hisD:On One Page

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

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Standard Name

hisD

Gene Synonym(s)

ECK2015, b2020, JW2002[1], JW2002

Product Desc.

HisD[2][3];

Component of HISTDEHYD-CPLX[2]

Histidinol dehydrogenase[4]

Product Synonyms(s)

bifunctional histidinal dehydrogenase and histidinol dehydrogenase[1], B2020[2][1], HisD[2][1] , ECK2015, JW2002, b2020

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): hisLGDCBHAFI[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

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Notes

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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

hisD

Mnemonic

Histidine

Synonyms

ECK2015, b2020, JW2002[1], JW2002

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Notes

Location(s) and DNA Sequence

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

Strain Map location Genome coordinates Genome browsers Sequence links

MG1655

45.03 minutes, 45.03 minutes 

MG1655: 2089121..2090425
<gbrowseImage> name=NC_000913:2089121..2090425 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2021162..2022403
<gbrowseImage> name=NC_012967:2021162..2022403 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1981604..1982908
<gbrowseImage> name=NC_012759:1981604..1982908 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2093234..2094538
<gbrowseImage> name=NC_007779:2093234..2094538 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2180129..2181433
<gbrowseImage> name=NC_010473:2180129..2181433 source=DH10B preset=GeneLocation </gbrowseImage>

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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 Type Strain Genomic Location Evidence Reference Notes

Coding Start (SO:0000323)

MG1655

2089124

Edman degradation

PMID:9298646


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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.

Allele Nt change(s) AA change(s) Phenotype: Type Phenotype: Description Reference Availability Comments

ΔhisD (Keio:JW2002)

deletion

deletion

Auxotrophies

Requires histidine for growth

PMID:16738554

Shigen

CGSC9648[5]

hisD::Tn5KAN-2 (FB20577)

Insertion at nt 551 in Minus orientation

Auxotrophies

Requires Histidine for growth

PMID:15262929

E. coli Genome Project:FB20577

does not contain pKD46

hisD::Tn5KAN-2 (FB20578)

Insertion at nt 551 in Minus orientation

Auxotrophies

Requires Histidine for growth

PMID:15262929

E. coli Genome Project:FB20578

contains pKD46

hisD4758(Stable)

Auxotrophies

Requires Histidine for growth

CGSC:5062

hisD4314

Auxotrophies

Requires Histidine for growth

CGSC:8527

hisD472

Auxotrophies

Requires Histidine for growth

CGSC:17204

ΔhisD789::kan

deletion

deletion

Auxotrophies

Requires Histidine for growth

PMID:16738554

CGSC:101366


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Notes

Genetic Interactions

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Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
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Notes

Genetic Resources

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

Resource Resource Type Source Notes/Reference

JW2002

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAGCTTTAACACAATCATTGA

Primer 2:CCTGCTTGCTCCTTAAGGGCGTT

6D9

Kohara Phage

Genobase

PMID:3038334

zef-3129::Tn10

Linked marker

CAG12099 = CGSC7397[5]

est. P1 cotransduction: 82% [6]
Synonyms:zee-3129::Tn10

zbd-3104::Tn10

Linked marker

CAG12021 = CGSC7344[5]

est. P1 cotransduction: % [6]
Synonyms:zbc-3105::Tn10, zbd-3105::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.

Database Accession Notes

EcoCyc

EcoCyc:EG10447

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10447

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000440

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946531

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0442

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006715

Escherichia coli str. K-12 substr. MG1655

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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

HisD

Synonyms

bifunctional histidinal dehydrogenase and histidinol dehydrogenase[1], B2020[2][1], HisD[2][1] , ECK2015, JW2002, b2020

Product description

HisD[2][3];

Component of HISTDEHYD-CPLX[2]

Histidinol dehydrogenase[4]

EC number (for enzymes)
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Notes

Function

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

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status

GO:0005737

cytoplasm

C

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0000105

histidine biosynthetic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01024

P

Seeded from EcoCyc (v14.0)

complete

GO:0000105

histidine biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001692

P

Seeded from EcoCyc (v14.0)

complete

GO:0000105

histidine biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012131

P

Seeded from EcoCyc (v14.0)

complete

GO:0000105

histidine biosynthetic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0368

P

Seeded from EcoCyc (v14.0)

complete

GO:0004399

histidinol dehydrogenase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01024

F

Seeded from EcoCyc (v14.0)

complete

GO:0004399

histidinol dehydrogenase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001692

F

Seeded from EcoCyc (v14.0)

complete

GO:0004399

histidinol dehydrogenase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012131

F

Seeded from EcoCyc (v14.0)

complete

GO:0004399

histidinol dehydrogenase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:1.1.1.23

F

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012131

F

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0862

F

Seeded from EcoCyc (v14.0)

complete

GO:0046872

metal ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0479

F

Seeded from EcoCyc (v14.0)

complete

GO:0051287

NAD or NADH binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012131

F

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR016161

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

P

Seeded from EcoCyc (v14.0)

complete

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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 Type Partner Notes References Evidence

Protein

Subunits of HISTDEHYD-CPLX

could be indirect

Protein

lacZ

PMID:16606699

Experiment(s):EBI-1141637

Protein

ygaD

PMID:16606699

Experiment(s):EBI-1141637

Protein

metH

PMID:16606699

Experiment(s):EBI-1141637

Protein

ahpC

PMID:16606699

Experiment(s):EBI-1141637

Protein

hipA

PMID:16606699

Experiment(s):EBI-1141637
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Notes

Localization

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

Compartment Description Evidence Reference/Source Notes
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Notes

Structure and Physical Properties

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

Name
Sequence

at EcoCyc 

MSFNTIIDWN SCTAEQQRQL LMRPAISASE SITRTVNDIL DNVKARGDEA LREYSAKFDK
TTVTALKVSA EEIAAASERL SDELKQAMAV AVKNIETFHT AQKLPPVDVE TQPGVRCQQV
TRPVASVGLY IPGGSAPLFS TVLMLATPAS IAGCKKVVLC SPPPIADEIL YAAQLCGVQD
VFNVGGAQAI AALAFGTESV PKVDKIFGPG NAFVTEAKRQ VSQRLDGAAI DMPAGPSEVL
VIADSGATPD FVASDLLSQA EHGPDSQVIL LTPAADMARR VAEAVERQLA ELPRAETARQ
ALNASRLIVT KDLAQCVEIS NQYGPEHLII QTRNARELVD SITSAGSVFL GDWSPESAGD
YASGTNHVLP TYGYTATCSS LGLADFQKRM TVQELSKEGF SALASTIETL AAAERLTAHK
NAVTLRVNAL KEQA
Length

434

Mol. Wt

46.109 kDa

pI

4.9 (calculated)

Extinction coefficient

21,430 - 22,305 (calc based on 7 Y, 2 W, and 7 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.

Type Residues Description Notes References

Initiator Methionine

1

Removed

UniProt:P06988

Domain

17..428

PF00815 Histidinol dehydrogenase

PMID:19920124

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

Structures

<beststructure> gene=hisD taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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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 type Source Notes/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.

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16129961

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946531

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006715

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P06988

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10447

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10447

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946531

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000440

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0442

Escherichia coli str. K-12 substr. MG1655

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Notes

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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

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)

Protein

E. coli K-12 MC4100

4.94E+02

molecules/cell

  • Medium: median data from rich and minimal media
  • Temperature (°C): 37
  • Doubling time (min): Growth Rate(min):
  • Growth phase: other:

emPAI

PMID:18304323

Protein

E. coli K-12 EMG2

220

molecules/cell

  • Medium: MOPS glucose minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • Growth phase: Exponential
  • OD: OD600 = 0.2 to 0.25
  • other: aerated

Quantitative protein sequencing

Spot ID: Ml26

PMID: 9298646

Protein

E. coli K-12 MG1655

1430

molecules/cell/generation

  • Medium: MOPS Complete
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

1353

molecules/cell/generation

  • Medium: MOPS Minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

1165

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

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Notes

Transcription and Transcriptional Regulation

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<protect>

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

Transcription unit(s)

hisLGDCBHAFI

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Figure courtesy of RegulonDB

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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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<protect><gbrowseImage> name=NC_000913:2089101..2089141 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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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

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

Allele Name Mutation Phenotype Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b2020 (EcoliWiki Page)

NCBI GEO profiles for hisD

microarray

GenExpDB:b2020 (EcoliWiki Page)

Summary of data for hisD 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 Name Resource Type Description Source Notes
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Notes

Accessions Related to hisD Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10447

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0442

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2020

EcoGene

EcoGene:EG10447

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000440

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006715

Escherichia coli str. K-12 substr. MG1655

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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.

Organism Homologs (Statistics) Comments

Arabidopsis thaliana

  • AT5G63890 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Oryza gramene

  • Q5NAY4 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YCL030C (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPBC17113 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00037599001 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000043204 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

HISD

From SHIGELLACYC

E. coli O157

HISD

From ECOO157CYC

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Do-It-Yourself Web Tools

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Notes

Families

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Database Accession Notes

Pfam (EcoliWiki Page)

PF00815 Histidinol dehydrogenase

Panther (EcoliWiki Page)

PTHR21256:SF2

Superfamily (EcoliWiki Page)

SUPERFAMILY:53720

EcoCyc

EcoCyc:EG10447

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10447

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000440

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0442

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006715

Escherichia coli str. K-12 substr. MG1655

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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. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 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 5.2 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).

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