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Protein

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

Gene

ispF

Organism
Shewanella oneidensis (strain MR-1)
Status
Reviewed-Annotation score: Annotation score: 4 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) (By similarity).By similarity

Catalytic activityi

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

Cofactori

a divalent metal cation1 PublicationNote: Binds 1 divalent metal cation per subunit.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 bindingi10Divalent metal cation1
Metal bindingi12Divalent metal cation1
Sitei36Transition state stabilizerBy similarity1
Metal bindingi44Divalent metal cation1
Binding sitei67Substrate; via carbonyl oxygenBy similarity1
Sitei135Transition state stabilizerBy similarity1
Binding sitei141Substrate; via carbonyl oxygenBy similarity1
Binding sitei144SubstrateBy similarity1

GO - Molecular functioni

  • 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity Source: TIGR
  • metal ion binding Source: UniProtKB-KW

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

Isoprene biosynthesis

Keywords - Ligandi

Metal-binding

Enzyme and pathway databases

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:SO_3437
OrganismiShewanella oneidensis (strain MR-1)
Taxonomic identifieri211586 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaAlteromonadalesShewanellaceaeShewanella
Proteomesi
  • UP000008186 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001895021 – 1592-C-methyl-D-erythritol 2,4-cyclodiphosphate synthaseAdd BLAST159

Proteomic databases

PaxDbiQ8EBR3.

Interactioni

Subunit structurei

Homotrimer.1 Publication

Protein-protein interaction databases

STRINGi211586.SO_3437.

Structurei

Secondary structure

1159
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 18Combined sources16
Beta strandi20 – 22Combined sources3
Beta strandi25 – 27Combined sources3
Beta strandi36 – 38Combined sources3
Helixi41 – 53Combined sources13
Helixi59 – 62Combined sources4
Helixi68 – 70Combined sources3
Helixi75 – 88Combined sources14
Beta strandi91 – 101Combined sources11
Beta strandi103 – 105Combined sources3
Helixi108 – 110Combined sources3
Helixi111 – 121Combined sources11
Helixi126 – 128Combined sources3
Beta strandi129 – 134Combined sources6
Helixi140 – 143Combined sources4
Beta strandi146 – 158Combined sources13

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1T0AX-ray1.60A/B/C1-159[»]
ProteinModelPortaliQ8EBR3.
SMRiQ8EBR3.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ8EBR3.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni10 – 12Substrate bindingBy similarity3
Regioni36 – 37Substrate bindingBy similarity2
Regioni40 – 48Substrate bindingBy similarity9
Regioni58 – 60Substrate bindingBy similarity3
Regioni63 – 67Substrate bindingBy similarity5
Regioni102 – 108Substrate bindingBy similarity7
Regioni133 – 137Substrate bindingBy similarity5
Regioni141 – 144Substrate binding4

Sequence similaritiesi

Belongs to the IspF family.Curated

Phylogenomic databases

eggNOGiENOG4108UH8. Bacteria.
COG0245. LUCA.
HOGENOMiHOG000239175.
KOiK01770.
OMAiIRIGNGY.
OrthoDBiPOG091H023X.
PhylomeDBiQ8EBR3.

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.

Q8EBR3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKIRIGHGFD VHKFGEPRPL ILCGVEVPYE TGLVAHSDGD VVLHAISDAI
60 70 80 90 100
LGAMALGDIG KHFPDTDAAY KGADSRVLLR HCYALAKAKG FELGNLDVTI
110 120 130 140 150
IAQAPKMAPH IEDMRQVLAA DLNADVADIN VKATTTEKLG FTGRKEGIAV

EAVVLLSRQ
Length:159
Mass (Da):16,996
Last modified:March 1, 2003 - v1
Checksum:iA16DC82586297501
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE014299 Genomic DNA. Translation: AAN56434.1.
RefSeqiNP_718990.1. NC_004347.2.
WP_011073293.1. NC_004347.2.

Genome annotation databases

EnsemblBacteriaiAAN56434; AAN56434; SO_3437.
GeneIDi1171112.
KEGGison:SO_3437.
PATRICi23526562. VBISheOne101494_3332.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE014299 Genomic DNA. Translation: AAN56434.1.
RefSeqiNP_718990.1. NC_004347.2.
WP_011073293.1. NC_004347.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1T0AX-ray1.60A/B/C1-159[»]
ProteinModelPortaliQ8EBR3.
SMRiQ8EBR3.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi211586.SO_3437.

Proteomic databases

PaxDbiQ8EBR3.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAN56434; AAN56434; SO_3437.
GeneIDi1171112.
KEGGison:SO_3437.
PATRICi23526562. VBISheOne101494_3332.

Phylogenomic databases

eggNOGiENOG4108UH8. Bacteria.
COG0245. LUCA.
HOGENOMiHOG000239175.
KOiK01770.
OMAiIRIGNGY.
OrthoDBiPOG091H023X.
PhylomeDBiQ8EBR3.

Enzyme and pathway databases

UniPathwayiUPA00056; UER00095.

Miscellaneous databases

EvolutionaryTraceiQ8EBR3.

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_SHEON
AccessioniPrimary (citable) accession number: Q8EBR3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 31, 2004
Last sequence update: March 1, 2003
Last modified: November 2, 2016
This is version 94 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.