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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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi9 – 91Divalent metal cation
Metal bindingi11 – 111Divalent metal cation
Sitei35 – 351Transition state stabilizerBy similarity
Metal bindingi43 – 431Divalent metal cation
Binding sitei66 – 661Substrate; via carbonyl oxygenBy similarity
Sitei134 – 1341Transition state stabilizerBy similarity
Binding sitei140 – 1401Substrate; via carbonyl oxygenBy similarity
Binding sitei143 – 1431SubstrateBy similarity

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)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 1581582-C-methyl-D-erythritol 2,4-cyclodiphosphate synthasePRO_0000189472Add
BLAST

Interactioni

Subunit structurei

Homotrimer.2 Publications

Protein-protein interaction databases

STRINGi71421.HI0671.

Structurei

Secondary structure

1
158
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 1211Combined sources
Beta strandi14 – 218Combined sources
Beta strandi24 – 329Combined sources
Helixi40 – 5213Combined sources
Helixi58 – 603Combined sources
Helixi64 – 674Combined sources
Beta strandi68 – 703Combined sources
Helixi74 – 8714Combined sources
Beta strandi90 – 10011Combined sources
Beta strandi102 – 1043Combined sources
Helixi107 – 12014Combined sources
Helixi125 – 1273Combined sources
Beta strandi128 – 1336Combined sources
Helixi139 – 1424Combined sources
Beta strandi145 – 15713Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 1-157.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP44815.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni9 – 113Substrate bindingBy similarity
Regioni35 – 362Substrate bindingBy similarity
Regioni39 – 479Substrate bindingBy similarity
Regioni57 – 593Substrate bindingBy similarity
Regioni62 – 665Substrate bindingBy similarity
Regioni101 – 1077Substrate bindingBy similarity
Regioni132 – 1365Substrate bindingBy similarity
Regioni140 – 1434Substrate binding

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
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. Positions 1-157.
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: September 7, 2016
This is version 117 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.