4-hydroxy-3-methylbut-2-enyl diphosphate reductase

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Reviewed, UniProtKB/Swiss-Prot P62623 (ISPH_ECOLI)

Last modified February 9, 2010. Version 54. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

Recommended name:
4-hydroxy-3-methylbut-2-enyl diphosphate reductase
EC=1.17.1.2

Gene names

Name:	ispH
Synonyms:	lytB, yaaE
Ordered Locus Names:	b0029, JW0027

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

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Protein attributes

Sequence length	316 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Function	Converts 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate into isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Is also involved in penicillin tolerance and control of the stringent response. Seems to directly or indirectly interact with relA to maintain it in an inactive form during normal growth. HAMAP MF_00191
Catalytic activity	Isopentenyl diphosphate + NAD(P)⁺ + H₂O = (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + NAD(P)H. Ref.9 Ref.11 Dimethylallyl diphosphate + NAD(P)⁺ + H₂O = (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + NAD(P)H. Ref.9 Ref.11
Cofactor	Binds 1 3Fe-4S cluster per subunit. HAMAP MF_00191
Enzyme regulation	Addition of Ca²⁺, Mg²⁺, Mn²⁺, Ni²⁺, Co²⁺ or Fe²⁺ decreases the activity. Addition of Zn²⁺ results in complete loss of activity. Ref.12
Pathway	Isoprenoid biosynthesis; dimethylallyl diphosphate biosynthesis; dimethylallyl diphosphate from (2E)-4-hydroxy-3-methylbutenyl diphosphate: step 1/1. Ref.7 Ref.8 Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 6/6. Ref.7 Ref.8
Subunit structure	Homodimer. Ref.10
Miscellaneous	Ref.10 authors have reported the presence of a 4Fe-4S iron-sulfur cluster. It could be due to experimental conditions. HAMAP MF_00191
Sequence similarities	Belongs to the ispH family.
Biophysicochemical properties	Kinetic parameters: K_M=30 µM for 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate Ref.12 pH dependence: Optimum pH is 7.0.

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Ontologies

Keywords
Biological process	Isoprene biosynthesis
Ligand	3Fe-4S Iron Iron-sulfur Metal-binding NADP
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway Inferred from electronic annotation. Source: HAMAP oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW response to antibiotic Ref.11 Inferred from direct assay. Source: UniProtKB terpenoid biosynthetic process Inferred from electronic annotation. Source: HAMAP ubiquinone biosynthetic process Ref.11 Inferred from direct assay. Source: UniProtKB
Molecular function	3 iron, 4 sulfur cluster binding Inferred from electronic annotation. Source: UniProtKB-KW 4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase activity Inferred from electronic annotation. Source: HAMAP hydroxymethylbutenyl pyrophosphate reductase activity Ref.11 Inferred from direct assay. Source: UniProtKB iron ion binding Inferred from electronic annotation. Source: UniProtKB-KW protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

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Binary interactions

With	Entry	#Exp.	IntAct	Notes
dnaK	P0A6Y8	1	EBI-554022,EBI-542092

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 316

316

4-hydroxy-3-methylbut-2-enyl diphosphate reductase HAMAP MF_00191

PRO_0000128812

Experimental info

Mutagenesis

C → S: Loss of activity. Ref.12

Mutagenesis

C → S: Loss of activity. Ref.12

Mutagenesis

197

C → S: Loss of activity. Ref.12

Secondary structure

316

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

P62623-1 [UniParc].

Last modified July 19, 2004. Version 1.
Checksum: 0E7B378BD49AB771
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FASTA

316

34,775

        10         20         30         40         50         60 
MQILLANPRG FCAGVDRAIS IVENALAIYG APIYVRHEVV HNRYVVDSLR ERGAIFIEQI 

        70         80         90        100        110        120 
SEVPDGAILI FSAHGVSQAV RNEAKSRDLT VFDATCPLVT KVHMEVARAS RRGEESILIG 

       130        140        150        160        170        180 
HAGHPEVEGT MGQYSNPEGG MYLVESPDDV WKLTVKNEEK LSFMTQTTLS VDDTSDVIDA 

       190        200        210        220        230        240 
LRKRFPKIVG PRKDDICYAT TNRQEAVRAL AEQAEVVLVV GSKNSSNSNR LAELAQRMGK 

       250        260        270        280        290        300 
RAFLIDDAKD IQEEWVKEVK CVGVTAGASA PDILVQNVVA RLQQLGGGEA IPLEGREENI 

       310 
VFEVPKELRV DIREVD

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Studies on the nonmevalonate terpene biosynthetic pathway: metabolic role of IspH (LytB) protein." Rohdich F., Hecht S., Gaertner K., Adam P., Krieger C., Amslinger S., Arigoni D., Bacher A., Eisenreich W. Proc. Natl. Acad. Sci. U.S.A. 99:1158-1163(2002) [PubMed: 11818558] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CHARACTERIZATION.
[2]	"Nucleotide sequence of the lsp-dapB interval in Escherichia coli." Bouvier J., Stragier P. Nucleic Acids Res. 19:180-180(1991) [PubMed: 2011499] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[3]	"Systematic sequencing of the Escherichia coli genome: analysis of the 0-2.4 min region." Yura T., Mori H., Nagai H., Nagata T., Ishihama A., Fujita N., Isono K., Mizobuchi K., Nakata A. Nucleic Acids Res. 20:3305-3308(1992) [PubMed: 1630901] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12.
[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: 9278503] [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: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[6]	"Identification of the Escherichia coli lytB gene, which is involved in penicillin tolerance and control of the stringent response." Gustafson C.E., Kaul S., Ishiguro E.E. J. Bacteriol. 175:1203-1205(1993) [PubMed: 8432714] [Abstract] Cited for: IDENTIFICATION.
[7]	"LytB, a novel gene of the 2-C-methyl-D-erythritol 4-phosphate pathway of isoprenoid biosynthesis in Escherichia coli." Altincicek B., Kollas A.-K., Eberl M., Wiesner J., Sanderbrand S., Hintz M., Beck E., Jomaa H. FEBS Lett. 499:37-40(2001) [PubMed: 11418107] [Abstract] Cited for: PATHWAY. Strain: K12 / ATCC 23716 / DSM 498.
[8]	"The lytB gene of Escherichia coli is essential and specifies a product needed for isoprenoid biosynthesis." McAteer S., Coulson A., McLennan N., Masters M. J. Bacteriol. 183:7403-7407(2001) [PubMed: 11717301] [Abstract] Cited for: PATHWAY.
[9]	"Biosynthesis of terpenes: studies on 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase." Adam P., Hecht S., Eisenreich W., Kaiser J., Graewert T., Arigoni D., Bacher A., Rohdich F. Proc. Natl. Acad. Sci. U.S.A. 99:12108-12113(2002) [PubMed: 12198182] [Abstract] Cited for: CATALYTIC ACTIVITY.
[10]	"Isoprenoid biosynthesis via the methylerythritol phosphate pathway: the (E)-4-hydroxy-3-methylbut-2-enyl diphosphate reductase (LytB/IspH) from Escherichia coli is a [4Fe-4S] protein." Wolff M., Seemann M., Tse Sum Bui B., Frapart Y., Tritsch D., Garcia Estrabot A., Rodriguez-Concepcion M., Boronat A., Marquet A., Rohmer M. FEBS Lett. 541:115-120(2003) [PubMed: 12706830] [Abstract] Cited for: IRON-SULFUR CLUSTER, SUBUNIT.
[11]	"The deoxyxylulose phosphate pathway of isoprenoid biosynthesis: studies on the mechanisms of the reactions catalyzed by IspG and IspH protein." Rohdich F., Zepeck F., Adam P., Hecht S., Kaiser J., Laupitz R., Graewert T., Amslinger S., Eisenreich W., Bacher A., Arigoni D. Proc. Natl. Acad. Sci. U.S.A. 100:1586-1591(2003) [PubMed: 12571359] [Abstract] Cited for: CATALYTIC ACTIVITY.
[12]	"IspH protein of Escherichia coli: studies on iron-sulfur cluster implementation and catalysis." Graewert T., Kaiser J., Zepeck F., Laupitz R., Hecht S., Amslinger S., Schramek N., Schleicher E., Weber S., Haslbeck M., Buchner J., Rieder C., Arigoni D., Bacher A., Eisenreich W., Rohdich F. J. Am. Chem. Soc. 126:12847-12855(2004) [PubMed: 15469281] [Abstract] Cited for: PRESENCE OF A 3FE-4S IRON-SULFUR CLUSTER, ENZYME REGULATION, KINETIC PARAMETERS, MUTAGENESIS OF CYS-12; CYS-96 AND CYS-197.

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Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AY062212 Genomic DNA. Translation: AAL38655.1.
X54945 Genomic DNA. Translation: CAA38707.1.
U00096 Genomic DNA. Translation: AAC73140.1.
AP009048 Genomic DNA. Translation: BAB96598.1.

PIR

JE0403.

RefSeq

AP_000693.1.
NP_414570.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3F7T	X-ray	1.80	A/B	1-316	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

P62623. 5 interactions.

STRING

P62623.

Proteomic databases

PRIDE

P62623.

Genome annotation databases

GeneID

944777.

GenomeReviews

Gene locus JW0027 in contig AP009048_GR.
Gene locus b0029 in contig U00096_GR.

KEGG

ecj:JW0027.
eco:b0029.

Organism-specific databases

EchoBASE

EB1073.

EcoGene

EG11081. ispH.

CMR

Search...

Phylogenomic databases

eggNOG

COG0761.

HOGENOM

HBG335228.

OMA

HMQVARA.

Enzyme and pathway databases

BioCyc

EcoCyc:EG11081-MONOMER.
ECOL168927:B0029-MONOMER.
MetaCyc:EG11081-MONOMER.

BRENDA

1.17.1.2. 246.

Gene expression databases

Genevestigator

P62623.

Family and domain databases

HAMAP

MF_00191. IspH.
[Tree]

InterPro

IPR003451. LytB.
[Graphical view]

Pfam

PF02401. LYTB. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00216. ispH_lytB. 1 hit.

ProtoNet

Search...

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Entry information

Entry name

ISPH_ECOLI

Accession

Primary (citable) accession number: P62623
Secondary accession number(s): P22565

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 19, 2004
Last sequence update:	July 19, 2004
Last modified:	February 9, 2010
This is version 54 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

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

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Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Entry information

Relevant documents