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Protein

Isopentenyl-diphosphate delta-isomerase

Gene

fni

Organism
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Status
Unreviewed-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
  • Mg2+UniRule annotation
  • NADPHUniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei95 – 951FMN; via amide nitrogenUniRule annotationCombined sources
Binding sitei123 – 1231FMNUniRule annotationCombined sources
Binding sitei152 – 1521FMNCombined sources
Binding sitei157 – 1571SubstrateUniRule annotation
Metal bindingi158 – 1581MagnesiumUniRule annotation
Binding sitei187 – 1871FMNUniRule annotation
Binding sitei217 – 2171FMN; via amide nitrogenUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi65 – 673FMNUniRule annotationCombined sources
Nucleotide bindingi187 – 1893FMNCombined sources
Nucleotide bindingi217 – 2193FMNCombined sources
Nucleotide bindingi263 – 2664FMNCombined sources
Nucleotide bindingi285 – 2862FMNUniRule annotationCombined sources

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

IsomeraseUniRule annotationImported

Keywords - Biological processi

Isoprene biosynthesisUniRule annotation

Keywords - Ligandi

Flavoprotein, FMNUniRule annotationCombined sources, MagnesiumUniRule annotation, Metal-bindingUniRule annotation, NADPUniRule annotation, Nucleotide-bindingCombined sources

Enzyme and pathway databases

BioCyciTTHE300852:GH8R-2133-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
Gene namesi
Name:fniUniRule annotation
Ordered Locus Names:TTHB110Imported
Encoded oniPlasmid pTT27Imported
OrganismiThermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Imported
Taxonomic identifieri300852 [NCBI]
Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus
Proteomesi
  • UP000000532 Componenti: Plasmid pTT27

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

CytoplasmUniRule annotation

Interactioni

Subunit structurei

Homooctamer. Dimer of tetramers.UniRule annotation

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3DH7X-ray2.97A/B/C/D1-332[»]
ProteinModelPortaliQ53W52.
SMRiQ53W52. Positions 9-332.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ53W52.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini4 – 9592FMN_dhInterPro annotationAdd
BLAST
Domaini171 – 325155FMN_dhInterPro annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni6 – 72Substrate bindingUniRule annotation
Regioni95 – 973Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the IPP isomerase type 2 family.UniRule annotation

Phylogenomic databases

HOGENOMiHOG000072126.
KOiK01823.
OMAiGSQRVML.
OrthoDBiEOG62C9GJ.
PhylomeDBiQ53W52.

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.

Q53W52-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNIRERKRKH LEACLEGEVA YQKTTTGLEG FRLRYQALAG LALSEVDLTT
60 70 80 90 100
PFLGKTLKAP FLIGAMTGGE ENGERINLAL AEAAEALGVG MMLGSGRILL
110 120 130 140 150
ERPEALRSFR VRKVAPKALL IANLGLAQLR RYGRDDLLRL VEMLEADALA
160 170 180 190 200
FHVNPLQEAV QRGDTDFRGL VERLAELLPL PFPVMVKEVG HGLSREAALA
210 220 230 240 250
LRDLPLAAVD VAGAGGTSWA RVEEWVRFGE VRHPELCEIG IPTARAILEV
260 270 280 290 300
REVLPHLPLV ASGGVYTGTD GAKALALGAD LLAVARPLLR PALEGAERVA
310 320 330
AWIGDYLEEL RTALFAIGAR NPKEARGRVE RV
Length:332
Mass (Da):36,019
Last modified:May 24, 2005 - v1
Checksum:iE07DA50B0A8C5D92
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP008227 Genomic DNA. Translation: BAD71906.1.
RefSeqiWP_011229187.1. NC_006462.1.
YP_145349.1. NC_006462.1.

Genome annotation databases

EnsemblBacteriaiBAD71906; BAD71906; BAD71906.
GeneIDi3169537.
KEGGittj:TTHB110.
PATRICi23959144. VBITheThe93045_2053.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP008227 Genomic DNA. Translation: BAD71906.1.
RefSeqiWP_011229187.1. NC_006462.1.
YP_145349.1. NC_006462.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3DH7X-ray2.97A/B/C/D1-332[»]
ProteinModelPortaliQ53W52.
SMRiQ53W52. Positions 9-332.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAD71906; BAD71906; BAD71906.
GeneIDi3169537.
KEGGittj:TTHB110.
PATRICi23959144. VBITheThe93045_2053.

Phylogenomic databases

HOGENOMiHOG000072126.
KOiK01823.
OMAiGSQRVML.
OrthoDBiEOG62C9GJ.
PhylomeDBiQ53W52.

Enzyme and pathway databases

BioCyciTTHE300852:GH8R-2133-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ53W52.

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

« Hide 'large scale' publications
  1. "Complete genome sequence of Thermus thermophilus HB8."
    Masui R., Kurokawa K., Nakagawa N., Tokunaga F., Koyama Y., Shibata T., Oshima T., Yokoyama S., Yasunaga T., Kuramitsu S.
    Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: HB8 / ATCC 27634 / DSM 579Imported.
  2. "Crystal structure of type 2 isopentenyl diphosphate isomerase from Thermus thermophilus in complex with inorganic pyrophosphate."
    de Ruyck J., Pouyez J., Rothman S.C., Poulter D., Wouters J.
    Biochemistry 47:9051-9053(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.97 ANGSTROMS) IN COMPLEX WITH FMN.

Entry informationi

Entry nameiQ53W52_THET8
AccessioniPrimary (citable) accession number: Q53W52
Entry historyi
Integrated into UniProtKB/TrEMBL: May 24, 2005
Last sequence update: May 24, 2005
Last modified: March 16, 2016
This is version 86 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

3D-structureCombined sources, Complete proteome, PlasmidImported, Reference proteomeImported

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.