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Gene |

Product(s) |

Expression|

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Standard Name	hybO
Gene Synonym(s)	ECK2991, b2997, JW2965, yghV, hyb0^[1]^[2]
Product Desc.	hydrogenase 2, small subunit^[2]^[3]; Component of hydrogenase 2^[2]^[3] Hydrogenase 2 [Ni, Fe], small subunit, periplasmic^[4]
Product Synonyms(s)	hydrogenase 2, small subunit^[1], B2997^[2]^[1], YghV^[2]^[1], HybO^[2]^[1] , ECK2991, JW2965, yghV, b2997
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): hybOABCDEFG^[2]
Regulation/Activity
Quick Links
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Notes

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Verified Tat substrate: HybO has a Tat-only (Class I) 37 aa signal peptide (Tullman-Ercek, 2007). Bound HybC is co-exported. HT_Cmplx26_Mem: HyaB+HybO.^[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	hybO
Mnemonic	Hydrogenase 2
Synonyms	ECK2991, b2997, JW2965, yghV, hyb0^[1]^[2]
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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	67.75 minutes	MG1655: 3144283..3143165 <gbrowseImage> name=NC_000913:3143165..3144283 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
BW2952		NC_012759: 3030313..3031431 <gbrowseImage> name=NC_012759:3030313..3031431 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3144917..3143799 <gbrowseImage> name=NC_007779:3143799..3144917 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3242028..3240910 <gbrowseImage> name=NC_010473:3240910..3242028 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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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	3143168	Edman degradation	PMID:9738917
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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)	Reference	Availability
ΔhybO (Keio:JW2965)	deletion	deletion	PMID:16738554	Shigen CGSC10280^[5]
ΔhybO770::kan			PMID:16738554	CGSC:101464
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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
JW2965	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCACTGGAGATAACACCCTCAT Primer 2:CCTTCTCCCCGTGAGTCAGCGTT
5C10	Kohara Phage	Genobase	PMID:3038334
nupG511::Tn10	Linked marker	CAG18472 = CGSC7433^[5]	est. P1 cotransduction: 19% ^[6]
metC162::Tn10	Linked marker	CAG18475 = CGSC7435^[5]	est. P1 cotransduction: 79% ^[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:G7554	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13006	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004114	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945902	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2828	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009834	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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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	HybO
Synonyms	hydrogenase 2, small subunit^[1], B2997^[2]^[1], YghV^[2]^[1], HybO^[2]^[1] , ECK2991, JW2965, yghV, b2997
Product description	hydrogenase 2, small subunit^[2]^[3]; Component of hydrogenase 2^[2]^[3] Hydrogenase 2 [Ni, Fe], small subunit, periplasmic^[4]
EC number (for enzymes)	1.18.99.1^[1]
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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:0031225	anchored to membrane				C	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	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:0006457	protein folding				P	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	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:0016020	membrane	PMID:16858726	IDA: Inferred from Direct Assay		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:0042597	periplasmic space	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0574	C	Seeded from EcoCyc (v14.0)	complete
	GO:0042597	periplasmic space	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0200	C	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 2	could be indirect
Protein	nadE		PMID:16606699	Experiment(s):EBI-1144528
Protein	pldA		PMID:16606699	Experiment(s):EBI-1144528
Protein	yghZ		PMID:16606699	Experiment(s):EBI-1144528
Protein	yhbO		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	Evidence	Reference/Source
plasma membrane
Inner Membrane	PMID:9738917	EchoLocation:hybO
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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 MTGDNTLIHS HGINRRDFMK LCAALAATMG LSSKAAAEMA ESVTNPQRPP VIWIGAQECT GCTESLLRAT HPTVENLVLE TISLEYHEVL SAAFGHQVEE NKHNALEKYK GQYVLVVDGS IPLKDNGIYC MVAGEPIVDH IRKAAEGAAA IIAIGSCSAW GGVAAAGVNP TGAVSLQEVL PGKTVINIPG CPPNPHNFLA TVAHIITYGK PPKLDDKNRP TFAYGRLIHE HCERRPHFDA GRFAKEFGDE GHREGWCLYH LGCKGPETYG NCSTLQFCDV GGVWPVAIGH PCYGCNEEGI GFHKGIHQLA NVENQTPRSQ KPDVNAKEGG NVSAGAIGLL GGVVGLVAGV SVMAVRELGR QQKKDNADSR GE
Length	372
Mol. Wt	39.65 kDa
pI	6.7 (calculated)
Extinction coefficient	35,410 - 37,035 (calc based on 9 Y, 4 W, and 13 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	1-37	UniProt Manual:Signal Peptides	UniProt:P69741
Domain	59..205	PF01058 NADH ubiquinone oxidoreductase, 20 Kd subunit		PMID:19920124
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<motif_map/>

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

Structures

<beststructure> gene=hybO 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:16130897	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945902	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009834	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P69741	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7554	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13006	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945902	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004114	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2828	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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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	Reference(s)
Protein	E. coli K-12 MG1655	191	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	15	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	105	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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See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)
hybOABCDEFG
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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_000913:3144263..3144303 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

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:b2997 (EcoliWiki Page)	NCBI GEO profiles for hybO
microarray	GenExpDB:b2997 (EcoliWiki Page)	Summary of data for hybO 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 (3144198..3144477) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ04; Well:D2^[7]
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Notes

Accessions Related to hybO Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7554	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2828	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2997
EcoGene	EcoGene:EG13006	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004114	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009834	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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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	S3245	From SHIGELLACYC
E. coli O157	Z4351	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.

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF01058 NADH ubiquinone oxidoreductase, 20 Kd subunit
Superfamily (EcoliWiki Page)	SUPERFAMILY:56770
EcoCyc	EcoCyc:G7554	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13006	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004114	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2828	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009834	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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

↑ ^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)
↑ ^2.00 ^2.01 ^2.02 ^2.03 ^2.04 ^2.05 ^2.06 ^2.07 ^2.08 ^2.09 ^2.10 ^2.11 ^2.12 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^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
↑ ^4.0 ^4.1 ^4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 ^5.2 CGSC: The Coli Genetics Stock Center
↑ ^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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

hybO:On One Page

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Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to hybO Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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