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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

References |

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Standard Name	hycE
Gene Synonym(s)	ECK2716, b2721, JW2691, hevE^[1], hevE
Product Desc.	hydrogenase 3, large subunit^[2]^[3]; Component of hydrogenase 3^[2]^[3]; formate hydrogenlyase complex^[2]^[3] Hydrogenase 3 large subunit, [NiFe] cluster; heterodimer^[4]
Product Synonyms(s)	hydrogenase 3, large subunit^[1], B2721^[2]^[1], HevE^[2]^[1], HycE^[2]^[1] , ECK2716, hevE, JW2691, b2721
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): hycABCDEFGHI^[2], OP00208
Regulation/Activity
Quick Links
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Notes

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FhlA regulon. Hydrogenase 3 is part of the formate hydrogenlyase complex. Residues 538-569 are removed to form mature protein. Unclipped C-terminus is required for Fe, Ni incorporation. FeNi incorporation is required for C-terminus processing and transport. C-terminal processing causes a conformational change that completes the maturation process.^[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	hycE
Mnemonic	Hydrogenase 3
Synonyms	ECK2716, b2721, JW2691, hevE^[1], hevE
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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	61.27 minutes	MG1655: 2844493..2842784 <gbrowseImage> name=NC_000913:2842784..2844493 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2741331..2739622 <gbrowseImage> name=NC_012967:2739622..2741331 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2728596..2730305 <gbrowseImage> name=NC_012759:2728596..2730305 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2845127..2843418 <gbrowseImage> name=NC_007779:2843418..2845127 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2937035..2935326 <gbrowseImage> name=NC_010473:2935326..2937035 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	2842784	Edman degradation	PMID:8125094
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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	Comments
ΔhycE (Keio:JW2691)	deletion	deletion	PMID:16738554	Shigen CGSC10120^[5]
hycE::Tn5KAN-I-SceI (FB20903)	Insertion at nt 790 in Minus orientation		PMID:15262929	E. coli Genome Project:FB20903	does not contain pKD46
hycE::Tn5KAN-I-SceI (FB20904)	Insertion at nt 790 in Minus orientation		PMID:15262929	E. coli Genome Project:FB20904	contains pKD46
ΔhycE725::kan			PMID:16738554	CGSC:101466
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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
JW2691	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCTCTGAAGAAAAATTAGGTCA Primer 2:CCTTTCAGCGGCGAGTTTTTACG
1B2	Kohara Phage	Genobase	PMID:3038334
12F2	Kohara Phage	Genobase	PMID:3038334
srlD3131::Tn10	Linked marker	CAG18642 = CGSC7423^[5]	est. P1 cotransduction: 54% ^[6] Synonyms:zfh-3131::Tn10, zfi-3131::Tn10
cysI95::Tn10	Linked marker	CAG12173 = CGSC7425^[5]	est. P1 cotransduction: 15% ^[6] Synonyms:cysC95::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:EG10478	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10478	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000471	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947396	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0473	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008944	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	HycE
Synonyms	hydrogenase 3, large subunit^[1], B2721^[2]^[1], HevE^[2]^[1], HycE^[2]^[1] , ECK2716, hevE, JW2691, b2721
Product description	hydrogenase 3, large subunit^[2]^[3]; Component of hydrogenase 3^[2]^[3]; formate hydrogenlyase complex^[2]^[3] Hydrogenase 3 large subunit, [NiFe] cluster; heterodimer^[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: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:0008137	NADH dehydrogenase (ubiquinone) activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001268	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008901	ferredoxin hydrogenase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001501	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016151	nickel ion binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001501	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016151	nickel ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0533	F	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:0016651	oxidoreductase activity, acting on NADH or NADPH	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001135	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:IPR001135	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051287	NAD or NADH binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001135	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: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:IPR001135	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001268	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001501	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 3	could be indirect
Protein	truA		PMID:16606699	Experiment(s):EBI-1143752
Protein	groL		PMID:16606699	Experiment(s):EBI-1143752
Protein	ade		PMID:16606699	Experiment(s):EBI-1143752
Protein	Subunits of formate hydrogenlyase complex	could be indirect
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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 MSEEKLGQHY LAALNEAFPG VVLDHAWQTK DQLTVTVKVN YLPEVVEFLY YKQGGWLSVL FGNDERKLNG HYAVYYVLSM EKGTKCWITV RVEVDANKPE YPSVTPRVPA AVWGEREVRD MYGLIPVGLP DERRLVLPDD WPDELYPLRK DSMDYRQRPA PTTDAETYEF INELGDKKNN VVPIGPLHVT SDEPGHFRLF VDGENIIDAD YRLFYVHRGM EKLAETRMGY NEVTFLSDRV CGICGFAHST AYTTSVENAM GIQVPERAQM IRAILLEVER LHSHLLNLGL ACHFTGFDSG FMQFFRVRET SMKMAEILTG ARKTYGLNLI GGIRRDLLKD DMIQTRQLAQ QMRREVQELV DVLLSTPNME QRTVGIGRLD PEIARDFSNV GPMVRASGHA RDTRADHPFV GYGLLPMEVH SEQGCDVISR LKVRINEVYT ALNMIDYGLD NLPGGPLMVE GFTYIPHRFA LGFAEAPRGD DIHWSMTGDN QKLYRWRCRA ATYANWPTLR YMLRGNTVSD APLIIGSLDP CYSCTDRMTV VDVRKKKSKV VPYKELERYS IERKNSPLK
Length	569
Mol. Wt	64.98 kDa
pI	6.6 (calculated)
Extinction coefficient	84,230 - 85,230 (calc based on 27 Y, 8 W, and 8 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	References
Domain	44..150	PF00329 Respiratory-chain NADH dehydrogenase, 30 Kd subunit	PMID:19920124
Domain	295..471	PF00346 Respiratory-chain NADH dehydrogenase, 49 Kd subunit	PMID:19920124
Domain	463..537	PF00346 Respiratory-chain NADH dehydrogenase, 49 Kd subunit	PMID:19920124
Domain	218..294	PF00374 Nickel-dependent hydrogenase	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=hycE 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:16130628	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947396	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008944	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P16431	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10478	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10478	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947396	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000471	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0473	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	Notes	Reference(s)
Protein	Ecoli K-12	1.628+/-0.11	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.001755413	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by RNA_Seq	PMID:20671182
Protein	E. coli K-12 MG1655	10	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	6	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	3^a	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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See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)
hycABCDEFGHI
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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_000913:2844473..2844513 source=MG1655 flip=1 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:b2721 (EcoliWiki Page)	NCBI GEO profiles for hycE
microarray	GenExpDB:b2721 (EcoliWiki Page)	Summary of data for hycE 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 hycE Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10478	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0473	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2721
EcoGene	EcoGene:EG10478	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000471	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008944	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
Gallus gallus	ENSGALP00000001067 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000043132 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	HYCE	From SHIGELLACYC
E. coli O157	HYCE	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)	PF00346 Respiratory-chain NADH dehydrogenase, 49 Kd subunit
Pfam (EcoliWiki Page)	PF00374 Nickel-dependent hydrogenase
Pfam (EcoliWiki Page)	PF00346 Respiratory-chain NADH dehydrogenase, 49 Kd subunit
Pfam (EcoliWiki Page)	PF00329 Respiratory-chain NADH dehydrogenase, 30 Kd subunit
Superfamily (EcoliWiki Page)	SUPERFAMILY:56762
Superfamily (EcoliWiki Page)	SUPERFAMILY:143243
EcoCyc	EcoCyc:EG10478	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10478	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000471	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0473	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008944	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 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 ^3.4 ^3.5 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).

hycE: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 hycE Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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