi73 – 731ManganeseUniRule annotation
Metal bindingi91 – 911MagnesiumUniRule annotation
Metal bindingi118 – 1181ManganeseUniRule annotation
Active sitei120 – 1201UniRule annotation
Metal bindingi120 – 1201ManganeseUniRule 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

BioCyciKRHI378753:GJ8F-310-MONOMER.
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:KRH_03040
OrganismiKocuria rhizophila (strain ATCC 9341 / DSM 348 / NBRC 103217 / DC2201)
Taxonomic identifieri378753 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaMicrococcalesMicrococcaceaeKocuria
Proteomesi
  • UP000008838 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 – 180180Isopentenyl-diphosphate Delta-isomerasePRO_1000204113Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi378753.KRH_03040.

Structurei

3D structure databases

ProteinModelPortaliB2GFH1.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the IPP isomerase type 1 family.UniRule annotation

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.

B2GFH1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSENSTPERV VLLDEQHQPT GTALKSEVHT EATPLHLAFS CHVLNPDGRV
60 70 80 90 100
LVTRRALSKR TWPGVWSNSF CGHPGPHESF EDAIARRARQ ELGLEIRNLT
110 120 130 140 150
VVVPEFQYRA TDATGVVENE FCPVFVAVTD TDPQPAESEV AEYAWTAPRD
160 170 180
LIAAVESAPY AFSPWLGDQV REPALREALG
Length:180
Mass (Da):19,902
Last modified:June 10, 2008 - v1
Checksum:iA69A9280FDDDB452
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP009152 Genomic DNA. Translation: BAG28651.1.
RefSeqiWP_012397378.1. NC_010617.1.

Genome annotation databases

EnsemblBacteriaiBAG28651; BAG28651; KRH_03040.
KEGGikrh:KRH_03040.
PATRICi22180826. VBIKocRhi5258_0292.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP009152 Genomic DNA. Translation: BAG28651.1.
RefSeqiWP_012397378.1. NC_010617.1.

3D structure databases

ProteinModelPortaliB2GFH1.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi378753.KRH_03040.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAG28651; BAG28651; KRH_03040.
KEGGikrh:KRH_03040.
PATRICi22180826. VBIKocRhi5258_0292.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayiUPA00059; UER00104.
BioCyciKRHI378753:GJ8F-310-MONOMER.

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: ATCC 9341 / DSM 348 / NBRC 103217 / DC2201.

Entry informationi

Entry nameiIDI_KOCRD
AccessioniPrimary (citable) accession number: B2GFH1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 22, 2009
Last sequence update: June 10, 2008
Last modified: November 11, 2015
This is version 55 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.