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Protein

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

Gene

ispF

Organism
Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
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 bindingi9Divalent metal cation1
Metal bindingi11Divalent metal cation1
Sitei35Transition state stabilizerBy similarity1
Metal bindingi43Divalent metal cation1
Binding sitei66Substrate; via carbonyl oxygenBy similarity1
Sitei134Transition state stabilizerBy similarity1
Binding sitei140Substrate; via carbonyl oxygenBy similarity1
Binding sitei143SubstrateBy similarity1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

Isoprene biosynthesis

Keywords - Ligandi

Manganese, Metal-binding

Enzyme and pathway databases

BRENDAi4.6.1.12. 2529.
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:HI_0671
OrganismiHaemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
Taxonomic identifieri71421 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPasteurellalesPasteurellaceaeHaemophilus
Proteomesi
  • UP000000579 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001894721 – 1582-C-methyl-D-erythritol 2,4-cyclodiphosphate synthaseAdd BLAST158

Interactioni

Subunit structurei

Homotrimer.2 Publications

Protein-protein interaction databases

STRINGi71421.HI0671.

Structurei

Secondary structure

1158
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 12Combined sources11
Beta strandi14 – 21Combined sources8
Beta strandi24 – 32Combined sources9
Helixi40 – 52Combined sources13
Helixi58 – 60Combined sources3
Helixi64 – 67Combined sources4
Beta strandi68 – 70Combined sources3
Helixi74 – 87Combined sources14
Beta strandi90 – 100Combined sources11
Beta strandi102 – 104Combined sources3
Helixi107 – 120Combined sources14
Helixi125 – 127Combined sources3
Beta strandi128 – 133Combined sources6
Helixi139 – 142Combined sources4
Beta strandi145 – 157Combined sources13

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1JN1X-ray2.90A/B/C1-158[»]
1VH8X-ray2.35A/B/C/D/E/F2-158[»]
1VHAX-ray2.35A/B/C/D/E/F2-158[»]
5ESVX-ray3.10E/F/G2-13[»]
E/F/G38-158[»]
5ESZX-ray4.19C/G2-14[»]
C/G38-158[»]
ProteinModelPortaliP44815.
SMRiP44815.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP44815.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni9 – 11Substrate bindingBy similarity3
Regioni35 – 36Substrate bindingBy similarity2
Regioni39 – 47Substrate bindingBy similarity9
Regioni57 – 59Substrate bindingBy similarity3
Regioni62 – 66Substrate bindingBy similarity5
Regioni101 – 107Substrate bindingBy similarity7
Regioni132 – 136Substrate bindingBy similarity5
Regioni140 – 143Substrate binding4

Sequence similaritiesi

Belongs to the IspF family.Curated

Phylogenomic databases

eggNOGiENOG4108UH8. Bacteria.
COG0245. LUCA.
KOiK01770.
OMAiIRIGNGY.
PhylomeDBiP44815.

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.

P44815-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIRIGHGFDV HAFGEDRPLI IGGVEVPYHT GFIAHSDGDV ALHALTDAIL
60 70 80 90 100
GAAALGDIGK LFPDTDMQYK NADSRGLLRE AFRQVQEKGY KIGNVDITII
110 120 130 140 150
AQAPKMRPHI DAMRAKIAED LQCDIEQVNV KATTTEKLGF TGRQEGIACE

AVALLIRQ
Length:158
Mass (Da):17,194
Last modified:November 1, 1995 - v1
Checksum:iDC34BF347DEC2EFF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L42023 Genomic DNA. Translation: AAC22331.1.
PIRiF64156.
RefSeqiNP_438831.1. NC_000907.1.
WP_005687916.1. NC_000907.1.

Genome annotation databases

EnsemblBacteriaiAAC22331; AAC22331; HI_0671.
GeneIDi950633.
KEGGihin:HI0671.
PATRICi20189959. VBIHaeInf48452_0701.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L42023 Genomic DNA. Translation: AAC22331.1.
PIRiF64156.
RefSeqiNP_438831.1. NC_000907.1.
WP_005687916.1. NC_000907.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1JN1X-ray2.90A/B/C1-158[»]
1VH8X-ray2.35A/B/C/D/E/F2-158[»]
1VHAX-ray2.35A/B/C/D/E/F2-158[»]
5ESVX-ray3.10E/F/G2-13[»]
E/F/G38-158[»]
5ESZX-ray4.19C/G2-14[»]
C/G38-158[»]
ProteinModelPortaliP44815.
SMRiP44815.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi71421.HI0671.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC22331; AAC22331; HI_0671.
GeneIDi950633.
KEGGihin:HI0671.
PATRICi20189959. VBIHaeInf48452_0701.

Phylogenomic databases

eggNOGiENOG4108UH8. Bacteria.
COG0245. LUCA.
KOiK01770.
OMAiIRIGNGY.
PhylomeDBiP44815.

Enzyme and pathway databases

UniPathwayiUPA00056; UER00095.
BRENDAi4.6.1.12. 2529.

Miscellaneous databases

EvolutionaryTraceiP44815.

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_HAEIN
AccessioniPrimary (citable) accession number: P44815
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: November 1, 1995
Last modified: November 2, 2016
This is version 119 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. Haemophilus influenzae
    Haemophilus influenzae (strain Rd): entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.