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Expression|

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Standard Name	pncA
Gene Synonym(s)	ECK1766, b1768, JW1757, nam, ydjB^[1], ydjB
Product Desc.	Nicotinamide deamidase^[2]
Product Synonyms(s)	nicotinamidase/pyrazinamidase^[1], B1768^[3]^[1], Nam^[3]^[1], YdjB^[3]^[1], PncA^[3]^[1] , ECK1766, JW1757, nam, ydjB, b1768
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ansA-pncA^[3]
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	pncA
Mnemonic	Pyridine nucleotide cycle
Synonyms	ECK1766, b1768, JW1757, nam, ydjB^[1], ydjB
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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	39.87 minutes	MG1655: 1849911..1850552 <gbrowseImage> name=NC_000913:1849911..1850552 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1829115..1829756 <gbrowseImage> name=NC_012967:1829115..1829756 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1741970..1742611 <gbrowseImage> name=NC_012759:1741970..1742611 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1853601..1854242 <gbrowseImage> name=NC_007779:1853601..1854242 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1940482..1941123 <gbrowseImage> name=NC_010473:1940482..1941123 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: Type	Phenotype: Description	Reference	Availability	Comments
ΔpncA (Keio:JW1757)	deletion	deletion			PMID:16738554	Shigen CGSC9477^[4]
ΔydjB::kan	deletion		Biolog:respiration	unable to respire N-Acetyl-D-glucosamine	PMID:16095938
ΔydjB::kan	deletion		Biolog:respiration	unable to respire Acetate	PMID:16095938
ΔydjB::kan	deletion		Biolog:respiration	unable to respire L-Aspartate	PMID:16095938
pncA1						CGSC:5567
pncA20						CGSC:39483
ΔpncA766::kan					PMID:16738554	CGSC:102386
pncA^-			Resistant to	Resistant to 6-amino-nicotinamide	CURRENT MICROBIOLOGY Volume 4, Number 1 (1980), 31-35, DOI: 10.1007/BF02602888	Strain: UTH7095	table 1
pncA^-			Resistant to	Resistant to 6-amino-nicotinamide	PMID:780339
pncA⁺			Growth Phenotype	Growth on media with nicotinamide as sole nitrogen source.	PMID:4399474	Mutant strain: W3889-nam11	Table 4
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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
JW1757	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCCCCCTCGCGCCCTGTTACT Primer 2:CCgCCCTGTGTCTCTTCCCAGTC
12H7	Kohara Phage	Genobase	PMID:3038334
3E12	Kohara Phage	Genobase	PMID:3038334
zdj-276::Tn10	Linked marker	CAG18464 = CGSC7387^[4]	est. P1 cotransduction: 54% ^[5] Synonyms:zdi-276::Tn10
zea-225::Tn10	Linked marker	CAG18465 = CGSC7388^[4]	est. P1 cotransduction: 49% ^[5] Synonyms:zdj-225::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:EG11135	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11135	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001119	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946276	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1125	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005891	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	PncA
Synonyms	nicotinamidase/pyrazinamidase^[1], B1768^[3]^[1], Nam^[3]^[1], YdjB^[3]^[1], PncA^[3]^[1] , ECK1766, JW1757, nam, ydjB, b1768
Product description	Nicotinamide deamidase^[2]
EC number (for enzymes)	3.5.1.19^[1] 3.5.1.-^[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:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000868	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008936	nicotinamidase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:3.5.1.19	F	Seeded from EcoCyc (v14.0)	complete
	GO:0019363	pyridine nucleotide biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0662	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	relE	PMID:16606699	Experiment(s):EBI-1140740
Protein	matC	PMID:16606699	Experiment(s):EBI-1140740
Protein	hemE	PMID:16606699	Experiment(s):EBI-1140740
Protein	rpsD	PMID:16606699	Experiment(s):EBI-1140740
Protein	tolA	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^[6]
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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 MIKETVMPPR ALLLVDLQND FCAGGALAVP EGDSTVDVAN RLIDWCQSRG EAVIASQDWH PANHGSFASQ HGVEPYTPGQ LDGLPQTFWP DHCVQNSEGA QLHPLLHQKA IAAVFHKGEN PLVDSYSAFF DNGRRQKTSL DDWLRDHEID ELIVMGLATD YCVKFTVLDA LQLGYKVNVI TDGCRGVNIQ PQDSAHAFME MSAAGATLYT LADWEETQG
Length	219
Mol. Wt	24.063 kDa
pI	4.5 (calculated)
Extinction coefficient	34,950 - 35,575 (calc based on 5 Y, 5 W, and 5 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	4..207	PF00857 Isochorismatase family		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=pncA 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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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:90111327	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946276	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005891	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P21369	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11135	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11135	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946276	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001119	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1125	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	18.786+/-0.171	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
Protein	E. coli K-12 MG1655	1341	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	391	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	648	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)
ansA-pncA
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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_000913:1849891..1849931 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:b1768 (EcoliWiki Page)	NCBI GEO profiles for pncA
microarray	GenExpDB:b1768 (EcoliWiki Page)	Summary of data for pncA 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 pncA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11135	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1125	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1768
EcoGene	EcoGene:EG11135	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001119	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005891	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
Apis mellifera	ENSAPMP00000015472 (score: 1.000; bootstrap: 100%) ENSAPMP00000023397 (score: 0.234)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00024864 (score: 1.000; bootstrap: 100%) WBGene00034545 (score: 0.243)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00021395 (score: 1.000; bootstrap: 100%) WBGene00013336 (score: 0.246)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000015300 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0231367 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0051216 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YGL037C (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPBC3650c (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	YDJB	From SHIGELLACYC
E. coli O157	YDJB	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)	PF00857 Isochorismatase family
Superfamily (EcoliWiki Page)	SUPERFAMILY:52499
Panther (EcoliWiki Page)	PTHR11080:SF2
EcoCyc	EcoCyc:EG11135	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11135	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001119	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1125	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005891	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 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).
↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7

pncA: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 pncA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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