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Gene |

Product(s) |

Expression|

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Standard Name	hemN
Gene Synonym(s)	ECK3860, b3867, JW3838, yihJ^[1], yihJ
Product Desc.	HEMN^[2]^[3] Coproporphyrinogen III oxidase, oxygen-independent, required for cytochrome B and cytochrome C synthesis during anaerobic growth^[4]
Product Synonyms(s)	coproporphyrinogen III oxidase, SAM and NAD(P)H dependent, oxygen-independent^[1], B3867^[2]^[1], YihJ^[2]^[1], HemN^[2]^[1] , ECK3860, JW3838, yihJ, b3867
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): hemN^[2]
Regulation/Activity
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Notes

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Radical SAM superfamily.^[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	hemN
Mnemonic	Hemin
Synonyms	ECK3860, b3867, JW3838, yihJ^[1], yihJ
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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	87.29 minutes	MG1655: 4050068..4051441 <gbrowseImage> name=NC_000913:4050068..4051441 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 4030342..4031715 <gbrowseImage> name=NC_012967:4030342..4031715 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3939737..3941110 <gbrowseImage> name=NC_012759:3939737..3941110 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3584636..3583263 <gbrowseImage> name=NC_007779:3583263..3584636 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4148988..4150361 <gbrowseImage> name=NC_010473:4148988..4150361 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
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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: Description	Reference	Availability	Comments
ΔhemN (Keio:JW3838)	deletion	deletion		PMID:16738554	Shigen CGSC10772^[5]
hemNH58L		H58L	Results in loss of iron-sulfur cluster and activity			seeded from UniProt:P32131
hemNC62S		C62S	Results in loss of iron-sulfur cluster and activity			seeded from UniProt:P32131
hemNC66S		C66S	Results in loss of iron-sulfur cluster and activity			seeded from UniProt:P32131
hemNF68L		F68L	No effect			seeded from UniProt:P32131
hemNC69S		C69S	Results in loss of iron-sulfur cluster and activity			seeded from UniProt:P32131
hemNC71S		C71S	No effect on iron-sulfur cluster, but results in activity loss			seeded from UniProt:P32131
hemNG111V		G111V	Loss of activity and much less iron-sulfur cluster formed; when associated with V-113			seeded from UniProt:P32131
hemNG113V		G113V	Loss of activity and much less iron-sulfur cluster formed; when associated with V-111			seeded from UniProt:P32131
hemNE145A,I		E145A,I	Loss of activity. Iron content reduced by about 80%			seeded from UniProt:P32131
hemNF310A,L		F310A,L	Loss of activity. Iron content reduced by about 50%. Can cleave up to one molecule of S-adenosyl-L-methionine (in vitro)			seeded from UniProt:P32131
hemNQ311A		Q311A	Loss of activity. No change in iron content. Can cleave up to one molecule of S-adenosyl-L-methionine (in vitro)			seeded from UniProt:P32131
hemNI329A		I329A	Loss of activity. No change in iron content. Can cleave up to one molecule of S-adenosyl-L-methionine (in vitro)			seeded from UniProt:P32131
hemNY56A,L		Y56A,L	Loss of activity			seeded from UniProt:P32131
hemNY56F		Y56F	Decreases activity by 50%			seeded from UniProt:P32131
ΔhemN728::kan				PMID:16738554	CGSC:101342
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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
JW3838	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCTCTGTACAGCAAATCGACTG Primer 2:CCAATCACCCGAGAGAACTGCTG
10F1	Kohara Phage	Genobase	PMID:3038334
8D12	Kohara Phage	Genobase	PMID:3038334
10H11	Kohara Phage	Genobase	PMID:3038334
fad-751::Tn10	Linked marker	CAG18496 = CGSC7465^[5]	est. P1 cotransduction: 43% ^[6] Synonyms:fadAB101::Tn10
zih-35::Tn10	Linked marker	CAG18495 = CGSC7467^[5]	est. P1 cotransduction: 61% ^[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:EG11836	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11836	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001767	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948362	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1782	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012629	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	HemN
Synonyms	coproporphyrinogen III oxidase, SAM and NAD(P)H dependent, oxygen-independent^[1], B3867^[2]^[1], YihJ^[2]^[1], HemN^[2]^[1] , ECK3860, JW3838, yihJ, b3867
Product description	HEMN^[2]^[3] Coproporphyrinogen III oxidase, oxygen-independent, required for cytochrome B and cytochrome C synthesis during anaerobic growth^[4]
EC number (for enzymes)	-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:0004109	coproporphyrinogen oxidase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004558	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004109	coproporphyrinogen oxidase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR010723	F	Seeded from EcoCyc (v14.0)	complete
	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:0005737	cytoplasm	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004558	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR010723	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0963	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0086	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: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:0051989	coproporphyrinogen dehydrogenase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:1.3.99.22	F	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004558	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR010723	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	References	Evidence
Protein	lacZ	PMID:16606699	Experiment(s):EBI-1146841
Protein	ycgE	PMID:16606699	Experiment(s):EBI-1146841
Protein	cysS	PMID:16606699	Experiment(s):EBI-1146841
Protein	narZ	PMID:16606699	Experiment(s):EBI-1146841
Protein	rplB	PMID:16606699	Experiment(s):EBI-1146841
Protein	ybgI	PMID:19402753	LCMS(ID Probability):99.6
Protein	phnI	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
cytoplasm			From EcoCyc^[3]
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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 MSMSVQQIDW DLALIQKYNY SGPRYTSYPT ALEFSEDFGE QAFLQAVARY PERPLSLYVH IPFCHKLCYF CGCNKIVTRQ QHKADQYLDA LEQEIVHRAP LFAGRHVSQL HWGGGTPTYL NKAQISRLMK LLRENFQFNA DAEISIEVDP REIELDVLDH LRAEGFNRLS MGVQDFNKEV QRLVNREQDE EFIFALLNHA REIGFTSTNI DLIYGLPKQT PESFAFTLKR VAELNPDRLS VFNYAHLPTI FAAQRKIKDA DLPSPQQKLD ILQETIAFLT QSGYQFIGMD HFARPDDELA VAQREGVLHR NFQGYTTQGD TDLLGMGVSA ISMIGDCYAQ NQKELKQYYQ QVDEQGNALW RGIALTRDDC IRRDVIKSLI CNFRLDYAPI EKQWDLHFAD YFAEDLKLLA PLAKDGLVDV DEKGIQVTAK GRLLIRNICM CFDTYLRQKA RMQQFSRVI
Length	459
Mol. Wt	52.948 kDa
pI	6.0 (calculated)
Extinction coefficient	50,310 - 51,435 (calc based on 19 Y, 4 W, and 9 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	56..229	PF04055 Radical SAM superfamily	PMID:19920124
Domain	311..431	PF06969 HemN C-terminal region	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=hemN taxon=562,83333 </beststructure>

Models

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Structure figures

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Notes

Gene Product Resources

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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:90111657	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948362	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012629	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P32131	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11836	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11836	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948362	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001767	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1782	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	10.046+/-0.086	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.03605244	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	873	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	305	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	368	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)
hemN
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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_000913:4050048..4050088 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:b3867 (EcoliWiki Page)	NCBI GEO profiles for hemN
microarray	GenExpDB:b3867 (EcoliWiki Page)	Summary of data for hemN 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 (4049345..4049674) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ07; Well:F7^[7]
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Notes

Accessions Related to hemN Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11836	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1782	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3867
EcoGene	EcoGene:EG11836	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001767	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012629	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
Xenopus tropicalis	ENSXETP00000014644 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	HEMN	From SHIGELLACYC
E. coli O157	HEMN	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)	PF04055 Radical SAM superfamily
Superfamily (EcoliWiki Page)	SUPERFAMILY:102114
Pfam (EcoliWiki Page)	PF06969 HemN C-terminal region
EcoCyc	EcoCyc:EG11836	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11836	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001767	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1782	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012629	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)
↑ ^2.0 ^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
↑ ^3.0 ^3.1 ^3.2 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

hemN: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 hemN Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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