Q4FM31 (ISPDF_PELUB) 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:	SAR11_0945

Organism

Pelagibacter ubique (strain HTCC1062) [Complete proteome] [HAMAP]

Taxonomic identifier

335992 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Alphaproteobacteria › Rickettsiales › SAR11 cluster › Candidatus Pelagibacter

Protein attributes

Sequence length	371 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 – 371	371	Bifunctional enzyme IspD/IspF HAMAP MF_01520		PRO_0000075672
Regions
	Region	1 – 214	214	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase HAMAP MF_01520
	Region	215 – 371	157	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase HAMAP MF_01520
Sites
	Metal binding	221	1	Divalent metal cation By similarity
	Metal binding	223	1	Divalent metal cation By similarity
	Metal binding	255	1	Divalent metal cation By similarity
	Site	15	1	Transition state stabilizer By similarity
	Site	22	1	Transition state stabilizer By similarity
	Site	148	1	Positions MEP for the nucleophilic attack By similarity
	Site	201	1	Positions MEP for the nucleophilic attack By similarity
	Site	247	1	Transition state stabilizer By similarity
	Site	346	1	Transition state stabilizer By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q4FM31 [UniParc]. Last modified August 30, 2005. Version 1. Checksum: F2B8D25AB6985FC8	FASTA	371	41,583
	10 20 30 40 50 60 MNSCFIILAG GESKRFNSNT PKPYTNYKGK PLLLHSIDKA KVFNKFNKIV LVVNKKHKNF 70 80 90 100 110 120 IKKLNIKNIR IITGGKTRAE SAYNALKSIK ENNFKNVIIH DAARPNFSLK LLNKLMNELK 130 140 150 160 170 180 LNDCVIPAIQ TADTVKQKIS NNVKNLKREN IYLIQTPQAF NYKKLFELQN NKSEEVTDDA 190 200 210 220 230 240 NLFVRAGKKI KIIKGETTNN KITINSDIKF NNLIKFGIGF DVHRLVPNKK LYLGGVKIPS 250 260 270 280 290 300 PIGTLGHSDG DPVLHAVTDA ILGACSMGDI GEKFSDKNKK FKNIRSTILL SEIIKQTLKK 310 320 330 340 350 360 GYLINNLDIN IITQKPKIQK YKKQILNCIA KICNISPTQI NIKGKTTEKL GVIGKEKAIA 370 CEVIASVIKN D

References

[1]

"Genome streamlining in a cosmopolitan oceanic bacterium." Giovannoni S.J., Tripp H.J., Givan S., Podar M., Vergin K.L., Baptista D., Bibbs L., Eads J., Richardson T.H., Noordewier M., Rappe M.S., Short J.M., Carrington J.C., Mathur E.J. Science 309:1242-1245(2005) [PubMed: 16109880] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: HTCC1062.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP000084 Genomic DNA. Translation: AAZ21757.1.
RefSeq	YP_266361.1. NC_007205.1.
3D structure databases
ProteinModelPortal	Q4FM31.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	3516956.
GenomeReviews	Gene locus SAR11_0945 in contig CP000084_GR.
KEGG	pub:SAR11_0945.
PATRIC	31991373. VBICanPel5618_0940.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG1211.
HOGENOM	HBG672839.
OMA	IVLIHDA.
PhylomeDB	Q4FM31.
Enzyme and pathway databases
BioCyc	CPEL335992:SAR11_0945-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_PELUB

Accession

Primary (citable) accession number: Q4FM31

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 6, 2005
Last sequence update:	August 30, 2005
Last modified:	January 25, 2012
This is version 45 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program