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P62623 (ISPH_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 89. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length316 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

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. Ref.13 Ref.14 Ref.15

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. Ref.13 Ref.14 Ref.15

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 Ref.13 Ref.14 Ref.15

Miscellaneous

Ref.10 and Ref.15 authors have reported the presence of a 4Fe-4S iron-sulfur cluster. It could be due to experimental conditions.

Sequence similarities

Belongs to the IspH family.

Biophysicochemical properties

Kinetic parameters:

KM=30 µM for 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate Ref.12

pH dependence:

Optimum pH is 7.0.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

dnaKP0A6Y81EBI-554022,EBI-542092

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 3163164-hydroxy-3-methylbut-2-enyl diphosphate reductase HAMAP-Rule MF_00191
PRO_0000128812

Regions

Region225 – 2273Substrate binding HAMAP-Rule MF_00191

Sites

Metal binding121Iron-sulfur (3Fe-4S)
Metal binding961Iron-sulfur (3Fe-4S)
Metal binding1971Iron-sulfur (3Fe-4S)
Binding site411Substrate
Binding site741Substrate
Binding site1241Substrate
Binding site1671Substrate
Binding site2691Substrate

Experimental info

Mutagenesis121C → S: Loss of activity. Ref.12 Ref.14
Mutagenesis411H → N: No effect on the activity. Ref.13
Mutagenesis741H → N: Reduces activity 2-fold. Ref.13
Mutagenesis961C → S: Loss of activity. Ref.12 Ref.14
Mutagenesis991V → A: No effect on the activity. Ref.13
Mutagenesis1241H → N: Reduces activity 100-fold. Ref.13
Mutagenesis1261E → D or Q: Reduces activity 100-fold. Ref.13 Ref.15
Mutagenesis1671T → C: Reduces activity 3-fold. Ref.13 Ref.15
Mutagenesis1671T → S: No effect on the activity. Ref.13 Ref.15
Mutagenesis1971C → S: Loss of activity. Ref.12 Ref.14
Mutagenesis2251S → C: Reduces activity 100-fold. Ref.13
Mutagenesis2271N → Q: Reduces activity 20-fold. Ref.13

Secondary structure

.............................................................. 316
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P62623 [UniParc].

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

FASTA31634,775
        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 

« Hide

References

« Hide '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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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 277:1453-1462(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]"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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [Abstract]
Cited for: PRESENCE OF A 3FE-4S IRON-SULFUR CLUSTER, ENZYME REGULATION, KINETIC PARAMETERS, MUTAGENESIS OF CYS-12; CYS-96 AND CYS-197.
[13]"Structure of active IspH enzyme from Escherichia coli provides mechanistic insights into substrate reduction."
Graewert T., Rohdich F., Span I., Bacher A., Eisenreich W., Eppinger J., Groll M.
Angew. Chem. Int. Ed. Engl. 48:5756-5759(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COMPLEX WITH IRON-SULFUR (3FE-4S), FUNCTION, COFACTOR, SUBUNIT, MUTAGENESIS OF HIS-41; HIS-74; VAL-99; HIS-124; GLU-126; THR-167; SER-225 AND ASN-227.
[14]"Probing the reaction mechanism of IspH protein by x-ray structure analysis."
Graewert T., Span I., Eisenreich W., Rohdich F., Eppinger J., Bacher A., Groll M.
Proc. Natl. Acad. Sci. U.S.A. 107:1077-1081(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) IN COMPLEX WITH SUBSTRATE AND IRON-SULFUR (3FE-4S), FUNCTION, COFACTOR, SUBUNIT, MUTAGENESIS OF CYS-12; CYS-96 AND CYS-197.
[15]"Crystal structures of mutant IspH proteins reveal a rotation of the substrate's hydroxymethyl group during catalysis."
Span I., Graewert T., Bacher A., Eisenreich W., Groll M.
J. Mol. Biol. 416:1-9(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.40 ANGSTROMS) IN COMPLEX WITH SUBSTRATE AND IRON-SULFUR (4FE-4S), FUNCTION, COFACTOR, SUBUNIT, MUTAGENESIS OF GLU-126 AND THR-167.
+Additional computationally mapped references.

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.
PIRJE0403.
RefSeqNP_414570.1. NC_000913.3.
YP_488335.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3F7TX-ray1.80A/B1-316[»]
3KE8X-ray1.70A/B1-316[»]
3KE9X-ray1.90A/B1-316[»]
3KEFX-ray1.70A/B1-316[»]
3KELX-ray1.80A/B1-316[»]
3KEMX-ray2.00A/B1-316[»]
3SZLX-ray1.60A/B1-316[»]
3SZOX-ray1.60A/B1-316[»]
3SZUX-ray1.40A/B1-316[»]
3T0FX-ray1.90A/B1-316[»]
3T0GX-ray2.10A/B1-316[»]
3URKX-ray1.50A/B1-316[»]
3UTCX-ray1.90A/B1-316[»]
3UTDX-ray1.70A/B1-316[»]
3UV3X-ray1.60A/B1-316[»]
3UV6X-ray1.70A/B1-316[»]
3UV7X-ray1.60A/B1-316[»]
3UWMX-ray1.80A/B1-316[»]
3ZGLX-ray1.68A/B1-316[»]
3ZGNX-ray1.95A/B1-316[»]
4EB3X-ray1.90A/B1-315[»]
4H4CX-ray1.80A/B1-315[»]
4H4DX-ray1.35A/B1-315[»]
4H4EX-ray1.70A/B1-315[»]
ProteinModelPortalP62623.
SMRP62623. Positions 1-310.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-35808N.
IntActP62623. 7 interactions.
STRING511145.b0029.

Proteomic databases

PaxDbP62623.
PRIDEP62623.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC73140; AAC73140; b0029.
BAB96598; BAB96598; BAB96598.
GeneID12933923.
944777.
KEGGecj:Y75_p0029.
eco:b0029.
PATRIC32115149. VBIEscCol129921_0026.

Organism-specific databases

EchoBASEEB1073.
EcoGeneEG11081. ispH.

Phylogenomic databases

eggNOGCOG0761.
HOGENOMHOG000220192.
KOK03527.
OMAGKYNHEE.
OrthoDBEOG6HF624.
PhylomeDBP62623.
ProtClustDBPRK01045.

Enzyme and pathway databases

BioCycEcoCyc:EG11081-MONOMER.
ECOL316407:JW0027-MONOMER.
MetaCyc:EG11081-MONOMER.
BRENDA1.17.1.2. 2026.
UniPathwayUPA00056; UER00097.
UPA00059; UER00105.

Gene expression databases

GenevestigatorP62623.

Family and domain databases

HAMAPMF_00191. IspH.
InterProIPR003451. LytB.
[Graphical view]
PfamPF02401. LYTB. 1 hit.
[Graphical view]
TIGRFAMsTIGR00216. ispH_lytB. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP62623.
PROP62623.

Entry information

Entry nameISPH_ECOLI
AccessionPrimary (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: April 16, 2014
This is version 89 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

Escherichia coli

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