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Protein

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

Gene

ispF

Organism
Yersinia pestis (strain Pestoides F)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

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).UniRule annotation

Catalytic activityi

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

Cofactori

a divalent metal cationUniRule annotationNote: Binds 1 divalent metal cation per subunit.UniRule annotation

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.UniRule annotation
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 cationUniRule annotation1
Metal bindingi10Divalent metal cationUniRule annotation1
Sitei36Transition state stabilizerUniRule annotation1
Metal bindingi44Divalent metal cationUniRule annotation1
Binding sitei67Substrate; via carbonyl oxygenUniRule annotation1
Sitei135Transition state stabilizerUniRule annotation1
Binding sitei141Substrate; via carbonyl oxygenUniRule annotation1
Binding sitei144SubstrateUniRule annotation1

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 synthaseUniRule annotation (EC:4.6.1.12UniRule annotation)
Short name:
MECDP-synthaseUniRule annotation
Short name:
MECPP-synthaseUniRule annotation
Short name:
MECPSUniRule annotation
Gene namesi
Name:ispFUniRule annotation
Ordered Locus Names:YPDSF_3000
OrganismiYersinia pestis (strain Pestoides F)
Taxonomic identifieri386656 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesYersiniaceaeYersinia

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000228951 – 1622-C-methyl-D-erythritol 2,4-cyclodiphosphate synthaseAdd BLAST162

Interactioni

Subunit structurei

Homotrimer.UniRule annotation

Structurei

3D structure databases

ProteinModelPortaliA4TPZ8.
SMRiA4TPZ8.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni8 – 10Substrate bindingUniRule annotation3
Regioni36 – 37Substrate bindingUniRule annotation2
Regioni40 – 48Substrate bindingUniRule annotation9
Regioni58 – 60Substrate bindingUniRule annotation3
Regioni63 – 67Substrate bindingUniRule annotation5
Regioni102 – 108Substrate bindingUniRule annotation7
Regioni133 – 137Substrate bindingUniRule annotation5

Sequence similaritiesi

Belongs to the IspF family.UniRule annotation

Phylogenomic databases

HOGENOMiHOG000239175.
KOiK01770.
OMAiIRIGNGY.

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.

A4TPZ8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRIGHGFDVH KFGENGSGPL IIGGVRIPYE KGLLAHSDGD VALHAATDAL
60 70 80 90 100
LGAAALGDIG KLFPDTDPAF KGADSRGLLR EAYRRILAKG YKLGNLDITI
110 120 130 140 150
IAQAPKMAPH IPQMRVNLAE DLQCHMDDIN VKATTTEQLG FTGRGEGIAC
160
EAVVLLVNVE QG
Length:162
Mass (Da):17,182
Last modified:May 15, 2007 - v1
Checksum:i9A295411D3DFB1EB
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000668 Genomic DNA. Translation: ABP41360.1.
RefSeqiWP_002209392.1. NZ_CP009715.1.

Genome annotation databases

EnsemblBacteriaiABP41360; ABP41360; YPDSF_3000.
KEGGiypp:YPDSF_3000.
PATRICi18615821. VBIYerPes122972_3789.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000668 Genomic DNA. Translation: ABP41360.1.
RefSeqiWP_002209392.1. NZ_CP009715.1.

3D structure databases

ProteinModelPortaliA4TPZ8.
SMRiA4TPZ8.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABP41360; ABP41360; YPDSF_3000.
KEGGiypp:YPDSF_3000.
PATRICi18615821. VBIYerPes122972_3789.

Phylogenomic databases

HOGENOMiHOG000239175.
KOiK01770.
OMAiIRIGNGY.

Enzyme and pathway databases

UniPathwayiUPA00056; UER00095.

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_YERPP
AccessioniPrimary (citable) accession number: A4TPZ8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: May 15, 2007
Last modified: November 2, 2016
This is version 67 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. 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.