Q3SSN8 (ISPDF_NITWN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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:	Nwi_1442

Organism

Nitrobacter winogradskyi (strain Nb-255 / ATCC 25391) [Complete proteome] [HAMAP]

Taxonomic identifier

323098 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Alphaproteobacteria › Rhizobiales › Bradyrhizobiaceae › Nitrobacter

Protein attributes

Sequence length	398 AA.
Sequence status	Complete.
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. 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.

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: InterPro
Molecular function	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity Inferred from electronic annotation. Source: EC 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity Inferred from electronic annotation. Source: EC 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 – 398	398	Bifunctional enzyme IspD/IspF HAMAP MF_01520		PRO_0000296750
Regions
	Region	1 – 234	234	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase HAMAP MF_01520
	Region	235 – 398	164	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase HAMAP MF_01520
Sites
	Metal binding	241	1	Divalent metal cation By similarity
	Metal binding	243	1	Divalent metal cation By similarity
	Metal binding	275	1	Divalent metal cation By similarity
	Site	19	1	Transition state stabilizer By similarity
	Site	26	1	Transition state stabilizer By similarity
	Site	156	1	Positions MEP for the nucleophilic attack By similarity
	Site	213	1	Positions MEP for the nucleophilic attack By similarity
	Site	267	1	Transition state stabilizer By similarity
	Site	366	1	Transition state stabilizer By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q3SSN8 [UniParc]. Last modified October 11, 2005. Version 1. Checksum: 2A51DA2EB5BC0930	FASTA	398	42,115
	10 20 30 40 50 60 MPSSKRTAAI IVAAGRGLRA GAGGPKQYRT IGGRTVISRA MEAFCQHPDV FAVQPVLNPD 70 80 90 100 110 120 DLSMFNQAAA QFRYRPPANG GATRQASVRA GLEALAADAP DIVLIHDAAR PFVTPALITR 130 140 150 160 170 180 AIDAADKAGA AVPAIAVTDT IKQVDESGAV NATPDRAKLR IAQTPQAFHF DMILDAHRRA 190 200 210 220 230 240 AREGRDDFTD DAALAEWVGL TVATFEGDAA NMKLTTPEDF VREEARLAAA LGDIRTGTGY 250 260 270 280 290 300 DVHAFGEGDH LMLCGVKVPH NCGFLAHSDG DVGLHALVDA ILGALADGDI GSHFPPSDPQ 310 320 330 340 350 360 WKGAASDKFL KYAVDRVTAR GGRVANLEVT MICQQPKIGP LRDQMRARIA DITGVAISRI 370 380 390 AVKATTSERL GFTGREEGIA ATASATIRLP WNDKGRDT

References

[1]

"Genome sequence of the chemolithoautotrophic nitrite-oxidizing bacterium Nitrobacter winogradskyi Nb-255." Starkenburg S.R., Chain P.S.G., Sayavedra-Soto L.A., Hauser L., Land M.L., Larimer F.W., Malfatti S.A., Klotz M.G., Bottomley P.J., Arp D.J., Hickey W.J. Appl. Environ. Microbiol. 72:2050-2063(2006) [PubMed: 16517654] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: Nb-255 / ATCC 25391.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP000115 Genomic DNA. Translation: ABA04703.1.
RefSeq	YP_318055.1. NC_007406.1.
3D structure databases
HSSP	HSSP built from PDB template 1H47 based on UniProtKB P62617.
ProteinModelPortal	Q3SSN8.
SMR	Q3SSN8. Positions 234-387.
ModBase	Search...
Protein-protein interaction databases
STRING	Q3SSN8.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	3677184.
GenomeReviews	Gene locus Nwi_1442 in contig CP000115_GR.
KEGG	nwi:Nwi_1442.
NMPDR	fig|323098.3.peg.1517.
PATRIC	22699564. VBINitWin102302_1613.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG1211.
HOGENOM	HBG672839.
OMA	IVLIHDA.
PhylomeDB	Q3SSN8.
ProtClustDB	CLSK911224.
Enzyme and pathway databases
BioCyc	NWIN323098:NWI_1442-MONOMER.
Family and domain databases
HAMAP	MF_01520. IspDF. [Tree]
InterPro	IPR023423. IpsF_dom. IPR001228. ISPD_synthase. IPR018294. ISPD_synthase_CS. IPR003526. MECDP_synthase. IPR020555. MECDP_synthase_CS. [Graphical view]
Gene3D	G3DSA:3.30.1330.50. MECDP_synthase_core. 1 hit.
KO	K12506.
Pfam	PF01128. IspD. 1 hit. PF02542. YgbB. 1 hit. [Graphical view]
SUPFAM	SSF69765. YgbB_synth. 1 hit.
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_NITWN

Accession

Primary (citable) accession number: Q3SSN8

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 24, 2007
Last sequence update:	October 11, 2005
Last modified:	January 25, 2012
This is version 46 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program