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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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei90 – 901FMN; via amide nitrogenUniRule annotation
Binding sitei117 – 1171FMNUniRule annotation
Binding sitei147 – 1471SubstrateUniRule annotation
Metal bindingi148 – 1481MagnesiumUniRule annotation
Binding sitei179 – 1791FMNUniRule annotation
Binding sitei204 – 2041FMNUniRule annotation
Binding sitei209 – 2091FMN; via amide nitrogenUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi60 – 623FMNUniRule annotation
Nucleotide bindingi253 – 2553FMNUniRule annotation
Nucleotide bindingi274 – 2752FMNUniRule annotation

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

Enzyme and pathway databases

BioCyciSPNE516950:GI38-385-MONOMER.

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)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 336336Isopentenyl-diphosphate delta-isomerasePRO_1000120546Add
BLAST

Interactioni

Subunit structurei

Homooctamer. Dimer of tetramers.UniRule annotation

Structurei

Secondary structure

1
336
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi3 – 1513Combined sources
Helixi22 – 254Combined sources
Beta strandi26 – 283Combined sources
Helixi38 – 403Combined sources
Beta strandi45 – 473Combined sources
Beta strandi50 – 589Combined sources
Helixi66 – 8217Combined sources
Beta strandi85 – 906Combined sources
Helixi92 – 965Combined sources
Turni106 – 1083Combined sources
Beta strandi113 – 1197Combined sources
Helixi124 – 13411Combined sources
Beta strandi139 – 1424Combined sources
Helixi145 – 1506Combined sources
Helixi161 – 17111Combined sources
Beta strandi176 – 1794Combined sources
Helixi187 – 19610Combined sources
Beta strandi200 – 2023Combined sources
Helixi211 – 2199Combined sources
Helixi223 – 2253Combined sources
Helixi232 – 2387Combined sources
Helixi240 – 2423Combined sources
Turni243 – 2453Combined sources
Beta strandi246 – 2538Combined sources
Helixi257 – 2659Combined sources
Beta strandi269 – 2746Combined sources
Helixi275 – 2839Combined sources
Helixi286 – 30621Combined sources
Helixi313 – 3175Combined sources
Beta strandi320 – 3223Combined sources
Helixi324 – 3318Combined sources

3D structure databases

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

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni5 – 62Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the IPP isomerase type 2 family.UniRule annotation

Phylogenomic databases

HOGENOMiHOG000072127.
KOiK01823.
OMAiGSQRVML.
OrthoDBiEOG62C9GJ.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_00354. Idi_2.
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
EntryMethodResolution (Å)ChainPositionsPDBsum
4N02X-ray1.40A2-336[»]
ProteinModelPortaliB2ILS5.
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.
OrthoDBiEOG62C9GJ.

Enzyme and pathway databases

BioCyciSPNE516950:GI38-385-MONOMER.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_00354. Idi_2.
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...

Publicationsi

  1. "Genome evolution driven by host adaptations results in a more virulent and antimicrobial-resistant Streptococcus pneumoniae serotype 14."
    Ding F., Tang P., Hsu M.-H., Cui P., Hu S., Yu J., Chiu C.-H.
    BMC Genomics 10:158-158(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: CGSP14.

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 11, 2015
This is version 49 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.