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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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei93 – 931FMN; via amide nitrogenUniRule annotation1 Publication
Binding sitei122 – 1221FMNUniRule annotation1 Publication
Binding sitei152 – 1521SubstrateUniRule annotation
Metal bindingi153 – 1531MagnesiumUniRule annotation
Binding sitei184 – 1841FMNUniRule annotation1 Publication
Binding sitei214 – 2141FMNUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi62 – 643FMN1 Publication
Nucleotide bindingi258 – 2592FMNUniRule annotation1 Publication
Nucleotide bindingi280 – 2812FMNUniRule annotation1 Publication

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)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 349349Isopentenyl-diphosphate delta-isomerasePRO_0000134404Add
BLAST

Proteomic databases

PaxDbiP50740.

Interactioni

Subunit structurei

Homooctamer. Dimer of tetramers.UniRule annotation1 Publication

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100012571.

Structurei

Secondary structure

1
349
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi25 – 273Combined sources
Beta strandi28 – 303Combined sources
Helixi40 – 423Combined sources
Beta strandi47 – 493Combined sources
Beta strandi52 – 554Combined sources
Beta strandi57 – 615Combined sources
Helixi68 – 8518Combined sources
Turni95 – 995Combined sources
Helixi101 – 11313Combined sources
Beta strandi115 – 1173Combined sources
Beta strandi119 – 1246Combined sources
Helixi129 – 13810Combined sources
Beta strandi142 – 1487Combined sources
Turni150 – 1534Combined sources
Helixi166 – 17611Combined sources
Beta strandi181 – 1888Combined sources
Helixi192 – 20110Combined sources
Beta strandi204 – 2096Combined sources
Helixi228 – 2314Combined sources
Helixi238 – 24811Combined sources
Beta strandi252 – 2598Combined sources
Helixi263 – 2719Combined sources
Beta strandi275 – 2795Combined sources
Helixi281 – 31333Combined sources
Helixi318 – 3214Combined sources
Beta strandi326 – 3283Combined sources
Helixi330 – 3389Combined sources
Helixi344 – 3485Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1P0KX-ray1.90A/B1-349[»]
1P0NX-ray2.80A/B1-349[»]
ProteinModelPortaliP50740.
SMRiP50740. Positions 22-349.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP50740.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni6 – 72Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the IPP isomerase type 2 family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4106UJV. Bacteria.
COG1304. LUCA.
HOGENOMiHOG000072127.
InParanoidiP50740.
KOiK01823.
OMAiGSQRVML.
OrthoDBiEOG62C9GJ.
PhylomeDBiP50740.

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. 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 AAC83963.1 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
EntryMethodResolution (Å)ChainPositionsPDBsum
1P0KX-ray1.90A/B1-349[»]
1P0NX-ray2.80A/B1-349[»]
ProteinModelPortaliP50740.
SMRiP50740. Positions 22-349.
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.
OrthoDBiEOG62C9GJ.
PhylomeDBiP50740.

Enzyme and pathway databases

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

Miscellaneous databases

EvolutionaryTraceiP50740.

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

Publicationsi

« Hide 'large scale' publications
  1. "Isopentenyl diphosphate isomerase from Bacillus subtilis."
    Kuzuyama T.
    Submitted (AUG-2000) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Sequence analysis of the Bacillus subtilis chromosome region between the serA and kdg loci cloned in a yeast artificial chromosome."
    Sorokin A.V., Azevedo V., Zumstein E., Galleron N., Ehrlich S.D., Serror P.
    Microbiology 142:2005-2016(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB 3610 / VKM B-501.
  3. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
    Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
    , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
    Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 168.
  4. "Crystal structure of the type II isopentenyl diphosphate:dimethylallyl diphosphate isomerase from Bacillus subtilis."
    Steinbacher S., Kaiser J., Gerhardt S., Eisenreich W., Huber R., Bacher A., Rohdich F.
    J. Mol. Biol. 329:973-982(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) IN COMPLEX WITH FMN, COFACTOR, SUBUNIT.

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: February 17, 2016
This is version 116 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.