hyaA: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

hyaA

Gene Synonym(s)

ECK0963, b0972, JW0954[1], JW0954

Product Desc.

hydrogenase 1, small subunit[2][3];

Component of hydrogenase 1[2][3]

Hydrogenase 1 small subunit [NiFe], periplasmic[4]

Product Synonyms(s)

hydrogenase 1, small subunit[1], B0972[2][1], HyaA[2][1] , ECK0963, JW0954, b0972

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): hyaABCDEF[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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Verified Tat substrate: HyaA has a Tat-only (Class I) 45 aa signal peptide (Tullman-Ercek, 2007). Bound HyaB is co-exported. Repressed during biofilm formation.[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

hyaA

Mnemonic

Hydrogenase 1

Synonyms

ECK0963, b0972, JW0954[1], JW0954

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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

22.23 minutes 

MG1655: 1031362..1032480
<gbrowseImage> name=NC_000913:1031362..1032480 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1049230..1050348
<gbrowseImage> name=NC_012967:1049230..1050348 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 934330..935448
<gbrowseImage> name=NC_012759:934330..935448 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1032561..1033679
<gbrowseImage> name=NC_007779:1032561..1033679 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1085290..1086408
<gbrowseImage> name=NC_010473:1085290..1086408 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

1031497

Edman degradation

PMID:2180913


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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

ΔhyaA (Keio:JW0954)

deletion

deletion

PMID:16738554

Shigen
CGSC8950[5]

hyaA::Tn5KAN-2 (FB20074)

Insertion at nt 834 in Plus orientation

PMID:15262929

E. coli Genome Project:FB20074

does not contain pKD46

ΔhyaA786::kan

PMID:16738554

CGSC:101444


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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

JW0954

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAATAACGAGGAAACATTTTA

Primer 2:CCTGCCTGTTTATCCTCATTGCC

4H9

Kohara Phage

Genobase

PMID:3038334

zcb-3059::Tn10

Linked marker

CAG12094 = CGSC7358[5]

est. P1 cotransduction: 32% [6]

zcc-282::Tn10

Linked marker

CAG18466 = CGSC7359[5]

est. P1 cotransduction: 29% [6]

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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:EG10468

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10468

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000461

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945579

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0463

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003286

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

HyaA

Synonyms

hydrogenase 1, small subunit[1], B0972[2][1], HyaA[2][1] , ECK0963, JW0954, b0972

Product description

hydrogenase 1, small subunit[2][3];

Component of hydrogenase 1[2][3]

Hydrogenase 1 small subunit [NiFe], periplasmic[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:0005506

iron ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0408

F

Seeded from EcoCyc (v14.0)

complete

GO:0005886

plasma membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0997

C

Seeded from EcoCyc (v14.0)

complete

GO:0005886

plasma membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-1003

C

Seeded from EcoCyc (v14.0)

complete

GO:0008137

NADH dehydrogenase (ubiquinone) activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006137

F

Seeded from EcoCyc (v14.0)

complete

GO:0008901

ferredoxin hydrogenase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001821

F

Seeded from EcoCyc (v14.0)

complete

GO:0009375

ferredoxin hydrogenase complex

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001821

C

Seeded from EcoCyc (v14.0)

complete

GO:0016020

membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0472

C

Seeded from EcoCyc (v14.0)

complete

GO:0016021

integral to membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0812

C

Seeded from EcoCyc (v14.0)

complete

GO:0016491

oxidoreductase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

F

Seeded from EcoCyc (v14.0)

complete

GO:0033748

hydrogenase (acceptor) activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:1.12.99.6

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:0048038

quinone binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006137

F

Seeded from EcoCyc (v14.0)

complete

GO:0051536

iron-sulfur cluster binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001821

F

Seeded from EcoCyc (v14.0)

complete

GO:0051536

iron-sulfur cluster binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0411

F

Seeded from EcoCyc (v14.0)

complete

GO:0051538

3 iron, 4 sulfur cluster binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0003

F

Seeded from EcoCyc (v14.0)

complete

GO:0051539

4 iron, 4 sulfur cluster binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006137

F

Seeded from EcoCyc (v14.0)

complete

GO:0051539

4 iron, 4 sulfur cluster binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0004

F

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001821

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006137

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 hydrogenase 1

could be indirect

Protein

slyD

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplB

PMID:19402753

LCMS(ID Probability):99.6

Protein

groS

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):25.333122

Protein

skp

PMID:19402753

LCMS(ID Probability):99.6

Protein

hyaB

PMID:19402753

MALDI(Z-score):27.571862

Protein

miaB

PMID:19402753

LCMS(ID Probability):99.6

Protein

secA

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):9.420503

Protein

rplX

PMID:19402753

LCMS(ID Probability):99.6

Protein

tufB

PMID:19402753

MALDI(Z-score):18.982033

Protein

dnaJ

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):10.058790

Protein

rplW

PMID:19402753

LCMS(ID Probability):99.6

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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

plasma membrane

C-terminus localized in the cytoplasm with 2 predicted transmembrane domains

Daley et al. (2005) [7]

membrane

Inner Membrane

PMID:2180913, PMID:1856178, PMID:9738917

EchoLocation:hyaA


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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 

MNNEETFYQA MRRQGVTRRS FLKYCSLAAT SLGLGAGMAP KIAWALENKP RIPVVWIHGL
ECTCCTESFI RSAHPLAKDV ILSLISLDYD DTLMAAAGTQ AEEVFEDIIT QYNGKYILAV
EGNPPLGEQG MFCISSGRPF IEKLKRAAAG ASAIIAWGTC ASWGCVQAAR PNPTQATPID
KVITDKPIIK VPGCPPIPDV MSAIITYMVT FDRLPDVDRM GRPLMFYGQR IHDKCYRRAH
FDAGEFVQSW DDDAARKGYC LYKMGCKGPT TYNACSSTRW NDGVSFPIQS GHGCLGCAEN
GFWDRGSFYS RVVDIPQMGT HSTADTVGLT ALGVVAAAVG VHAVASAVDQ RRRHNQQPTE
TEHQPGNEDK QA
Length

372

Mol. Wt

40.68 kDa

pI

7.1 (calculated)

Extinction coefficient

56,380 - 58,130 (calc based on 12 Y, 7 W, and 14 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

motif

1-45

UniProt Manual:Signal Peptides

UniProt:P69739

Domain

62..208

PF01058 NADH ubiquinone oxidoreductase, 20 Kd subunit

PMID:19920124

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<motif_map/>

tmhmm.php?gene=hyaA&show=pic&.jpg
Click the image to view raw output from TMHMM.

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

Structures

<beststructure> gene=hyaA 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:16128938

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945579

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003286

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P69739

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10468

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10468

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945579

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000461

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0463

Escherichia coli str. K-12 substr. MG1655

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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

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

Protein

E. coli K-12 MG1655

1a

molecules/cell/generation

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

Ribosome Profiling

Low confidence in the sequencing data set.

PMID: 24766808

Protein

E. coli K-12 MG1655

7

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

0a

molecules/cell/generation

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

Ribosome Profiling

Low confidence in the sequencing data set.

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)

hyaABCDEF

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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_000913:1031342..1031382 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:b0972 (EcoliWiki Page)

NCBI GEO profiles for hyaA

microarray

GenExpDB:b0972 (EcoliWiki Page)

Summary of data for hyaA 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

GFP Fusion

Intergenic region (1030841..1031434) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ08; Well:A6[8]

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Notes

Accessions Related to hyaA Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10468

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0463

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0972

EcoGene

EcoGene:EG10468

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000461

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003286

Escherichia coli str. K-12 substr. MG1655

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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.

Organism Homologs (Statistics) Comments

Shigella flexneri

HYAA

From SHIGELLACYC

E. coli O157

HYAA

From ECOO157CYC

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Do-It-Yourself Web Tools

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Notes

Families

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

Database Accession Notes

Pfam (EcoliWiki Page)

PF01058 NADH ubiquinone oxidoreductase, 20 Kd subunit

Superfamily (EcoliWiki Page)

SUPERFAMILY:56770

EcoCyc

EcoCyc:EG10468

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10468

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000461

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0463

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003286

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 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 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 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).
  7. ↑ Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed
  8. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

Categories

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