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Protein

Isopentenyl-diphosphate delta-isomerase

Gene

fni

Organism
Streptococcus pneumoniae (strain CGSP14)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

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

Catalytic activityi

Isopentenyl diphosphate = dimethylallyl diphosphate.UniRule annotation

Cofactori

Protein has several cofactor binding sites:
  • FMNUniRule annotation
  • NADPHUniRule annotation
  • Mg2+UniRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei90FMN; via amide nitrogenUniRule annotation1
Binding sitei117FMNUniRule annotation1
Binding sitei147SubstrateUniRule annotation1
Metal bindingi148MagnesiumUniRule annotation1
Binding sitei179FMNUniRule annotation1
Binding sitei204FMNUniRule annotation1
Binding sitei209FMN; via amide nitrogenUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi60 – 62FMNUniRule annotation3
Nucleotide bindingi253 – 255FMNUniRule annotation3
Nucleotide bindingi274 – 275FMNUniRule annotation2

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

Isoprene biosynthesis

Keywords - Ligandi

Flavoprotein, FMN, Magnesium, Metal-binding, NADP

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):
Isopentenyl diphosphate:dimethylallyl diphosphate isomeraseUniRule annotation
Isopentenyl pyrophosphate isomeraseUniRule annotation
Type 2 isopentenyl diphosphate isomeraseUniRule annotation
Short name:
IDI-2UniRule annotation
Gene namesi
Name:fniUniRule annotation
Ordered Locus Names:SPCG_0379
OrganismiStreptococcus pneumoniae (strain CGSP14)
Taxonomic identifieri516950 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesStreptococcaceaeStreptococcus
Proteomesi
  • UP000001682 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10001205461 – 336Isopentenyl-diphosphate delta-isomeraseAdd BLAST336

Interactioni

Subunit structurei

Homooctamer. Dimer of tetramers.UniRule annotation

Structurei

Secondary structure

1336
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi3 – 15Combined sources13
Helixi22 – 25Combined sources4
Beta strandi26 – 28Combined sources3
Helixi38 – 40Combined sources3
Beta strandi45 – 47Combined sources3
Beta strandi50 – 58Combined sources9
Helixi66 – 82Combined sources17
Beta strandi85 – 90Combined sources6
Helixi92 – 96Combined sources5
Turni106 – 108Combined sources3
Beta strandi113 – 119Combined sources7
Helixi124 – 134Combined sources11
Beta strandi139 – 142Combined sources4
Helixi145 – 150Combined sources6
Helixi161 – 171Combined sources11
Beta strandi176 – 179Combined sources4
Helixi187 – 196Combined sources10
Beta strandi200 – 202Combined sources3
Helixi211 – 219Combined sources9
Helixi223 – 225Combined sources3
Helixi232 – 238Combined sources7
Helixi240 – 242Combined sources3
Turni243 – 245Combined sources3
Beta strandi246 – 253Combined sources8
Helixi257 – 265Combined sources9
Beta strandi269 – 274Combined sources6
Helixi275 – 283Combined sources9
Helixi286 – 306Combined sources21
Helixi313 – 317Combined sources5
Beta strandi320 – 322Combined sources3
Helixi324 – 331Combined sources8

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4N02X-ray1.40A2-336[»]
ProteinModelPortaliB2ILS5.
SMRiB2ILS5.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni5 – 6Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the IPP isomerase type 2 family.UniRule annotation

Phylogenomic databases

HOGENOMiHOG000072127.
KOiK01823.
OMAiGSQRVML.

Family and domain databases

CDDicd02811. IDI-2_FMN. 1 hit.
Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_00354. Idi_2. 1 hit.
InterProiIPR013785. Aldolase_TIM.
IPR000262. FMN-dep_DH.
IPR011179. IPdP_isomerase.
[Graphical view]
PANTHERiPTHR10578:SF3. PTHR10578:SF3. 2 hits.
PfamiPF01070. FMN_dh. 2 hits.
[Graphical view]
PIRSFiPIRSF003314. IPP_isomerase. 1 hit.
TIGRFAMsiTIGR02151. IPP_isom_2. 1 hit.

Sequencei

Sequence statusi: Complete.

B2ILS5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTTNRKDEHI LYALEQKSSY NSFDEVELIH SSLPLYNLDE IDLSTEFAGR
60 70 80 90 100
KWDFPFYINA MTGGSNKGRE INQKLAQVAE SCGILFVTGS YSAALKNPTD
110 120 130 140 150
DSFSVKSSHP NLLLGTNIGL DKPVELGLQT VEEMNPVLLQ VHVNVMQELL
160 170 180 190 200
MPEGERKFRS WQSHLADYSK QIPVPIVLKE VGFGMDAKTI ERAYEFGVRT
210 220 230 240 250
VDLSGRGGTS FAYIENRRSG QRDYLNQWGQ STMQALLNAQ EWKDKVELLV
260 270 280 290 300
SGGVRNPLDM IKCLVFGAKA VGLSRTVLEL VETYTVEEVI GIVQGWKADL
310 320 330
RLIMCSLNCA TIADLQKVDY LLYGKLKEAK DQMKKA
Length:336
Mass (Da):37,687
Last modified:June 10, 2008 - v1
Checksum:i47F79E51BF2A5934
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001033 Genomic DNA. Translation: ACB89631.1.
RefSeqiWP_000210618.1. NC_010582.1.

Genome annotation databases

EnsemblBacteriaiACB89631; ACB89631; SPCG_0379.
KEGGispw:SPCG_0379.
PATRICi19676895. VBIStrPne123335_0408.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001033 Genomic DNA. Translation: ACB89631.1.
RefSeqiWP_000210618.1. NC_010582.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4N02X-ray1.40A2-336[»]
ProteinModelPortaliB2ILS5.
SMRiB2ILS5.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACB89631; ACB89631; SPCG_0379.
KEGGispw:SPCG_0379.
PATRICi19676895. VBIStrPne123335_0408.

Phylogenomic databases

HOGENOMiHOG000072127.
KOiK01823.
OMAiGSQRVML.

Family and domain databases

CDDicd02811. IDI-2_FMN. 1 hit.
Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_00354. Idi_2. 1 hit.
InterProiIPR013785. Aldolase_TIM.
IPR000262. FMN-dep_DH.
IPR011179. IPdP_isomerase.
[Graphical view]
PANTHERiPTHR10578:SF3. PTHR10578:SF3. 2 hits.
PfamiPF01070. FMN_dh. 2 hits.
[Graphical view]
PIRSFiPIRSF003314. IPP_isomerase. 1 hit.
TIGRFAMsiTIGR02151. IPP_isom_2. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiIDI2_STRPS
AccessioniPrimary (citable) accession number: B2ILS5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 14, 2009
Last sequence update: June 10, 2008
Last modified: November 30, 2016
This is version 53 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

3D-structure, Complete proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  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.