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Gene |

Product(s) |

Expression|

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Standard Name	hcaB
Gene Synonym(s)	ECK2538, b2541, JW2525, dig, phd, hcaA2, phdD, yfhX^[1], yfhX
Product Desc.	Probable 3-phenylpropionate-dihydrodiol dehydrogenase; hca genes catabolize 3-phenylpropionate and cinnamic acid, feeding the products into the the mhp pathway^[2]
Product Synonyms(s)	2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase^[1], B2541^[3]^[1], YfhX^[3]^[1], PhdD^[3]^[1], HcaB^[3]^[1] , ECK2538, JW2525, phdD, yfhX, b2541
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): hcaEFCBD^[3]
Regulation/Activity
Quick Links
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Notes

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Hydrocinnamic acid is a synonym for 3-phenylpropionic acid. HcaB is also called 2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase. HcaB also likely has cinnamic acid-dihydrodiol dehydrogenase activity.^[2]

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	hcaB
Mnemonic	Hydrocinnamic acid
Synonyms	ECK2538, b2541, JW2525, dig, phd, hcaA2, phdD, yfhX^[1], yfhX
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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	57.53 minutes	MG1655: 2669247..2670059 <gbrowseImage> name=NC_000913:2669247..2670059 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2591924..2592736 <gbrowseImage> name=NC_012967:2591924..2592736 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2555052..2555864 <gbrowseImage> name=NC_012759:2555052..2555864 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2669881..2670693 <gbrowseImage> name=NC_007779:2669881..2670693 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2761012..2761824 <gbrowseImage> name=NC_010473:2761012..2761824 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)	Reference	Availability
ΔhcaB (Keio:JW2525)	deletion	deletion	PMID:16738554	Shigen CGSC10011^[4]
ΔhcaB786::kan			PMID:16738554	CGSC:101306
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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
JW2525	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAGCGATCTGCATAACGAGTC Primer 2:CCAAGATCCAGCCCAGCCGCTAC
6F10	Kohara Phage	Genobase	PMID:3038334
8E12	Kohara Phage	Genobase	PMID:3038334
zfh-208::Tn10	Linked marker	CAG18481 = CGSC7417^[4]	est. P1 cotransduction: 82% ^[5] Synonyms:zff-208::Tn10
nadB51::Tn10	Linked marker	CAG18480 = CGSC7419^[4]	est. P1 cotransduction: 18% ^[5]
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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:G7335	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13459	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003905	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945346	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3232	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008361	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	HcaB
Synonyms	2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase^[1], B2541^[3]^[1], YfhX^[3]^[1], PhdD^[3]^[1], HcaB^[3]^[1] , ECK2538, JW2525, phdD, yfhX, b2541
Product description	Probable 3-phenylpropionate-dihydrodiol dehydrogenase; hca genes catabolize 3-phenylpropionate and cinnamic acid, feeding the products into the the mhp pathway^[2]
EC number (for enzymes)	1.3.1.-^[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:0005737	cytoplasm				C	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016040	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005488	binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016040	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002198	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002347	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016040	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01647	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002198	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002347	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020904	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:0016628	oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:1.3.1	F	Seeded from EcoCyc (v14.0)	complete
	GO:0018498	2,3-dihydroxy-2,3-dihydro-phenylpropionate dehydrogenase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01647	F	Seeded from EcoCyc (v14.0)	complete
	GO:0019439	aromatic compound catabolic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01647	P	Seeded from EcoCyc (v14.0)	complete
	GO:0019439	aromatic compound catabolic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0058	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002347	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	glsA2	PMID:16606699	Experiment(s):EBI-1143201
Protein	slyD	PMID:16606699	Experiment(s):EBI-1143201
Protein	ppiB	PMID:16606699	Experiment(s):EBI-1143201
Protein	hldD	PMID:16606699	Experiment(s):EBI-1143201
Protein	groL	PMID:16606699	Experiment(s):EBI-1143201
Protein	lpxH	PMID:16606699	Experiment(s):EBI-1143201
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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 MSDLHNESIF ITGGGSGLGL ALVERFIEEG AQVATLELSA AKVASLRQRF GEHILAVEGN VTCYADYQRA VDQILTRSGK LDCFIGNAGI WDHNASLVNT PAETLETGFH ELFNVNVLGY LLGAKACAPA LIASEGSMIF TLSNAAWYPG GGGPLYTASK HAATGLIRQL AYELAPKVRV NGVGPCGMAS DLRGPQALGQ SETSIMQSLT PEKIAAILPL QFFPQPADFT GPYVMLTSRR NNRALSGVMI NADAGLAIRG IRHVAAGLDL
Length	270
Mol. Wt	28.499 kDa
pI	6.2 (calculated)
Extinction coefficient	21,430 - 21,930 (calc based on 7 Y, 2 W, and 4 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
Domain	7..175	PF00106 short chain dehydrogenase		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=hcaB 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:16130466	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945346	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008361	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P77646	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7335	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13459	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945346	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003905	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3232	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	E. coli K-12 MG1655	7^a	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	11	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	0^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)
hcaEFCBD
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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_000913:2669227..2669267 source=MG1655 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:b2541 (EcoliWiki Page)	NCBI GEO profiles for hcaB
microarray	GenExpDB:b2541 (EcoliWiki Page)	Summary of data for hcaB 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 hcaB Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7335	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3232	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2541
EcoGene	EcoGene:EG13459	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003905	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008361	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	HCAB	From SHIGELLACYC
E. coli O157	HCAB	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)	PF00106 short chain dehydrogenase
Superfamily (EcoliWiki Page)	SUPERFAMILY:51735
Panther (EcoliWiki Page)	PTHR24322:SF31
EcoCyc	EcoCyc:G7335	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13459	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003905	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3232	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008361	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 ^1.13 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^3.0 ^3.1 ^3.2 ^3.3 ^3.4 ^3.5 ^3.6 ^3.7 ^3.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 CGSC: The Coli Genetics Stock Center
↑ ^5.0 ^5.1 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).

hcaB: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 hcaB Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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