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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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi10 – 101Divalent metal cation
Metal bindingi12 – 121Divalent metal cation
Sitei36 – 361Transition state stabilizerBy similarity
Metal bindingi44 – 441Divalent metal cation
Binding sitei67 – 671Substrate; via carbonyl oxygenBy similarity
Sitei135 – 1351Transition state stabilizerBy similarity
Binding sitei141 – 1411Substrate; via carbonyl oxygenBy similarity
Binding sitei144 – 1441SubstrateBy similarity

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

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)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 1591592-C-methyl-D-erythritol 2,4-cyclodiphosphate synthasePRO_0000189502Add
BLAST

Proteomic databases

PaxDbiQ8EBR3.

Interactioni

Subunit structurei

Homotrimer.1 Publication

Protein-protein interaction databases

STRINGi211586.SO_3437.

Structurei

Secondary structure

1
159
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 1816Combined sources
Beta strandi20 – 223Combined sources
Beta strandi25 – 273Combined sources
Beta strandi36 – 383Combined sources
Helixi41 – 5313Combined sources
Helixi59 – 624Combined sources
Helixi68 – 703Combined sources
Helixi75 – 8814Combined sources
Beta strandi91 – 10111Combined sources
Beta strandi103 – 1053Combined sources
Helixi108 – 1103Combined sources
Helixi111 – 12111Combined sources
Helixi126 – 1283Combined sources
Beta strandi129 – 1346Combined sources
Helixi140 – 1434Combined sources
Beta strandi146 – 15813Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1T0AX-ray1.60A/B/C1-159[»]
ProteinModelPortaliQ8EBR3.
SMRiQ8EBR3. Positions 2-159.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ8EBR3.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni10 – 123Substrate bindingBy similarity
Regioni36 – 372Substrate bindingBy similarity
Regioni40 – 489Substrate bindingBy similarity
Regioni58 – 603Substrate bindingBy similarity
Regioni63 – 675Substrate bindingBy similarity
Regioni102 – 1087Substrate bindingBy similarity
Regioni133 – 1375Substrate bindingBy similarity
Regioni141 – 1444Substrate binding

Sequence similaritiesi

Belongs to the IspF family.Curated

Phylogenomic databases

eggNOGiENOG4108UH8. Bacteria.
COG0245. LUCA.
HOGENOMiHOG000239175.
KOiK01770.
OMAiIRIGNGY.
OrthoDBiEOG6J48RZ.
PhylomeDBiQ8EBR3.

Family and domain databases

Gene3Di3.30.1330.50. 1 hit.
HAMAPiMF_00107. IspF.
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
EntryMethodResolution (Å)ChainPositionsPDBsum
1T0AX-ray1.60A/B/C1-159[»]
ProteinModelPortaliQ8EBR3.
SMRiQ8EBR3. Positions 2-159.
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.
OrthoDBiEOG6J48RZ.
PhylomeDBiQ8EBR3.

Enzyme and pathway databases

UniPathwayiUPA00056; UER00095.

Miscellaneous databases

EvolutionaryTraceiQ8EBR3.

Family and domain databases

Gene3Di3.30.1330.50. 1 hit.
HAMAPiMF_00107. IspF.
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...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: MR-1.
  2. "Structure of 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase from Shewanella oneidensis at 1.6 A: identification of farnesyl pyrophosphate trapped in a hydrophobic cavity."
    Ni S., Robinson H., Marsing G.C., Bussiere D.E., Kennedy M.A.
    Acta Crystallogr. D 60:1949-1957(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS AND DIVALENT CATIONS, COFACTOR, SUBUNIT.

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: March 16, 2016
This is version 91 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.