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ispH:On One Page

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Quickview | Gene | Product(s) | Expression| Evolution | References |

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Standard Name

ispH

Gene Synonym(s)

ECK0030, b0029, JW0027, lytB, yaaE[1]

Product Desc.

1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase[2][3]

Last, branched, step of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) synthesis from 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate; alternative nonmevalonate (DXP) pathway for terpenoid biosynthesis[4]

Product Synonyms(s)

1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase, 4Fe-4S protein[1], B0029[2][1], YaaE[2][1], LytB[2][1], IspH[2][1]

Function from GO

Molecular Function

Biological Process

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): lsp-fkpB-ispH[2], ribF-ileS-lspA-fkpB-ispH[2], ileS-lsp, ileS-lspA-lytB, ribF-ileS-lspA-slpA-lytB

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(ispH)    Textpresso(ispH)

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Notes

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The ispH gene is essential. IspH contains a [4Fe-4S] cluster. IspH affects penicillin tolerance and the stringent response.[4]



Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

ispH

Mnemonic

Isoprenoid

Synonyms

ECK0030, b0029, JW0027, lytB, yaaE[1]

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Notes

Location(s) and DNA Sequence

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See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

0.57 minutes 

MG1655: 26277..27227
gbrowse_img.php?coord=26277..27227&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 30349..31299
gbrowse_img.php?coord=30349..31299&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 26277..27227
gbrowse_img.php?coord=26277..27227&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 26277..27227
gbrowse_img.php?coord=26277..27227&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

BW2952

NC_012759: 26277..27227
gbrowse_img.php?coord=26277..27227&genome=BW2952&name=NC_012759&trackset=0&width=300&.png

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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature typeLocationDescription
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

AlleleNt change(s)AA change(s)Phenotype: TypePhenotype: DescriptionReferenceAvailabilityComments

ispHC197S

C197S

Loss of activity

seeded from UniProt:P62623

ispHC12S

C12S

Loss of activity

seeded from UniProt:P62623

ispHC96S

C96S

Loss of activity

seeded from UniProt:P62623

ΔispH3::kan

CGSC:84187


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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

ResourceResource TypeSourceNotes/Reference

JW0027

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCCAGATCCTGTTGGCCAACCC

Primer 2:CCATCGACTTCACGAATATCGAC

thrA34::Tn10

Linked marker

CAG18442 = CGSC7320[5]

est. P1 cotransduction: 37% [6]
Synonyms:thr-34::Tn10

carB96::Tn10

Linked marker

CAG12093 = CGSC7322[5]

est. P1 cotransduction: 81% [6]
Synonyms:car-96::Tn10

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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG11081

EchoBASE (EcoliWiki Page)

EchoBASE:EB1073

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0029

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0033

EcoGene (EcoliWiki Page)

EcoGene:EG11081

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:LYTB

CGSC (EcoliWiki Page)

CGSC:34696

ASAP (EcoliWikiPage)

ASAP:ABE-0000103


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Notes

Links

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Product(s)

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Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

IspH

Synonyms

1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase, 4Fe-4S protein[1], B0029[2][1], YaaE[2][1], LytB[2][1], IspH[2][1]

Product description

1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase[2][3]

Last, branched, step of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) synthesis from 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate; alternative nonmevalonate (DXP) pathway for terpenoid biosynthesis[4]

EC number (for enzymes)
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Notes

Function

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Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

QualifierGO IDGO term nameReference(s)Evidence Codewith/fromAspectNotesStatus

GO:0005515

protein binding

PMID:16606699

IPI: Inferred from Physical Interaction

UniProtKB:P0A6Y8

F

Seeded from EcoCyc [7]

complete

GO:0006744

ubiquinone biosynthetic process

PMID:12571359

IDA: Inferred from Direct Assay

P

Seeded from EcoCyc [7]

complete

GO:0042380

hydroxymethylbutenyl pyrophosphate reductase activity

PMID:12571359

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc [7]

complete

GO:0046677

response to antibiotic

PMID:12571359

IDA: Inferred from Direct Assay

P

Seeded from EcoCyc [7]

complete

GO:0005506

iron ion binding

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0408

F

Seeded from EcoCyc [7]

complete

GO:0008299

isoprenoid biosynthetic process

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0414

P

Seeded from EcoCyc [7]

complete

GO:0016114

terpenoid biosynthetic process

GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00191

P

Seeded from EcoCyc [7]

complete

GO:0019288

isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway

GO_REF:0000002
GO_REF:0000020

IEA: Inferred from Electronic Annotation

InterPro:IPR003451
HAMAP:MF_00191

P

Seeded from EcoCyc 12.5 [8]

complete

GO:0046872

metal ion binding

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0479

F

Seeded from EcoCyc [7]

complete

GO:0051536

iron-sulfur cluster binding

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0411

F

Seeded from EcoCyc [7]

complete

GO:0051538

3 iron, 4 sulfur cluster binding

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0003

F

Seeded from EcoCyc [7]

complete

GO:0051745

4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase activity

GO_REF:0000003
GO_REF:0000020

IEA: Inferred from Electronic Annotation

EC:1.17.1.2
HAMAP:MF_00191

F

Seeded from EcoCyc 12.5 [8]

complete

GO:0005737

cytoplasm

C

Seeded from EcoCyc 11.1[3].

required fields missing

GO:0016491

oxidoreductase activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

F

Seeded from EcoCyc [7]

complete

GO:0055114

oxidation reduction

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

P

Seeded from EcoCyc [7]

complete

GO:0042493

response to drug

P

Seeded from EcoCyc 11.1[3].

required fields missing

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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner TypePartnerNotesReferencesEvidence

Protein

dnaK

PMID:16606699

Experiment(s):EBI-1135373

Protein

groL

PMID:15690043

Experiment(s):EBI-892784

Protein

rplD

PMID:15690043

Experiment(s):EBI-892784

Protein

rplL

PMID:15690043

Experiment(s):EBI-892784

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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

CompartmentDescriptionEvidenceSourceNotes
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Notes

Structure and Physical Properties

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Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Sequence

at EcoCyc 

MQILLANPRG FCAGVDRAIS IVENALAIYG APIYVRHEVV HNRYVVDSLR ERGAIFIEQI
SEVPDGAILI FSAHGVSQAV RNEAKSRDLT VFDATCPLVT KVHMEVARAS RRGEESILIG
HAGHPEVEGT MGQYSNPEGG MYLVESPDDV WKLTVKNEEK LSFMTQTTLS VDDTSDVIDA
LRKRFPKIVG PRKDDICYAT TNRQEAVRAL AEQAEVVLVV GSKNSSNSNR LAELAQRMGK
RAFLIDDAKD IQEEWVKEVK CVGVTAGASA PDILVQNVVA RLQQLGGGEA IPLEGREENI
VFEVPKELRV DIREVD
Length

316

Mol. Wt

34.773 kDa

pI

5.1 (calculated)

Extinction coefficient

19,940 - 20,440 (calc based on 6 Y, 2 W, and 4 C residues)

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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

TypeResiduesDescriptionNotesReferences
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Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures
Models

View models at:

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Structure figures

Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource typeSourceNotes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG11081-MONOMER

UniProt (EcoliWiki Page)

UniProt:P62623

PFAM (EcoliWiki Page)

PFAM:PF02401

RefSeq (EcoliWiki Page)

RefSeq:NP_414570


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Notes

Links

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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.


Cellular Levels

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See Help:Cellular levels

MoleculeOrganism or StrainCellular levelUnitsMediumTemperature °COther (e.g. anaerobic)Growth rateAssay usedNotesReference(s)
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Notes

Transcription and Transcriptional Regulation

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See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)

lsp-fkpB-ispH

ribF-ileS-lspA-fkpB-ispH

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Figure courtesy of RegulonDB

Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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gbrowse_img.php?coord=26257..26297&genome=ecoli&name=MG1655&trackset=Gene+DNA_+Protein&width=400&figure=Nterm&.png
This picture shows the sequence around the N-terminus.

Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele NameMutationPhenotypeReference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

TypeReferenceNotes

microarray

GEO Profiles:b0029 (EcoliWiki Page)

NCBI GEO profiles for ispH

microarray

GenExpDB:b0029 (EcoliWiki Page)

Summary of data for ispH from multiple microarray studies

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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource NameResource TypeDescriptionSourceNotes
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Notes

Accessions Related to ispH Expression

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG11081

EchoBASE (EcoliWiki Page)

EchoBASE:EB1073

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0029

EcoGene (EcoliWiki Page)

EcoGene:EG11081


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Notes

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Evolution

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Homologs in Other Organisms

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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

OrganismHomologs (Statistics)Comments

Anopheles gambiae

  • ENSANGP00000000823 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT4G34350 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Oryza gramene

  • Q6AVG6 (score: 1.000; bootstrap: 100%)
  • Q6AVG7 (score: 0.361)
  • Q6AVH0 (score: 0.122)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000002190 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

LYTB

From SHIGELLACYC

E. coli O157

LYTB

From ECOO157CYC

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Do-It-Yourself Web Tools

Notes

Families

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF02401


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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 2.11 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 3.2 3.3 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ 5.0 5.1 CGSC: The Coli Genetics Stock Center
  6. ↑ 6.0 6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).
  7. ↑ 7.00 7.01 7.02 7.03 7.04 7.05 7.06 7.07 7.08 7.09 7.10 7.11 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70
  8. ↑ 8.0 8.1 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7

Categories

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