Reviewed, UniProtKB/Swiss-Prot A1B890 (ISPDF_PARDP)

Names and origin

Protein names

Recommended name:
    Bifunctional enzyme ispD/ispF
Including the following 2 domains:
    1- Recommended name:
            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- Recommended name:
            2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
                Short name=MECPS
                Short name=MECDP-synthase
              EC=4.6.1.12

Gene names

Name:	ispDF
Ordered Locus Names:	Pden_3667

Organism

Paracoccus denitrificans (strain Pd 1222) [Complete proteome] [HAMAP]

Taxonomic identifier

318586 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Alphaproteobacteria › Rhodobacterales › Rhodobacteraceae › Paracoccus

Protein attributes

Sequence length	380 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Inferred 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.
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.
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.

Ontologies

Keywords
Biological process	Isoprene biosynthesis
Ligand	Metal-binding
Molecular function	Lyase Nucleotidyltransferase Transferase
Technical term	Complete proteome Multifunctional enzyme
Gene Ontology (GO)
Biological process	terpenoid biosynthetic process Inferred from electronic annotation. Source: HAMAP
Molecular function	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity Inferred from electronic annotation. Source: HAMAP 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity Inferred from electronic annotation. Source: HAMAP metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 380	380	Bifunctional enzyme ispD/ispF HAMAP MF_01520		PRO_0000292858
Regions
	Region	1 – 224	224	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase HAMAP MF_01520
	Region	225 – 380	156	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase HAMAP MF_01520
Sites
	Metal binding	231	1	Divalent metal cation By similarity
	Metal binding	233	1	Divalent metal cation By similarity
	Metal binding	265	1	Divalent metal cation By similarity
	Site	19	1	Transition state stabilizer By similarity
	Site	26	1	Transition state stabilizer By similarity
	Site	151	1	Positions MEP for the nucleophilic attack By similarity
	Site	204	1	Positions MEP for the nucleophilic attack By similarity
	Site	257	1	Transition state stabilizer By similarity
	Site	356	1	Transition state stabilizer By similarity

Sequences

	Sequence		Length	Mass (Da)
	A1B890-1 [UniParc]. Last modified June 26, 2007. Version 2. Checksum: FF37E37D79F81468	FASTA	380	39,647
	10 20 30 40 50 60 MTIPATYAAI ITAAGRGTRA GDGPPKQWRP LAGQSVLERS IAAFAGFPRV VVTLAPEDMA 70 80 90 100 110 120 RGVAELSGPV VLVAGGATRS DSVRAALESL EGSGVTHVLI HDGARPLVSR RVIGGVIEAL 130 140 150 160 170 180 QSGAPAAAPA LPVTDALWRA QDGCVTATAS REGLFRAQTP QGFALDAILA AHRAHPEGAA 190 200 210 220 230 240 DDVELAIRAG LPVTVTPGDE DNLKLTWPGD FARAERILGD AMDIRLGNGF DVHAFTTGDH 250 260 270 280 290 300 VWLCGVKIPH DKALLGHSDA DVGMHALTDA IYGALAQGDI GRHFPPSDPQ WKGAESHIFL 310 320 330 340 350 360 RHAAMLARQM GYEISNADVT LICERPKVGP HAGAMALRLS EIIGVEPDRV SVKATTSERL 370 380 GFTGREEGIA SIATATLVKG

References

[1]

"Complete sequence of chromosome 2 of Paracoccus denitrificans PD1222." Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S., Munk A.C., Brettin T., Bruce D., Han C., Tapia R., Gilna P., Schmutz J. , Larimer F., Land M., Hauser L., Kyrpides N., Lykidis A., Spiro S., Richardson D.J., Moir J.W.B., Ferguson S.J., van Spanning R.J.M., Richardson P. Submitted (DEC-2006) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Cross-references

Sequence databases
EMBLGenBankDDBJ	CP000490 Genomic DNA. Translation: ABL71734.1. Different initiation.
RefSeq	YP_917430.1.
3D structure databases
ModBase	Search...
Protein-protein interaction databases
STRING	A1B890.
Genome annotation databases
GeneID	4582219.
GenomeReviews	Gene locus Pden_3667 in contig CP000490_GR.
KEGG	pde:Pden_3667.
Organism-specific databases
CMR	Search...
Family and domain databases
HAMAP	MF_01520. [Tree]
InterPro	IPR001228. ISPD_synthase. IPR018294. ISPD_synthase_CS. IPR003526. MECDP_synthase_core. IPR020555. MECDP_synthase_CS. [Graphical view]
Pfam	PF01128. IspD. 1 hit. PF02542. YgbB. 1 hit. [Graphical view]
TIGRFAMs	TIGR00453. ispD. 1 hit. TIGR00151. ispF. 1 hit.
PROSITE	PS01295. ISPD. 1 hit. PS01350. ISPF. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

ISPDF_PARDP

Accession

Primary (citable) accession number: A1B890

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 26, 2007
Last sequence update:	June 26, 2007
Last modified:	October 13, 2009
This is version 16 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)