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Protein

Bifunctional enzyme IspD/IspF

Gene

ispDF

Organism
Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Bifunctional enzyme that catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate (MEP) (IspD), and 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) (IspF).UniRule annotation

Catalytic activityi

CTP + 2-C-methyl-D-erythritol 4-phosphate = diphosphate + 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol.UniRule annotation1 Publication
2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol = 2-C-methyl-D-erythritol 2,4-cyclodiphosphate + CMP.UniRule annotation1 Publication

Cofactori

a divalent metal cationUniRule annotation1 Publication

Pathwayi: isopentenyl diphosphate biosynthesis via DXP pathway

This protein is involved in step 2 and 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. Bifunctional enzyme IspD/IspF (ispDF)
  3. 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (ispE)
  4. Bifunctional enzyme IspD/IspF (ispDF)
  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
Sitei16 – 161Transition state stabilizerUniRule annotation
Sitei23 – 231Transition state stabilizerUniRule annotation
Sitei139 – 1391Positions MEP for the nucleophilic attackUniRule annotation
Sitei191 – 1911Positions MEP for the nucleophilic attackUniRule annotation
Metal bindingi217 – 2171Divalent metal cationUniRule annotation
Metal bindingi219 – 2191Divalent metal cationUniRule annotation
Sitei243 – 2431Transition state stabilizerUniRule annotation
Metal bindingi251 – 2511Divalent metal cationUniRule annotation
Binding sitei274 – 2741Substrate; via carbonyl oxygenUniRule annotation
Sitei342 – 3421Transition state stabilizerUniRule annotation
Binding sitei348 – 3481Substrate; via carbonyl oxygenUniRule annotation
Binding sitei351 – 3511SubstrateUniRule annotation

GO - Molecular functioni

GO - Biological processi

Keywords - Molecular functioni

Lyase, Nucleotidyltransferase, Transferase

Keywords - Biological processi

Isoprene biosynthesis

Keywords - Ligandi

Metal-binding

Enzyme and pathway databases

BioCyciCJEJ192222:GJTS-1566-MONOMER.
UniPathwayiUPA00056; UER00093.
UPA00056; UER00095.

Names & Taxonomyi

Protein namesi
Recommended name:
Bifunctional enzyme IspD/IspFUniRule annotation
Including the following 2 domains:
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferaseUniRule annotation (EC:2.7.7.60UniRule annotation)
Alternative name(s):
4-diphosphocytidyl-2C-methyl-D-erythritol synthaseUniRule annotation
MEP cytidylyltransferaseUniRule annotation
Short name:
MCTUniRule annotation
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:ispDFUniRule annotation
Ordered Locus Names:Cj1607
OrganismiCampylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)
Taxonomic identifieri192222 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaEpsilonproteobacteriaCampylobacteralesCampylobacteraceaeCampylobacter
Proteomesi
  • UP000000799 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 371371Bifunctional enzyme IspD/IspFPRO_0000075662Add
BLAST

Proteomic databases

PaxDbiQ9PM68.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
fliNO323701EBI-1192039,EBI-1191320

Protein-protein interaction databases

IntActiQ9PM68. 27 interactions.
MINTiMINT-6485480.
STRINGi192222.Cj1607.

Structurei

Secondary structure

1
371
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 96Combined sources
Turni15 – 173Combined sources
Beta strandi19 – 213Combined sources
Helixi23 – 253Combined sources
Beta strandi27 – 293Combined sources
Helixi33 – 4210Combined sources
Beta strandi50 – 556Combined sources
Helixi57 – 615Combined sources
Beta strandi65 – 717Combined sources
Helixi76 – 849Combined sources
Beta strandi89 – 968Combined sources
Helixi104 – 1118Combined sources
Helixi112 – 1165Combined sources
Beta strandi118 – 1247Combined sources
Beta strandi130 – 1323Combined sources
Beta strandi135 – 1373Combined sources
Helixi139 – 1413Combined sources
Beta strandi149 – 1524Combined sources
Helixi153 – 1597Combined sources
Helixi169 – 1746Combined sources
Turni175 – 1773Combined sources
Beta strandi180 – 1845Combined sources
Helixi187 – 1893Combined sources
Helixi195 – 2006Combined sources
Beta strandi210 – 22516Combined sources
Beta strandi227 – 2293Combined sources
Beta strandi232 – 2409Combined sources
Beta strandi243 – 2453Combined sources
Helixi248 – 26013Combined sources
Helixi266 – 2694Combined sources
Beta strandi272 – 2743Combined sources
Turni276 – 2794Combined sources
Helixi282 – 29514Combined sources
Beta strandi298 – 30811Combined sources
Beta strandi310 – 3123Combined sources
Helixi315 – 3173Combined sources
Helixi318 – 32912Combined sources
Helixi333 – 3353Combined sources
Beta strandi336 – 3416Combined sources
Helixi347 – 3504Combined sources
Beta strandi353 – 36513Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1W55X-ray2.30A1-371[»]
1W57X-ray3.09A1-371[»]
ProteinModelPortaliQ9PM68.
SMRiQ9PM68. Positions 2-370.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9PM68.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 2102102-C-methyl-D-erythritol 4-phosphate cytidylyltransferaseAdd
BLAST
Regioni211 – 3711612-C-methyl-D-erythritol 2,4-cyclodiphosphate synthaseAdd
BLAST
Regioni217 – 2193Substrate bindingUniRule annotation
Regioni243 – 2442Substrate bindingUniRule annotation
Regioni247 – 2559Substrate bindingUniRule annotation
Regioni265 – 2673Substrate bindingUniRule annotation
Regioni270 – 2745Substrate bindingUniRule annotation
Regioni340 – 3445Substrate bindingUniRule annotation

Sequence similaritiesi

In the N-terminal section; belongs to the IspD family.UniRule annotation
In the C-terminal section; belongs to the IspF family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4108UH8. Bacteria.
COG0245. LUCA.
COG1211. LUCA.
HOGENOMiHOG000252034.
KOiK12506.
OMAiCGAGDIG.
OrthoDBiEOG6J48RZ.

Family and domain databases

Gene3Di3.30.1330.50. 1 hit.
3.90.550.10. 1 hit.
HAMAPiMF_00107. IspF.
MF_01520. IspDF.
InterProiIPR001228. IspD.
IPR026596. IspD/F.
IPR018294. ISPD_synthase_CS.
IPR003526. MECDP_synthase.
IPR020555. MECDP_synthase_CS.
IPR029044. Nucleotide-diphossugar_trans.
[Graphical view]
PfamiPF01128. IspD. 1 hit.
PF02542. YgbB. 1 hit.
[Graphical view]
SUPFAMiSSF53448. SSF53448. 1 hit.
SSF69765. SSF69765. 1 hit.
TIGRFAMsiTIGR00453. ispD. 1 hit.
TIGR00151. ispF. 1 hit.
PROSITEiPS01295. ISPD. 1 hit.
PS01350. ISPF. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9PM68-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSEMSLIMLA AGNSTRFNTK VKKQFLRLGN DPLWLYATKN LSSFYPFKKI
60 70 80 90 100
VVTSSNITYM KKFTKNYEFI EGGDTRAESL KKALELIDSE FVMVSDVARV
110 120 130 140 150
LVSKNLFDRL IENLDKADCI TPALKVADTT LFDNEALQRE KIKLIQTPQI
160 170 180 190 200
SKTKLLKKAL DQNLEFTDDS TAIAAMGGKI WFVEGEENAR KLTFKEDLKK
210 220 230 240 250
LDLPTPSFEI FTGNGFDVHE FGENRPLLLA GVQIHPTMGL KAHSDGDVLA
260 270 280 290 300
HSLTDAILGA AGLGDIGELY PDTDMKFKNA NSMELLKQAY DKVREIGFEL
310 320 330 340 350
INIDICVMAQ SPKLKDFKQA MQSNIAHTLD LDEFRINVKA TTTEKLGFIG
360 370
RKEGMAVLSS VNLKYFDWTR L
Length:371
Mass (Da):41,690
Last modified:October 1, 2000 - v1
Checksum:iBAD0087B19905FAF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL111168 Genomic DNA. Translation: CAL35704.1.
PIRiE81256.
RefSeqiWP_002851397.1. NC_002163.1.
YP_002344976.1. NC_002163.1.

Genome annotation databases

EnsemblBacteriaiCAL35704; CAL35704; Cj1607.
GeneIDi905874.
KEGGicje:Cj1607.
PATRICi20060174. VBICamJej33762_1583.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL111168 Genomic DNA. Translation: CAL35704.1.
PIRiE81256.
RefSeqiWP_002851397.1. NC_002163.1.
YP_002344976.1. NC_002163.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1W55X-ray2.30A1-371[»]
1W57X-ray3.09A1-371[»]
ProteinModelPortaliQ9PM68.
SMRiQ9PM68. Positions 2-370.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiQ9PM68. 27 interactions.
MINTiMINT-6485480.
STRINGi192222.Cj1607.

Proteomic databases

PaxDbiQ9PM68.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAL35704; CAL35704; Cj1607.
GeneIDi905874.
KEGGicje:Cj1607.
PATRICi20060174. VBICamJej33762_1583.

Phylogenomic databases

eggNOGiENOG4108UH8. Bacteria.
COG0245. LUCA.
COG1211. LUCA.
HOGENOMiHOG000252034.
KOiK12506.
OMAiCGAGDIG.
OrthoDBiEOG6J48RZ.

Enzyme and pathway databases

UniPathwayiUPA00056; UER00093.
UPA00056; UER00095.
BioCyciCJEJ192222:GJTS-1566-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ9PM68.

Family and domain databases

Gene3Di3.30.1330.50. 1 hit.
3.90.550.10. 1 hit.
HAMAPiMF_00107. IspF.
MF_01520. IspDF.
InterProiIPR001228. IspD.
IPR026596. IspD/F.
IPR018294. ISPD_synthase_CS.
IPR003526. MECDP_synthase.
IPR020555. MECDP_synthase_CS.
IPR029044. Nucleotide-diphossugar_trans.
[Graphical view]
PfamiPF01128. IspD. 1 hit.
PF02542. YgbB. 1 hit.
[Graphical view]
SUPFAMiSSF53448. SSF53448. 1 hit.
SSF69765. SSF69765. 1 hit.
TIGRFAMsiTIGR00453. ispD. 1 hit.
TIGR00151. ispF. 1 hit.
PROSITEiPS01295. ISPD. 1 hit.
PS01350. ISPF. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700819 / NCTC 11168.
  2. "Biosynthesis of isoprenoids. A bifunctional IspDF enzyme from Campylobacter jejuni."
    Gabrielsen M., Rohdich F., Eisenreich W., Graewert T., Hecht S., Bacher A., Hunter W.N.
    Eur. J. Biochem. 271:3028-3035(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 1-22, CATALYTIC ACTIVITY, COFACTOR, IDENTIFICATION BY MASS SPECTROMETRY.

Entry informationi

Entry nameiISPDF_CAMJE
AccessioniPrimary (citable) accession number: Q9PM68
Secondary accession number(s): Q0P821
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 11, 2001
Last sequence update: October 1, 2000
Last modified: January 20, 2016
This is version 112 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, Direct protein sequencing, Multifunctional enzyme, 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.