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Protein

Isopentenyl-diphosphate delta-isomerase

Gene

fni

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 5 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 annotation1 Publication
  • NADPHUniRule annotation
  • Mg2+UniRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei93FMN; via amide nitrogenUniRule annotation1 Publication1
Binding sitei122FMNUniRule annotation1 Publication1
Binding sitei152SubstrateUniRule annotation1
Metal bindingi153MagnesiumUniRule annotation1
Binding sitei184FMNUniRule annotation1 Publication1
Binding sitei214FMNUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi62 – 64FMN1 Publication3
Nucleotide bindingi258 – 259FMNUniRule annotation1 Publication2
Nucleotide bindingi280 – 281FMNUniRule annotation1 Publication2

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

BioCyciBSUB:BSU22870-MONOMER.
BRENDAi5.3.3.2. 658.

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
Synonyms:idi, ypgA
Ordered Locus Names:BSU22870
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001570 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_00001344041 – 349Isopentenyl-diphosphate delta-isomeraseAdd BLAST349

Proteomic databases

PaxDbiP50740.

Interactioni

Subunit structurei

Homooctamer. Dimer of tetramers.UniRule annotation1 Publication

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100012571.

Structurei

Secondary structure

1349
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi25 – 27Combined sources3
Beta strandi28 – 30Combined sources3
Helixi40 – 42Combined sources3
Beta strandi47 – 49Combined sources3
Beta strandi52 – 55Combined sources4
Beta strandi57 – 61Combined sources5
Helixi68 – 85Combined sources18
Turni95 – 99Combined sources5
Helixi101 – 113Combined sources13
Beta strandi115 – 117Combined sources3
Beta strandi119 – 124Combined sources6
Helixi129 – 138Combined sources10
Beta strandi142 – 148Combined sources7
Turni150 – 153Combined sources4
Helixi166 – 176Combined sources11
Beta strandi181 – 188Combined sources8
Helixi192 – 201Combined sources10
Beta strandi204 – 209Combined sources6
Helixi228 – 231Combined sources4
Helixi238 – 248Combined sources11
Beta strandi252 – 259Combined sources8
Helixi263 – 271Combined sources9
Beta strandi275 – 279Combined sources5
Helixi281 – 313Combined sources33
Helixi318 – 321Combined sources4
Beta strandi326 – 328Combined sources3
Helixi330 – 338Combined sources9
Helixi344 – 348Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1P0KX-ray1.90A/B1-349[»]
1P0NX-ray2.80A/B1-349[»]
ProteinModelPortaliP50740.
SMRiP50740.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP50740.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni6 – 7Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the IPP isomerase type 2 family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4106UJV. Bacteria.
COG1304. LUCA.
HOGENOMiHOG000072127.
InParanoidiP50740.
KOiK01823.
OMAiGSQRVML.
PhylomeDBiP50740.

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. 1 hit.
[Graphical view]
PIRSFiPIRSF003314. IPP_isomerase. 1 hit.
TIGRFAMsiTIGR02151. IPP_isom_2. 1 hit.

Sequencei

Sequence statusi: Complete.

P50740-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTRAERKRQH INHALSIGQK RETGLDDITF VHVSLPDLAL EQVDISTKIG
60 70 80 90 100
ELSSSSPIFI NAMTGGGGKL TYEINKSLAR AASQAGIPLA VGSQMSALKD
110 120 130 140 150
PSERLSYEIV RKENPNGLIF ANLGSEATAA QAKEAVEMIG ANALQIHLNV
160 170 180 190 200
IQEIVMPEGD RSFSGALKRI EQICSRVSVP VIVKEVGFGM SKASAGKLYE
210 220 230 240 250
AGAAAVDIGG YGGTNFSKIE NLRRQRQISF FNSWGISTAA SLAEIRSEFP
260 270 280 290 300
ASTMIASGGL QDALDVAKAI ALGASCTGMA GHFLKALTDS GEEGLLEEIQ
310 320 330 340
LILEELKLIM TVLGARTIAD LQKAPLVIKG ETHHWLTERG VNTSSYSVR
Length:349
Mass (Da):37,221
Last modified:April 27, 2001 - v2
Checksum:i3EA275B6EDEAB587
GO

Sequence cautioni

The sequence AAC83963 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB047343 Genomic DNA. Translation: BAB32625.1.
L47648 Genomic DNA. Translation: AAC83963.1. Different initiation.
AL009126 Genomic DNA. Translation: CAB14203.2.
PIRiD69935.
RefSeqiNP_390168.3. NC_000964.3.
WP_004399098.1. NZ_JNCM01000036.1.

Genome annotation databases

EnsemblBacteriaiCAB14203; CAB14203; BSU22870.
GeneIDi938985.
KEGGibsu:BSU22870.
PATRICi18976389. VBIBacSub10457_2385.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB047343 Genomic DNA. Translation: BAB32625.1.
L47648 Genomic DNA. Translation: AAC83963.1. Different initiation.
AL009126 Genomic DNA. Translation: CAB14203.2.
PIRiD69935.
RefSeqiNP_390168.3. NC_000964.3.
WP_004399098.1. NZ_JNCM01000036.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1P0KX-ray1.90A/B1-349[»]
1P0NX-ray2.80A/B1-349[»]
ProteinModelPortaliP50740.
SMRiP50740.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100012571.

Proteomic databases

PaxDbiP50740.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB14203; CAB14203; BSU22870.
GeneIDi938985.
KEGGibsu:BSU22870.
PATRICi18976389. VBIBacSub10457_2385.

Phylogenomic databases

eggNOGiENOG4106UJV. Bacteria.
COG1304. LUCA.
HOGENOMiHOG000072127.
InParanoidiP50740.
KOiK01823.
OMAiGSQRVML.
PhylomeDBiP50740.

Enzyme and pathway databases

BioCyciBSUB:BSU22870-MONOMER.
BRENDAi5.3.3.2. 658.

Miscellaneous databases

EvolutionaryTraceiP50740.

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. 1 hit.
[Graphical view]
PIRSFiPIRSF003314. IPP_isomerase. 1 hit.
TIGRFAMsiTIGR02151. IPP_isom_2. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiIDI2_BACSU
AccessioniPrimary (citable) accession number: P50740
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: April 27, 2001
Last modified: November 2, 2016
This is version 119 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.