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Protein

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

Gene

ispF

Organism
Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
Status
Unreviewed-Annotation score: Annotation score: 3 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).UniRule annotationSAAS annotation

Catalytic activityi

2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol = 2-C-methyl-D-erythritol 2,4-cyclodiphosphate + CMP.UniRule annotationSAAS 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 annotationSAAS 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), 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), 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (ispH1)
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 bindingi11 – 111Divalent metal cationUniRule annotation
Metal bindingi11 – 111ZincCombined sources
Metal bindingi13 – 131Divalent metal cationUniRule annotation
Metal bindingi13 – 131Zinc; via tele nitrogenCombined sources
Sitei37 – 371Transition state stabilizerUniRule annotation
Metal bindingi45 – 451Divalent metal cationUniRule annotation
Metal bindingi45 – 451Zinc; via pros nitrogenCombined sources
Sitei133 – 1331Transition state stabilizerUniRule annotation
Binding sitei142 – 1421SubstrateUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi11 – 133CDPCombined sources
Nucleotide bindingi59 – 613CDPCombined sources
Nucleotide bindingi103 – 1097CDPCombined sources
Nucleotide bindingi131 – 1333CDPCombined sources

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

LyaseUniRule annotationSAAS annotationImported

Keywords - Biological processi

Isoprene biosynthesisUniRule annotationSAAS annotation

Keywords - Ligandi

Metal-bindingUniRule annotationCombined sourcesSAAS annotation, Nucleotide-bindingCombined sources, ZincCombined sources

Enzyme and pathway databases

BioCyciMSME246196:GJ4Y-6074-MONOMER.
UniPathwayiUPA00056; UER00095.

Names & Taxonomyi

Protein namesi
Recommended name:
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthaseUniRule annotationSAAS annotation (EC:4.6.1.12UniRule annotationSAAS annotation)
Short name:
MECDP-synthaseUniRule annotation
Short name:
MECPP-synthaseUniRule annotation
Short name:
MECPSUniRule annotation
Gene namesi
Name:ispFUniRule annotationImported
Ordered Locus Names:MSMEG_6075Imported
OrganismiMycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Imported
Taxonomic identifieri246196 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesMycobacteriaceaeMycobacterium
Proteomesi
  • UP000000757 Componenti: Chromosome

Interactioni

Subunit structurei

Homotrimer.UniRule annotationSAAS annotation

Protein-protein interaction databases

STRINGi246196.MSMEG_6075.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2UZHX-ray2.20A/B/C1-163[»]
ProteinModelPortaliA0R559.
SMRiA0R559. Positions 3-146.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiA0R559.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini5 – 154150YgbBInterPro annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni11 – 133Substrate bindingUniRule annotation
Regioni37 – 382Substrate bindingUniRule annotation
Regioni41 – 499Substrate bindingUniRule annotation
Regioni59 – 613Substrate bindingUniRule annotation
Regioni131 – 1355Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the IspF family.UniRule annotationSAAS annotation

Phylogenomic databases

eggNOGiENOG4108UH8. Bacteria.
COG0245. LUCA.
HOGENOMiHOG000239175.
KOiK01770.
OMAiHFGTGRP.
OrthoDBiEOG6J1DJS.

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.

A0R559-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MMLPRVGLGT DVHPIEAGRP CRLLCLEFDD ADGCAGHSDG DVAAHALCDA
60 70 80 90 100
LLSAAGLGDL GTIFGTDRPQ WRGASGADMI RHVRGLVENA GFVIGNATVQ
110 120 130 140 150
VIGNRPKVGP RREEAQQVLS ELVGAPVSVS ATTTDGLGLT GRGEGLAAIA
160
TALVAAEPVG DAK
Length:163
Mass (Da):16,547
Last modified:January 9, 2007 - v1
Checksum:iEE974948A1D56A64
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000480 Genomic DNA. Translation: ABK73227.1.
RefSeqiWP_011731018.1. NZ_CP009494.1.
YP_890297.1. NC_008596.1.

Genome annotation databases

EnsemblBacteriaiABK73227; ABK73227; MSMEG_6075.
GeneIDi4536746.
KEGGimsb:LJ00_30040.
msm:MSMEG_6075.
PATRICi18084387. VBIMycSme59918_5913.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000480 Genomic DNA. Translation: ABK73227.1.
RefSeqiWP_011731018.1. NZ_CP009494.1.
YP_890297.1. NC_008596.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2UZHX-ray2.20A/B/C1-163[»]
ProteinModelPortaliA0R559.
SMRiA0R559. Positions 3-146.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi246196.MSMEG_6075.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABK73227; ABK73227; MSMEG_6075.
GeneIDi4536746.
KEGGimsb:LJ00_30040.
msm:MSMEG_6075.
PATRICi18084387. VBIMycSme59918_5913.

Phylogenomic databases

eggNOGiENOG4108UH8. Bacteria.
COG0245. LUCA.
HOGENOMiHOG000239175.
KOiK01770.
OMAiHFGTGRP.
OrthoDBiEOG6J1DJS.

Enzyme and pathway databases

UniPathwayiUPA00056; UER00095.
BioCyciMSME246196:GJ4Y-6074-MONOMER.

Miscellaneous databases

EvolutionaryTraceiA0R559.

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

  1. Hayward D., Fahey B.
    Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700084 / mc(2)155Imported.

Entry informationi

Entry nameiA0R559_MYCS2
AccessioniPrimary (citable) accession number: A0R559
Entry historyi
Integrated into UniProtKB/TrEMBL: January 9, 2007
Last sequence update: January 9, 2007
Last modified: July 6, 2016
This is version 90 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

3D-structureCombined sources, Complete proteome, 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.