P62617 (ISPF_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Short name=MECDP-synthase
Short name=MECPP-synthase
Short name=MECPS
EC=4.6.1.12

Gene names

Name:	ispF
Synonyms:	mecS, ygbB
Ordered Locus Names:	b2746, JW2716

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	159 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Involved in the biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), two major building blocks of isoprenoid compounds. Catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-CPP) with a corresponding release of cytidine 5-monophosphate (CMP). Also converts 4-diphosphocytidyl-2-C-methyl-D-erythritol into 2-C-methyl-D-erythritol 3,4-cyclophosphate and CMP. Ref.2 Ref.8
Catalytic activity	2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol = 2-C-methyl-D-erythritol 2,4-cyclodiphosphate + CMP. Ref.2 Ref.8
Cofactor	Binds 1 divalent metal cation per subunit. Ref.2 Ref.9 Ref.10 Ref.11 Ref.12 Ref.13 Ref.14 Ref.15
Enzyme regulation	Activated by 2C-methyl-D-erythritol 4-phosphate (MEP). Ref.8
Pathway	Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 4/6. HAMAP-Rule MF_00107
Subunit structure	Homotrimer. Ref.9 Ref.10 Ref.11 Ref.12 Ref.14 Ref.15
Disruption phenotype	Cells lacking this gene reveal a filamentous phenotype. Ref.7
Sequence similarities	Belongs to the IspF family.
Biophysicochemical properties	Kinetic parameters: kcat is 61 min(-1) for CDP-ME2P (at pH 7.4). KM=339 µM for CDP-ME2P (at pH 7.4) Ref.8

Ontologies

Keywords
Biological process	Isoprene biosynthesis
Ligand	Metal-binding
Molecular function	Lyase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway Inferred from electronic annotation. Source: UniProtKB-UniPathway terpenoid biosynthetic process Inferred from electronic annotation. Source: HAMAP ubiquinone biosynthetic process Inferred from direct assay Ref.2. Source: EcoCyc
Molecular_function	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity Inferred from direct assay Ref.2. Source: EcoCyc metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
hldD	P67910	1	EBI-562321,EBI-543760

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 159

159

2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase HAMAP-Rule MF_00107

PRO_0000189464

Regions

Region

8 – 10

3

Substrate binding HAMAP-Rule MF_00107

Region

34 – 35

2

Substrate binding HAMAP-Rule MF_00107

Region

38 – 46

9

Substrate binding HAMAP-Rule MF_00107

Region

56 – 58

3

Substrate binding HAMAP-Rule MF_00107

Region

61 – 65

5

Substrate binding HAMAP-Rule MF_00107

Region

100 – 106

7

Substrate binding HAMAP-Rule MF_00107

Region

131 – 135

5

Substrate binding HAMAP-Rule MF_00107

Sites

Metal binding

8

1

Divalent metal cation

Metal binding

10

1

Divalent metal cation

Metal binding

42

1

Divalent metal cation

Binding site

65

1

Substrate; via carbonyl oxygen

Binding site

139

1

Substrate; via carbonyl oxygen

Binding site

142

1

Substrate

Site

34

1

Transition state stabilizer

Site

133

1

Transition state stabilizer

Experimental info

Mutagenesis

8

1

D → S: Loss of activity. Ref.10

Mutagenesis

42

1

H → S: Loss of activity. Ref.10

Mutagenesis

56

1

D → S: 35% decrease of activity. Ref.10

Mutagenesis

142

1

R → M: Little effect on the overall structure; when associated with L-144. Ref.13

Mutagenesis

144

1

E → L: Little effect on the overall structure; when associated with M-142. Ref.13

Secondary structure

1

.

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159

Helix Strand Turn

Details...

Beta strand

1 – 16

16

Beta strand

18 – 20

3

Beta strand

23 – 25

3

Beta strand

28 – 31

4

Beta strand

33 – 35

3

Helix

39 – 51

13

Helix

57 – 60

4

Beta strand

63 – 65

3

Helix

66 – 68

3

Beta strand

69 – 71

3

Helix

73 – 86

14

Beta strand

90 – 99

10

Beta strand

101 – 103

3

Helix

106 – 108

3

Helix

109 – 119

11

Helix

124 – 126

3

Beta strand

127 – 132

6

Helix

138 – 141

4

Beta strand

144 – 155

12

Sequences

	Sequence		Length	Mass (Da)
	P62617 [UniParc]. Last modified July 19, 2004. Version 1. Checksum: 9FC5563623A62939	FASTA	159	16,898
	10 20 30 40 50 60 MRIGHGFDVH AFGGEGPIII GGVRIPYEKG LLAHSDGDVA LHALTDALLG AAALGDIGKL 70 80 90 100 110 120 FPDTDPAFKG ADSRELLREA WRRIQAKGYT LGNVDVTIIA QAPKMLPHIP QMRVFIAEDL 130 140 150 GCHMDDVNVK ATTTEKLGFT GRGEGIACEA VALLIKATK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"A new gene involved in stationary-phase survival located at 59 minutes on the Escherichia coli chromosome." Li C., Ichikawa J.K., Ravetto J.J., Kuo H.-C., Fu J.C., Clarke S. J. Bacteriol. 176:6015-6022(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: MP180.
[2]	"Biosynthesis of terpenoids: YgbB protein converts 4-diphosphocytidyl-2C-methyl-D-erythritol 2-phosphate to 2C-methyl-D-erythritol 2,4-cyclodiphosphate." Herz S., Wungsintaweekul J., Schuhr C.A., Hecht S., Luettgen H., Sagner S., Fellermeier M., Eisenreich W., Zenk M.H., Bacher A., Rohdich F. Proc. Natl. Acad. Sci. U.S.A. 97:2486-2490(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE, FUNCTION AS AN MECDP-SYNTHASE, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, COFACTOR.
[3]	"Studies on the nonmevalonate pathway: formation of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate from 2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol." Takagi M., Kuzuyama T., Kaneda K., Watanabe H., Dairi T., Seto H. Tetrahedron Lett. 41:3395-3398(2000) Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CHARACTERIZATION.
[4]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[5]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[6]	"Enrichment of low abundance proteins of Escherichia coli by hydroxyapatite chromatography." Fountoulakis M., Takacs M.-F., Berndt P., Langen H., Takacs B. Electrophoresis 20:2181-2195(1999) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY. Strain: B / BL21.
[7]	"Characterization of the depletion of 2-C-methyl-D-erythritol-2,4-cyclodiphosphate synthase in Escherichia coli and Bacillus subtilis." Campbell T.L., Brown E.D. J. Bacteriol. 184:5609-5618(2002) [PubMed] [Europe PMC] [Abstract] Cited for: DISRUPTION PHENOTYPE.
[8]	"2C-Methyl-d-erythritol 4-phosphate enhances and sustains cyclodiphosphate synthase IspF activity." Bitok J.K., Meyers C.F. ACS Chem. Biol. 7:1702-1710(2012) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION AS AN MECDP-SYNTHASE, CATALYTIC ACTIVITY, ENZYME REGULATION, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES.
[9]	"Structure and mechanism of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase. An enzyme in the mevalonate-independent isoprenoid biosynthetic pathway." Richard S.B., Ferrer J.-L., Bowman M.E., Lillo A.M., Tetzlaff C.N., Cane D.E., Noel J.P. J. Biol. Chem. 277:8667-8672(2002) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS AND DIVALENT CATIONS, COFACTOR, SUBUNIT. Strain: K12.
[10]	"Structure of 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase involved in mevalonate-independent biosynthesis of isoprenoids." Steinbacher S., Kaiser J., Wungsintaweekul J., Hecht S., Eisenreich W., Gerhardt S., Bacher A., Rohdich F. J. Mol. Biol. 316:79-88(2002) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS AND DIVALENT CATIONS, MUTAGENESIS OF ASP-8; HIS-42 AND ASP-56, COFACTOR, SUBUNIT.
[11]	"Structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase: an essential enzyme for isoprenoid biosynthesis and target for antimicrobial drug development." Kemp L.E., Bond C.S., Hunter W.N. Proc. Natl. Acad. Sci. U.S.A. 99:6591-6596(2002) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS AND DIVALENT CATIONS, COFACTOR, SUBUNIT.
[12]	"The identification of isoprenoids that bind in the intersubunit cavity of Escherichia coli 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase by complementary biophysical methods." Kemp L.E., Alphey M.S., Bond C.S., Ferguson M.A., Hecht S., Bacher A., Eisenreich W., Rohdich F., Hunter W.N. Acta Crystallogr. D 61:45-52(2005) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS AND DIVALENT CATIONS, COFACTOR, SUBUNIT.
[13]	"A double mutation of Escherichia coli2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase disrupts six hydrogen bonds with, yet fails to prevent binding of, an isoprenoid diphosphate." Sgraja T., Kemp L.E., Ramsden N., Hunter W.N. Acta Crystallogr. F 61:625-629(2005) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.11 ANGSTROMS) OF DOUBLE MUTANT MET-142/LEU-144 IN COMPLEX WITH SUBSTRATE ANALOGS AND DIVALENT CATIONS, MUTAGENESIS OF ARG-142 AND GLU-144, COFACTOR.
[14]	"Fluorescent inhibitors for IspF, an enzyme in the non-mevalonate pathway for isoprenoid biosynthesis and a potential target for antimalarial therapy." Crane C.M., Kaiser J., Ramsden N.L., Lauw S., Rohdich F., Eisenreich W., Hunter W.N., Bacher A., Diederich F. Angew. Chem. Int. Ed. 45:1069-1074(2006) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS AND ZINC IONS, COFACTOR, SUBUNIT.
[15]	"A structure-based approach to ligand discovery for 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase: a target for antimicrobial therapy." Ramsden N.L., Buetow L., Dawson A., Kemp L.A., Ulaganathan V., Brenk R., Klebe G., Hunter W.N. J. Med. Chem. 52:2531-2542(2009) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS AND ZINC IONS, COFACTOR, SUBUNIT.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

L07942 Genomic DNA. Translation: AAA79837.1.
AF230738 Genomic DNA. Translation: AAF44656.1.
AB038256 Genomic DNA. Translation: BAA95145.1.
U29579 Genomic DNA. Translation: AAA69256.1.
U00096 Genomic DNA. Translation: AAC75788.1.
AP009048 Genomic DNA. Translation: BAE76823.1.

PIR

I55083.

RefSeq

NP_417226.1. NC_000913.2.
YP_490955.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1GX1	X-ray	1.80	A/B/C	1-159	[»]
1H47	X-ray	2.00	A/B/C/D/E/F	1-159	[»]
1H48	X-ray	2.30	A/B/C/D/E/F	1-159	[»]
1JY8	X-ray	2.50	A	1-159	[»]
1KNJ	X-ray	2.80	A	1-159	[»]
1KNK	X-ray	2.80	A	1-159	[»]
1U3L	X-ray	2.50	A	1-159	[»]
1U3P	X-ray	2.85	A	1-159	[»]
1U40	X-ray	2.80	A	1-159	[»]
1U43	X-ray	3.20	A	1-159	[»]
1YQN	X-ray	3.11	A	1-159	[»]
2AMT	X-ray	2.30	A/B/C/D/E/F	1-159	[»]
2GZL	X-ray	2.50	A	1-157	[»]
3ELC	X-ray	2.50	A/B/C	1-159	[»]
3EOR	X-ray	2.90	A	1-159	[»]
3ERN	X-ray	2.10	A/B/C/D/E/F	1-159	[»]
3ESJ	X-ray	2.70	A	1-159	[»]
3FBA	X-ray	3.10	A	1-159	[»]

ProteinModelPortal

P62617.

SMR

P62617. Positions 1-156.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-48029N.

IntAct

P62617. 6 interactions.

STRING

511145.b2746.

Proteomic databases

PaxDb

P62617.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC75788; AAC75788; b2746.
BAE76823; BAE76823; BAE76823.

GeneID

12933285.
945057.

KEGG

ecj:Y75_p2684.
eco:b2746.

PATRIC

32120898. VBIEscCol129921_2841.

Organism-specific databases

EchoBASE

EB1763.

EcoGene

EG11816. ispF.

Phylogenomic databases

eggNOG

COG0245.

HOGENOM

HOG000239175.

KO

K01770.

OMA

HKFGGEG.

ProtClustDB

PRK00084.

Enzyme and pathway databases

BioCyc

EcoCyc:EG11816-MONOMER.
ECOL316407:JW2716-MONOMER.
MetaCyc:EG11816-MONOMER.

BRENDA

4.6.1.12. 2026.

UniPathway

UPA00056; UER00095.

Gene expression databases

Genevestigator

P62617.

Family and domain databases

Gene3D

3.30.1330.50. 1 hit.

HAMAP

MF_00107. IspF.

InterPro

IPR003526. MECDP_synthase.
IPR020555. MECDP_synthase_CS.
[Graphical view]

Pfam

PF02542. YgbB. 1 hit.
[Graphical view]

SUPFAM

SSF69765. YgbB_synth. 1 hit.

TIGRFAMs

TIGR00151. ispF. 1 hit.

PROSITE

PS01350. ISPF. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

BindingDB

P62617.

EvolutionaryTrace

P62617.

Entry information

Entry name

ISPF_ECOLI

Accession

Primary (citable) accession number: P62617
Secondary accession number(s): P36663, Q2MA83

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 19, 2004
Last sequence update:	July 19, 2004
Last modified:	May 1, 2013
This is version 97 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program