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B5ZNB6 (ISPDF_RHILW) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 29. 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:Rleg2_1616
OrganismRhizobium leguminosarum bv. trifolii (strain WSM2304) [Complete proteome] [HAMAP]
Taxonomic identifier395492 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Alphaproteobacteria › Rhizobiales › Rhizobiaceae › Rhizobium/Agrobacterium group › Rhizobium

Protein attributes

Sequence length406 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 – 406406Bifunctional enzyme IspD/IspF HAMAP MF_01520
PRO_1000191078

Regions

Region1 – 2462462-C-methyl-D-erythritol 4-phosphate cytidylyltransferase HAMAP MF_01520
Region247 – 4061602-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
B5ZNB6 [UniParc].

Last modified November 25, 2008. Version 1.
Checksum: 333E916307F49CFC

FASTA40643,577
        10         20         30         40         50         60 
MLQMPSKQPI SAGIVIVAAG RGERAGSSKE GPKQYRMIGG KPVIVHTLEN FMTWEPATEI 

        70         80         90        100        110        120 
VVVIHPDDEA LFARALRHII SATPIETVHG GPTRQQSVLA GLRHLKDKRI SHVLIHDAVR 

       130        140        150        160        170        180 
PFFDHVLLDR IAESLDNGAQ AVLPAIPVTD TLKRADSAGT VLTTVSREHL YAAQTPQSFA 

       190        200        210        220        230        240 
FETILDAHEK AAASGRSDFT DDASIAEWAG IPVTIVAGTP DNVKLTVKKD IAMADDKLSA 

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

       310        320        330        340        350        360 
DIGDHFPPSD PQWKGAASRI FIEHAARIVR EHGGTIMNAD VSLIAEAPKV GPHRESMRMR 

       370        380        390        400 
LSEYLGIDIE RCSVKATTNE TIGFVGRREG IAAIATATVV YRGVKR

« Hide

References

[1]"Complete sequence of chromosome of Rhizobium leguminosarum bv. trifolii WSM2304."
Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Pitluck S., Chain P., Malfatti S., Shin M., Vergez L., Lang D., Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N., Yates R. expand/collapse author list , Ardley J., Tiwari R.P., O'Hara G., Howieson J., Brau L., Reeve W.
Submitted (OCT-2008) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: WSM2304.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		CP001191 Genomic DNA. Translation: ACI54906.1.
RefSeqYP_002281132.1. NC_011369.1.

3D structure databases

ProteinModelPortalB5ZNB6.
ModBaseSearch...

Protein-protein interaction databases

STRINGB5ZNB6.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID6980352.
GenomeReviewsGene locus Rleg2_1616 in contig CP001191_GR.
KEGGrlt:Rleg2_1616.
PATRIC23127230. VBIRhiLeg95088_3440.

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_RHILW
AccessionPrimary (citable) accession number: B5ZNB6
Entry history
Integrated into UniProtKB/Swiss-Prot: April 14, 2009
Last sequence update: November 25, 2008
Last modified: January 25, 2012
This is version 29 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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