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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

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Standard Name	hemB
Gene Synonym(s)	ECK0366, b0369, JW0361, ncf^[1], ncf
Product Desc.	porphobilinogen synthase^[2]^[3]; Component of porphobilinogen synthase^[2]^[3] 5-aminolevulinate dehydratase; binds Zn(II)^[4]
Product Synonyms(s)	porphobilinogen synthase^[1], B0369^[2]^[1], Ncf^[2]^[1], HemB^[2]^[1] , ECK0366, JW0361, ncf, b0369
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): hemB^[2]
Regulation/Activity
Quick Links
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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	hemB
Mnemonic	Hemin
Synonyms	ECK0366, b0369, JW0361, ncf^[1], ncf
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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	8.36 minutes	MG1655: 388951..387977 <gbrowseImage> name=NC_000913:387977..388951 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 358635..357661 <gbrowseImage> name=NC_012967:357661..358635 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 290736..291710 <gbrowseImage> name=NC_012759:290736..291710 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 388951..387977 <gbrowseImage> name=NC_007779:387977..388951 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 328282..327308 <gbrowseImage> name=NC_010473:327308..328282 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	387980	Edman degradation	PMID:8439296
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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	Phenotype: Type	Phenotype: Description	Reference	Availability	Comments
hemB3				CGSC:11612
hemB1			PMID:1987138	CGSC:11608
hemB220				CGSC:23022
hemB-201	Auxotrophies	δ-aminolevulinate auxotrophy	PMID:1987138	Experimental strain: GE1360 Parental strain: K12	δ-aminolevulinate auxotrophy is usually associated with hemA mutants.
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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
JW0361	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCACAGACTTAATCCAACGCCC Primer 2:CCACGCAGAATCTTCTTCTCAGC
8F10	Kohara Phage	Genobase	PMID:3038334
6E2	Kohara Phage	Genobase	PMID:3038334
mhpC281::Tn10	Linked marker	CAG12080 = CGSC7333^[5]	est. P1 cotransduction: 55% ^[6] Synonyms:zah-281::Tn10
zai-3053::Tn10	Linked marker	CAG18091 = CGSC7336^[5]	est. P1 cotransduction: 81% ^[6] Synonyms:zaj-3053::Tn10 nnnCAG18091 also carries proC9999 (CGSC).
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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:EG10428	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10428	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000421	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945017	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0423	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001266	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	HemB
Synonyms	porphobilinogen synthase^[1], B0369^[2]^[1], Ncf^[2]^[1], HemB^[2]^[1] , ECK0366, JW0361, ncf, b0369
Product description	porphobilinogen synthase^[2]^[3]; Component of porphobilinogen synthase^[2]^[3] 5-aminolevulinate dehydratase; binds Zn(II)^[4]
EC number (for enzymes)	4.2.1.24^[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:0005737	cytoplasm				C	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	GO:0000287	magnesium ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0460	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013785	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004655	porphobilinogen synthase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001731	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004655	porphobilinogen synthase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:4.2.1.24	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004655	porphobilinogen synthase activity	PMID:3276659	IMP: Inferred from Mutant Phenotype		F	Seeded from EcoCyc (v14.0)	complete
	GO:0005829	cytosol	PMID:16858726	IDA: Inferred from Direct Assay		C	Seeded from EcoCyc (v14.0)	complete
	GO:0006779	porphyrin biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0627	P	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:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001731	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004655	porphobilinogen synthase activity	PMID:3276659	IMP: Inferred from Mutant Phenotype		F	A hemB mutant was mutagenized and selected for heme permeability before testing for porphobilinogen synthase activity.	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:0006783	heme biosynthetic process	PMID:3276659	IMP: Inferred from Mutant Phenotype		P		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 porphobilinogen synthase	could be indirect
Protein	sanA		PMID:16606699	Experiment(s):EBI-1136394
Protein	hisJ		PMID:16606699	Experiment(s):EBI-1136394
Protein	fadH		PMID:16606699	Experiment(s):EBI-1136394
Protein	rpsN		PMID:19402753	LCMS(ID Probability):99.6
Protein	yfiD		PMID:19402753	LCMS(ID Probability):99.6
Protein	groS		PMID:19402753	LCMS(ID Probability):99.6
Protein	ahpC		PMID:19402753	LCMS(ID Probability):99.6
Protein	hupA		PMID:19402753	LCMS(ID Probability):99.6
Protein	ppsA		PMID:19402753	LCMS(ID Probability):99.6
Protein	degQ		PMID:19402753	LCMS(ID Probability):99.6
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Notes

Localization

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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 MPLDSTNIRQ TMTDLIQRPR RLRKSPALRA MFEETTLSLN DLVLPIFVEE EIDDYKAVEA MPGVMRIPEK HLAREIERIA NAGIRSVMTF GISHHTDETG SDAWREDGLV ARMSRICKQT VPEMIVMSDT CFCEYTSHGH CGVLCEHGVD NDATLENLGK QAVVAAAAGA DFIAPSAAMD GQVQAIRQAL DAAGFKDTAI MSYSTKFASS FYGPFREAAG SALKGDRKSY QMNPMNRREA IRESLLDEAQ GADCLMVKPA GAYLDIVREL RERTELPIGA YQVSGEYAMI KFAALAGAID EEKVVLESLG SIKRAGADLI FSYFALDLAE KKILR
Length	335
Mol. Wt	36.882 kDa
pI	5.2 (calculated)
Extinction coefficient	18,910 - 19,660 (calc based on 9 Y, 1 W, and 6 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:P0ACB2
Domain	3..321	PF00490 Delta-aminolevulinic acid dehydratase		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=hemB 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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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:90111123	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945017	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001266	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0ACB2	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10428	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10428	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945017	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000421	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0423	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 MC4100	9.24E+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 MG1655	3626	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	1093	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	1897	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)
hemB
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Figure courtesy of RegulonDB

</protect>

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_000913:388931..388971 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:b0369 (EcoliWiki Page)	NCBI GEO profiles for hemB
microarray	GenExpDB:b0369 (EcoliWiki Page)	Summary of data for hemB 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 (388886..389151) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ07; Well:A3^[7]
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Notes

Accessions Related to hemB Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10428	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0423	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0369
EcoGene	EcoGene:EG10428	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000421	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001266	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
Anopheles gambiae	ENSANGP00000012449 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000001781 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT1G69740 (score: 1.000; bootstrap: 100%) AT1G44318 (score: 0.419)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000000315 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000004817 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000010338 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-050417-123 (score: 1.000; bootstrap: 100%) ZDB-CDNA-050417-124 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0231415 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0036271 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila pseudoobscura	GA10250-PA (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000014392 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000277315 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000005411 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Mus musculus	MGI:96853 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Oryza gramene	Q5Z8V9 (score: 1.000; bootstrap: 100%) Q42836 (score: 0.831)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000036346 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000020625 (score: 1.000; bootstrap: 100%) ENSRNOP00000041533 (score: 0.247)	From Inparanoid:20070104
Saccharomyces cerevisiae	YGL040C (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAC18056c (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000154331 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00009256001 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000050679 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	HEMB	From SHIGELLACYC
E. coli O157	HEMB	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)	PF00490 Delta-aminolevulinic acid dehydratase
Superfamily (EcoliWiki Page)	SUPERFAMILY:51569
Panther (EcoliWiki Page)	PTHR11458:SF0
PFAM (EcoliWiki Page)	PFAM:PF00490
EcoCyc	EcoCyc:EG10428	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10428	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000421	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0423	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001266	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 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 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 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 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

hemB: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 hemB Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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