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B3PYS4 (ISPDF_RHIE6) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 28. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
Bifunctional enzyme IspD/IspF

Including the following 2 domains:

  1. 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
    EC=2.7.7.60
    Alternative name(s):
    4-diphosphocytidyl-2C-methyl-D-erythritol synthase
    MEP cytidylyltransferase
    Short name=MCT
  2. 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
    Short name=MECDP-synthase
    Short name=MECPS
    EC=4.6.1.12
Gene names
Name:ispDF
Ordered Locus Names:RHECIAT_CH0002043
OrganismRhizobium etli (strain CIAT 652) [Complete proteome] [HAMAP]
Taxonomic identifier491916 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Alphaproteobacteria › Rhizobiales › Rhizobiaceae › Rhizobium/Agrobacterium group › Rhizobium

Protein attributes

Sequence length405 AA.
Sequence statusComplete.
Protein existenceInferred from homology

General annotation (Comments)

Function

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 converts 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate into 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MECDP) and CMP (IspF) By similarity. HAMAP MF_01520

Catalytic activity

CTP + 2-C-methyl-D-erythritol 4-phosphate = diphosphate + 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol. HAMAP MF_01520

2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol = 2-C-methyl-D-erythritol 2,4-cyclodiphosphate + CMP. HAMAP MF_01520

Cofactor

Divalent metal cations By similarity. HAMAP MF_01520

Pathway

Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 2/6. HAMAP MF_01520

Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 4/6.

Sequence similarities

In the N-terminal section; belongs to the IspD family.

In the C-terminal section; belongs to the IspF family.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 405405Bifunctional enzyme IspD/IspF HAMAP MF_01520
PRO_1000191077

Regions

Region1 – 2462462-C-methyl-D-erythritol 4-phosphate cytidylyltransferase HAMAP MF_01520
Region247 – 4051592-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase HAMAP MF_01520

Sites

Metal binding2531Divalent metal cation By similarity
Metal binding2551Divalent metal cation By similarity
Metal binding2871Divalent metal cation By similarity
Site241Transition state stabilizer By similarity
Site331Transition state stabilizer By similarity
Site1671Positions MEP for the nucleophilic attack By similarity
Site2241Positions MEP for the nucleophilic attack By similarity
Site2791Transition state stabilizer By similarity
Site3781Transition state stabilizer By similarity

Sequences

Sequence LengthMass (Da)Tools
B3PYS4 [UniParc].

Last modified September 2, 2008. Version 1.
Checksum: 7D7F683704BE4FBC

FASTA40543,262
        10         20         30         40         50         60 
MLQMPSKQPI SAGIVIVAAG RGERAGSPTE GPKQYRPIGG KPVIVHTLEN FMTWEPATAI 

        70         80         90        100        110        120 
VVVIHPDDEA LFAKAFRHII SATPIETVHG GPTRQRSVLA GLRYLKDKHV SHVLIHDAVR 

       130        140        150        160        170        180 
PFFDHTLLDR IAENLANGAL AVLPAMPVTD TLKRADGAGT VLTTVSREQL FAAQTPQSFA 

       190        200        210        220        230        240 
FETILDAHEK AAASGRSDFT DDASIAEWLG IPVTIVEGTG DNVKLTVKKD IAMADDKLSA 

       250        260        270        280        290        300 
SLLPDVRTGN GYDVHQLEAG DGVTLCGVFI PHDQKLKGHS DADVALHALT DALLATCGAG 

       310        320        330        340        350        360 
DIGDHFPPSD PQWKGAASRI FIEHAARIVR ERGGTIMNAD VSLIAEAPKV GPHREAMRAN 

       370        380        390        400 
LSEYLGIDLE RCSVKATTNE TIGFVGRREG IAAIATATVV YRGRT

« Hide

References

[1]"Genome diversity and DNA divergence of Rhizobium etli."
Gonzalez V., Acosta J.L., Santamaria R.I., Bustos P., Hernandez-Gonzalez I.L., Fernandez J.L., Diaz R., Flores M., Mora J., Palacios R., Davila G.
Submitted (APR-2008) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: CIAT 652.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		CP001074 Genomic DNA. Translation: ACE91003.1.
RefSeqYP_001978181.1. NC_010994.1.

3D structure databases

ProteinModelPortalB3PYS4.
ModBaseSearch...

Protein-protein interaction databases

STRINGB3PYS4.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID6400130.
GenomeReviewsGene locus ispDF in contig CP001074_GR.
KEGGrec:RHECIAT_CH0002043.
PATRIC23097557. VBIRhiEtl120572_2016.

Organism-specific databases

CMRSearch...

Phylogenomic databases

HOGENOMHBG672839.
OMAIVLIHDA.
ProtClustDBPRK09382.

Family and domain databases

HAMAPMF_01520. IspDF.
[Tree]
InterProIPR023423. IpsF_dom.
IPR001228. ISPD_synthase.
IPR018294. ISPD_synthase_CS.
IPR003526. MECDP_synthase.
IPR020555. MECDP_synthase_CS.
[Graphical view]
Gene3DG3DSA:3.30.1330.50. MECDP_synthase_core. 1 hit.
KOK12506.
PfamPF01128. IspD. 1 hit.
PF02542. YgbB. 1 hit.
[Graphical view]
SUPFAMSSF69765. YgbB_synth. 1 hit.
TIGRFAMsTIGR00453. IspD. 1 hit.
TIGR00151. IspF. 1 hit.
PROSITEPS01295. ISPD. 1 hit.
PS01350. ISPF. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameISPDF_RHIE6
AccessionPrimary (citable) accession number: B3PYS4
Entry history
Integrated into UniProtKB/Swiss-Prot: April 14, 2009
Last sequence update: September 2, 2008
Last modified: January 25, 2012
This is version 28 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

PATHWAY comments

Index of metabolic and biosynthesis pathways

SIMILARITY comments

Index of protein domains and families

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