Q1CU78 (ISPDF_HELPH) 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:	HPAG1_0427

Organism

Helicobacter pylori (strain HPAG1) [Complete proteome] [HAMAP]

Taxonomic identifier

357544 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Epsilonproteobacteria › Campylobacterales › Helicobacteraceae › Helicobacter

Protein attributes

Sequence length	406 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 – 406	406	Bifunctional enzyme IspD/IspF HAMAP MF_01520		PRO_0000296747
Regions
	Region	1 – 247	247	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase HAMAP MF_01520
	Region	248 – 406	159	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase HAMAP MF_01520
Sites
	Metal binding	254	1	Divalent metal cation By similarity
	Metal binding	256	1	Divalent metal cation By similarity
	Metal binding	288	1	Divalent metal cation By similarity
	Site	48	1	Transition state stabilizer By similarity
	Site	55	1	Transition state stabilizer By similarity
	Site	175	1	Positions MEP for the nucleophilic attack By similarity
	Site	227	1	Positions MEP for the nucleophilic attack By similarity
	Site	280	1	Transition state stabilizer By similarity
	Site	379	1	Transition state stabilizer By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q1CU78 [UniParc]. Last modified July 11, 2006. Version 1. Checksum: F798BABA3C78313E	FASTA	406	45,590
	10 20 30 40 50 60 MSLIRVNGEA FKFSLESLEE DPFETKETLE ILVKQTSVVL LAAGESRRFS QTIKKQWLRS 70 80 90 100 110 120 NHTPLWLSVY ESFKEALDFK EIVLVVSELD YIYIQRHYPE IKLIKGGASR QESVRNALKI 130 140 150 160 170 180 IDSAYTLTSD VARGLANMET LKSLFLTLQQ TSHYCIAPYL PCYDTAIYYN EALDREAIKL 190 200 210 220 230 240 IQTPQLSHTK TLQSALNQGD FKDESSAILQ AFPNSVSYIE GSKDLHKLTT SDDLKHFAFF 250 260 270 280 290 300 FNPAKDTFIG MGFDTHAFIK DKPMVLGGVV LDCEFGLKAH SDGDALLHAV IDAVLGAIKG 310 320 330 340 350 360 GDIGEWFPDN DPKYKNASSK ELLKIVLDFS QSIGFELFEM GATIFSEIPK ITPYKPAILE 370 380 390 400 NLSQLLGLEK SQISLKATTM EKMGFIGKQE GLLVQAHVSM RYKQKL

References

[1]

"The complete genome sequence of a chronic atrophic gastritis Helicobacter pylori strain: evolution during disease progression." Oh J.D., Kling-Baeckhed H., Giannakis M., Xu J., Fulton R.S., Fulton L.A., Cordum H.S., Wang C., Elliott G., Edwards J., Mardis E.R., Engstrand L.G., Gordon J.I. Proc. Natl. Acad. Sci. U.S.A. 103:9999-10004(2006) [PubMed: 16788065] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: HPAG1.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP000241 Genomic DNA. Translation: ABF84494.1.
RefSeq	YP_627168.1. NC_008086.1.
3D structure databases
ProteinModelPortal	Q1CU78.
ModBase	Search...
Protein-protein interaction databases
STRING	Q1CU78.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	4098804.
GenomeReviews	Gene locus HPAG1_0427 in contig CP000241_GR.
KEGG	hpa:HPAG1_0427.
PATRIC	20602195. VBIHelPyl56048_0446.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG1211.
HOGENOM	HBG672839.
OMA	GGDIGEW.
ProtClustDB	PRK09382.
Enzyme and pathway databases
BioCyc	HPYL357544:HPAG1_0427-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_HELPH

Accession

Primary (citable) accession number: Q1CU78

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 24, 2007
Last sequence update:	July 11, 2006
Last modified:	January 25, 2012
This is version 41 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program