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Standard Name	panD
Gene Synonym(s)	ECK0130, b0131, JW0127^[1], JW0127
Product Desc.	PanD α & β cleavage products^[2]^[3]; Component of aspartate 1-decarboxylase^[3] Aspartate 1-decarboxylase; pantothenate biosynthesis; residues 1-24 cleaved, constitute the beta chain; C-terminal (102aa) constitutes alpha chain^[4]
Product Synonyms(s)	aspartate 1-decarboxylase^[1], B0131^[2]^[1] , ECK0130, JW0127, b0131
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): panD^[2]
Regulation/Activity
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Notes

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Mutants have altered acyl-CoA pools. N-terminus of alpha subunit (Ser25) is modified to pyruvic acid and involved in catalysis. Replacing normally modified Ser25 with an alanine inactivates PanD. Sequencing citation: Merkel,W.K. and Nichols,B.P., Nucleotide sequence of the Escherichia coli panBCD gene cluster, unpublished (1993) as cited in GenBank accession number L17086. Aspartate decarboxylase activity was confirmed in K-12 when it was first shown to be PanD (Cronan, 1980).^[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	panD
Mnemonic	Pantothenate
Synonyms	ECK0130, b0131, JW0127^[1], JW0127
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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	3.15 minutes	MG1655: 146694..146314 <gbrowseImage> name=NC_000913:146314..146694 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 149497..149117 <gbrowseImage> name=NC_012967:149117..149497 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 146313..146693 <gbrowseImage> name=NC_012759:146313..146693 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 146694..146314 <gbrowseImage> name=NC_007779:146314..146694 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 120798..120418 <gbrowseImage> name=NC_010473:120418..120798 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	146314	Edman degradation	PMID:9169598
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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
panD(del) (Keio:JW0127)	deletion	deletion	PMID:16738554	Shigen CGSC8404^[5]
panD1				CGSC:6017
panD2				CGSC:6021
panD3				CGSC:6023
panD748(del)::kan			PMID:16738554	CGSC:102250
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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
JW0127	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCATTCGCACGATGCTGCAGGG Primer 2:CCAGCAACCTGTACCGGAATCGC
17C11	Kohara Phage	Genobase	PMID:3038334
11C5	Kohara Phage	Genobase	PMID:3038334
leuO3051::Tn10	Linked marker	CAG12095 = CGSC7324^[5]	est. P1 cotransduction: 3% ^[6] Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).
zad-220::Tn10	Linked marker	CAG12025 = CGSC7326^[5]	est. P1 cotransduction: 93% ^[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:EG11747	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11747	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001685	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945686	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1697	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000459	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	PanD
Synonyms	aspartate 1-decarboxylase^[1], B0131^[2]^[1] , ECK0130, JW0127, b0131
Product description	PanD α & β cleavage products^[2]^[3]; Component of aspartate 1-decarboxylase^[3] Aspartate 1-decarboxylase; pantothenate biosynthesis; residues 1-24 cleaved, constitute the beta chain; C-terminal (102aa) constitutes alpha chain^[4]
EC number (for enzymes)	4.1.1.11^[1]
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Notes

Function

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<protect> Gene Ontology

PanD product

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:0004068	aspartate 1-decarboxylase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00446	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004068	aspartate 1-decarboxylase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003190	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004068	aspartate 1-decarboxylase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:4.1.1.11	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005488	binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR009010	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00446	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:0006523	alanine biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003190	P	Seeded from EcoCyc (v14.0)	complete
	GO:0015940	pantothenate biosynthetic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00446	P	Seeded from EcoCyc (v14.0)	complete
	GO:0015940	pantothenate biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0566	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016829	lyase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0456	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016831	carboxy-lyase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0210	F	Seeded from EcoCyc (v14.0)	complete
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Interactions

PanD product

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 aspartate 1-decarboxylase	could be indirect
Protein	panC		PMID:16606699	Experiment(s):EBI-1135679
Protein	lacZ		PMID:16606699	Experiment(s):EBI-1135679
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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 MIRTMLQGKL HRVKVTHADL HYEGSCAIDQ DFLDAAGILE NEAIDIWNVT NGKRFSTYAI AAERGSRIIS VNGAAAHCAS VGDIVIIASF VTMPDEEART WRPNVAYFEG DNEMKRTAKA IPVQVA
Length	126
Mol. Wt	13.833 kDa
pI	5.7 (calculated)
Extinction coefficient	15,470 - 15,720 (calc based on 3 Y, 2 W, and 2 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	1..116	PF02261 Aspartate decarboxylase		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=panD taxon=562,83333 </beststructure>

Models

View models at:

PSI-PRED (P0A790)
Genomes TO Protein (P0A790) (GTOP)

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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:16128124	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945686	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000459	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A790	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11747	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11747	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945686	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001685	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1697	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	2.11E+03	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	15147	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	5227	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	6124	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)
panD
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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_000913:146674..146714 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:b0131 (EcoliWiki Page)	NCBI GEO profiles for panD
microarray	GenExpDB:b0131 (EcoliWiki Page)	Summary of data for panD 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 (146610..146978) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ18; Well:B12^[7]
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Notes

Accessions Related to panD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11747	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1697	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0131
EcoGene	EcoGene:EG11747	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001685	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000459	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	PAND	From SHIGELLACYC
E. coli O157	PAND	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)	PF02261 Aspartate decarboxylase
Superfamily (EcoliWiki Page)	SUPERFAMILY:50692
EcoCyc	EcoCyc:EG11747	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11747	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001685	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1697	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000459	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.

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 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 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 ^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

panD:On One Page

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Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

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Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

PanD product

PanD product

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 panD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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