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Protein

2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

Gene

ispF

Organism
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), two major building blocks of isoprenoid compounds. Catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-CPP) with a corresponding release of cytidine 5-monophosphate (CMP).1 Publication

Catalytic activityi

2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol = 2-C-methyl-D-erythritol 2,4-cyclodiphosphate + CMP.1 Publication

Cofactori

a divalent metal cation1 PublicationNote: Binds 1 divalent metal cation per subunit.1 Publication

Temperature dependencei

Thermostable.1 Publication

Pathwayi: isopentenyl diphosphate biosynthesis via DXP pathway

This protein is involved in step 4 of the subpathway that synthesizes isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate.
Proteins known to be involved in the 6 steps of the subpathway in this organism are:
  1. 1-deoxy-D-xylulose 5-phosphate reductoisomerase (dxr)
  2. 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (ispD)
  3. 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (ispE)
  4. 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (ispF)
  5. 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (flavodoxin) (ispG)
  6. 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (ispH)
This subpathway is part of the pathway isopentenyl diphosphate biosynthesis via DXP pathway, which is itself part of Isoprenoid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate, the pathway isopentenyl diphosphate biosynthesis via DXP pathway and in Isoprenoid biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi8Divalent metal cation1
Metal bindingi10Divalent metal cation1
Sitei34Transition state stabilizerBy similarity1
Metal bindingi42Divalent metal cation1
Binding sitei65Substrate; via carbonyl oxygenBy similarity1
Sitei133Transition state stabilizer1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

Isoprene biosynthesis

Keywords - Ligandi

Metal-binding

Enzyme and pathway databases

BRENDAi4.6.1.12. 2305.
UniPathwayiUPA00056; UER00095.

Names & Taxonomyi

Protein namesi
Recommended name:
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC:4.6.1.12)
Short name:
MECDP-synthase
Short name:
MECPP-synthase
Short name:
MECPS
Gene namesi
Name:ispF
Ordered Locus Names:TTHA1790
OrganismiThermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Taxonomic identifieri300852 [NCBI]
Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus
Proteomesi
  • UP000000532 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001895111 – 1522-C-methyl-D-erythritol 2,4-cyclodiphosphate synthaseAdd BLAST152

Interactioni

Subunit structurei

Homotrimer.1 Publication

Protein-protein interaction databases

STRINGi300852.TTHA1790.

Structurei

Secondary structure

1152
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 14Combined sources12
Beta strandi18 – 20Combined sources3
Beta strandi23 – 25Combined sources3
Beta strandi28 – 31Combined sources4
Beta strandi33 – 35Combined sources3
Helixi39 – 50Combined sources12
Turni51 – 53Combined sources3
Helixi57 – 60Combined sources4
Turni66 – 70Combined sources5
Helixi73 – 86Combined sources14
Beta strandi91 – 99Combined sources9
Beta strandi101 – 103Combined sources3
Helixi106 – 108Combined sources3
Helixi109 – 120Combined sources12
Helixi124 – 126Combined sources3
Beta strandi127 – 132Combined sources6
Beta strandi141 – 150Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1IV1X-ray1.65A/B/C/D/E/F1-152[»]
1IV2X-ray1.55A/B/C/D/E/F1-152[»]
1IV3X-ray1.52A/B/C/D/E/F1-152[»]
1IV4X-ray1.55A/B/C/D/E/F1-152[»]
ProteinModelPortaliQ8RQP5.
SMRiQ8RQP5.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ8RQP5.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni8 – 10Substrate binding3
Regioni34 – 35Substrate bindingBy similarity2
Regioni38 – 46Substrate bindingBy similarity9
Regioni56 – 58Substrate binding3
Regioni61 – 65Substrate bindingBy similarity5
Regioni100 – 106Substrate binding7
Regioni131 – 135Substrate binding5

Sequence similaritiesi

Belongs to the IspF family.Curated

Phylogenomic databases

eggNOGiENOG4108UH8. Bacteria.
COG0245. LUCA.
HOGENOMiHOG000239175.
KOiK01770.
OMAiHFGTGRP.
PhylomeDBiQ8RQP5.

Family and domain databases

CDDicd00554. MECDP_synthase. 1 hit.
Gene3Di3.30.1330.50. 1 hit.
HAMAPiMF_00107. IspF. 1 hit.
InterProiIPR003526. MECDP_synthase.
IPR020555. MECDP_synthase_CS.
[Graphical view]
PfamiPF02542. YgbB. 1 hit.
[Graphical view]
SUPFAMiSSF69765. SSF69765. 1 hit.
TIGRFAMsiTIGR00151. ispF. 1 hit.
PROSITEiPS01350. ISPF. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q8RQP5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRIGYGEDSH RLEEGRPLYL CGLLIPSPVG ALAHSDGDAA LHALTDALLS
60 70 80 90 100
AYGLGDIGLL FPDTDPRWRG ERSEVFLREA LRLVEARGAK LLQASLVLTL
110 120 130 140 150
DRPKLGPHRK ALVDSLSRLL RLPQDRIGLT FKTSEGLAPS HVQARAVVLL

DG
Length:152
Mass (Da):16,520
Last modified:June 1, 2002 - v1
Checksum:i0114C0E440DC28F3
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB082126 Genomic DNA. Translation: BAB86885.1.
AP008226 Genomic DNA. Translation: BAD71613.1.
RefSeqiWP_011228919.1. NC_006461.1.
YP_145056.1. NC_006461.1.

Genome annotation databases

EnsemblBacteriaiBAD71613; BAD71613; BAD71613.
GeneIDi3169480.
KEGGittj:TTHA1790.
PATRICi23958547. VBITheThe93045_1761.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB082126 Genomic DNA. Translation: BAB86885.1.
AP008226 Genomic DNA. Translation: BAD71613.1.
RefSeqiWP_011228919.1. NC_006461.1.
YP_145056.1. NC_006461.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1IV1X-ray1.65A/B/C/D/E/F1-152[»]
1IV2X-ray1.55A/B/C/D/E/F1-152[»]
1IV3X-ray1.52A/B/C/D/E/F1-152[»]
1IV4X-ray1.55A/B/C/D/E/F1-152[»]
ProteinModelPortaliQ8RQP5.
SMRiQ8RQP5.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi300852.TTHA1790.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAD71613; BAD71613; BAD71613.
GeneIDi3169480.
KEGGittj:TTHA1790.
PATRICi23958547. VBITheThe93045_1761.

Phylogenomic databases

eggNOGiENOG4108UH8. Bacteria.
COG0245. LUCA.
HOGENOMiHOG000239175.
KOiK01770.
OMAiHFGTGRP.
PhylomeDBiQ8RQP5.

Enzyme and pathway databases

UniPathwayiUPA00056; UER00095.
BRENDAi4.6.1.12. 2305.

Miscellaneous databases

EvolutionaryTraceiQ8RQP5.

Family and domain databases

CDDicd00554. MECDP_synthase. 1 hit.
Gene3Di3.30.1330.50. 1 hit.
HAMAPiMF_00107. IspF. 1 hit.
InterProiIPR003526. MECDP_synthase.
IPR020555. MECDP_synthase_CS.
[Graphical view]
PfamiPF02542. YgbB. 1 hit.
[Graphical view]
SUPFAMiSSF69765. SSF69765. 1 hit.
TIGRFAMsiTIGR00151. ispF. 1 hit.
PROSITEiPS01350. ISPF. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiISPF_THET8
AccessioniPrimary (citable) accession number: Q8RQP5
Secondary accession number(s): Q5SHE0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 31, 2004
Last sequence update: June 1, 2002
Last modified: November 2, 2016
This is version 90 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, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  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.