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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)DescriptionActionsGraphical viewLength
Sitei16Transition state stabilizerUniRule annotation1
Sitei23Transition state stabilizerUniRule annotation1
Sitei139Positions MEP for the nucleophilic attackUniRule annotation1
Sitei191Positions MEP for the nucleophilic attackUniRule annotation1
Metal bindingi217Divalent metal cationUniRule annotation1
Metal bindingi219Divalent metal cationUniRule annotation1
Sitei243Transition state stabilizerUniRule annotation1
Metal bindingi251Divalent metal cationUniRule annotation1
Binding sitei274Substrate; via carbonyl oxygenUniRule annotation1
Sitei342Transition state stabilizerUniRule annotation1
Binding sitei348Substrate; via carbonyl oxygenUniRule annotation1
Binding sitei351SubstrateUniRule annotation1

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-1508-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)DescriptionActionsGraphical viewLength
ChainiPRO_00000756621 – 371Bifunctional enzyme IspD/IspFAdd BLAST371

Proteomic databases

PaxDbiQ9PM68.

Interactioni

Protein-protein interaction databases

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

Structurei

Secondary structure

1371
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 9Combined sources6
Turni15 – 17Combined sources3
Beta strandi19 – 21Combined sources3
Helixi23 – 25Combined sources3
Beta strandi27 – 29Combined sources3
Helixi33 – 42Combined sources10
Beta strandi50 – 55Combined sources6
Helixi57 – 61Combined sources5
Beta strandi65 – 71Combined sources7
Helixi76 – 84Combined sources9
Beta strandi89 – 96Combined sources8
Helixi104 – 111Combined sources8
Helixi112 – 116Combined sources5
Beta strandi118 – 124Combined sources7
Beta strandi130 – 132Combined sources3
Beta strandi135 – 137Combined sources3
Helixi139 – 141Combined sources3
Beta strandi149 – 152Combined sources4
Helixi153 – 159Combined sources7
Helixi169 – 174Combined sources6
Turni175 – 177Combined sources3
Beta strandi180 – 184Combined sources5
Helixi187 – 189Combined sources3
Helixi195 – 200Combined sources6
Beta strandi210 – 225Combined sources16
Beta strandi227 – 229Combined sources3
Beta strandi232 – 240Combined sources9
Beta strandi243 – 245Combined sources3
Helixi248 – 260Combined sources13
Helixi266 – 269Combined sources4
Beta strandi272 – 274Combined sources3
Turni276 – 279Combined sources4
Helixi282 – 295Combined sources14
Beta strandi298 – 308Combined sources11
Beta strandi310 – 312Combined sources3
Helixi315 – 317Combined sources3
Helixi318 – 329Combined sources12
Helixi333 – 335Combined sources3
Beta strandi336 – 341Combined sources6
Helixi347 – 350Combined sources4
Beta strandi353 – 365Combined sources13

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiQ9PM68.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 2102-C-methyl-D-erythritol 4-phosphate cytidylyltransferaseAdd BLAST210
Regioni211 – 3712-C-methyl-D-erythritol 2,4-cyclodiphosphate synthaseAdd BLAST161
Regioni217 – 219Substrate bindingUniRule annotation3
Regioni243 – 244Substrate bindingUniRule annotation2
Regioni247 – 255Substrate bindingUniRule annotation9
Regioni265 – 267Substrate bindingUniRule annotation3
Regioni270 – 274Substrate bindingUniRule annotation5
Regioni340 – 344Substrate bindingUniRule annotation5

Sequence similaritiesi

In the N-terminal section; belongs to the IspD/TarI cytidylyltransferase family. IspD subfamily.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.

Family and domain databases

CDDicd02516. CDP-ME_synthetase. 1 hit.
cd00554. MECDP_synthase. 1 hit.
Gene3Di3.30.1330.50. 1 hit.
3.90.550.10. 1 hit.
HAMAPiMF_01520. IspDF. 1 hit.
MF_00107. IspF. 1 hit.
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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1W55X-ray2.30A1-371[»]
1W57X-ray3.09A1-371[»]
ProteinModelPortaliQ9PM68.
SMRiQ9PM68.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiQ9PM68. 27 interactors.
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.

Enzyme and pathway databases

UniPathwayiUPA00056; UER00093.
UPA00056; UER00095.
BioCyciCJEJ192222:GJTS-1508-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ9PM68.

Family and domain databases

CDDicd02516. CDP-ME_synthetase. 1 hit.
cd00554. MECDP_synthase. 1 hit.
Gene3Di3.30.1330.50. 1 hit.
3.90.550.10. 1 hit.
HAMAPiMF_01520. IspDF. 1 hit.
MF_00107. IspF. 1 hit.
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...

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: November 2, 2016
This is version 116 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.