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Expression|

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Standard Name	waaA
Gene Synonym(s)	kdtA, ECK3623, b3633, JW3608^[1]^[2], JW3608
Product Desc.	3-deoxy-D-manno-octulosonate(Kdo)-lipid A transferase^[3]
Product Synonyms(s)	3-deoxy-D-manno-octulosonic-acid transferase (KDO transferase)^[1], B3633^[4]^[1], WaaA^[4]^[1], KdtA^[4]^[1] , ECK3623, JW3608, kdtA, b3633
Function from GO	<GO_nr />
Knock-Out Phenotype	lethal (see PMID:7499229)
Regulation/Expression	transcription unit(s): kdtA^[4], kdtA-coaD^[4], kdtAB, waaA-coaD
Regulation/Activity
Quick Links
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Notes

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WaaA adds 2 Kdo residues to lipid IVA. waaA is an essential gene. Mutagenesis eliminated ATG a codon 52 as a start codon (Belunis and Raetz, 1992).^[3]

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	waaA
Mnemonic	Systematic nomenclature
Synonyms	kdtA, ECK3623, b3633, JW3608^[1]^[2], JW3608
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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	82.04 minutes	MG1655: 3806563..3807840 <gbrowseImage> name=NC_000913:3806563..3807840 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3746895..3748172 <gbrowseImage> name=NC_012967:3746895..3748172 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3694889..3696166 <gbrowseImage> name=NC_012759:3694889..3696166 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3831875..3830598 <gbrowseImage> name=NC_007779:3830598..3831875 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	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
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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
	Plasmid clone	Shigen	PMID:16769691 Status: Primer 1: Primer 2:
2A6	Kohara Phage	Genobase	PMID:3038334
4D2	Kohara Phage	Genobase	PMID:3038334
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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:EG10520	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10520	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000513	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:949048	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0515	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011873	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	WaaA
Synonyms	3-deoxy-D-manno-octulosonic-acid transferase (KDO transferase)^[1], B3633^[4]^[1], WaaA^[4]^[1], KdtA^[4]^[1] , ECK3623, JW3608, kdtA, b3633
Product description	3-deoxy-D-manno-octulosonate(Kdo)-lipid A transferase^[3]
EC number (for enzymes)	-2^[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:0005529	sugar binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR007507	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0997	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-1003	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0472	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0812	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-9904	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016740	transferase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR007507	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016740	transferase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0808	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016740	transferase activity	PMID:2651435	IDA: Inferred from Direct Assay		F		complete
	GO:0016020	membrane	PMID:2651435	IDA: Inferred from Direct Assay		C		complete
	GO:0009245	lipid A biosynthetic process	PMID:7499229	IMP: Inferred from Mutant Phenotype		P		complete
	GO:0016740	transferase activity	PMID:1577828	IDA: Inferred from Direct Assay		F		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	entB	PMID:15690043	Experiment(s):EBI-883387
Protein	rplA	PMID:15690043	Experiment(s):EBI-883387
Protein	rplE	PMID:15690043	Experiment(s):EBI-883387
Protein	rplL	PMID:15690043	Experiment(s):EBI-883387
Protein	rplM	PMID:15690043	Experiment(s):EBI-883387
Protein	rplS	PMID:15690043	Experiment(s):EBI-883387
Protein	rplT	PMID:15690043	Experiment(s):EBI-883387
Protein	rplU	PMID:15690043	Experiment(s):EBI-883387
Protein	rplV	PMID:15690043	Experiment(s):EBI-883387
Protein	rpmG	PMID:15690043	Experiment(s):EBI-883387
Protein	rpsB	PMID:15690043	Experiment(s):EBI-883387
Protein	rpsE	PMID:15690043	Experiment(s):EBI-883387
Protein	rpsJ	PMID:15690043	Experiment(s):EBI-883387
Protein	murE	PMID:15690043	Experiment(s):EBI-883387
Protein	murE	PMID:19402753	LCMS(ID Probability):99.0
Protein	tufB	PMID:19402753	MALDI(Z-score):22.989507
Protein	tig	PMID:19402753	MALDI(Z-score):38.502574
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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 MLELLYTALL YLIQPLIWIR LWVRGRKAPA YRKRWGERYG FYRHPLKPGG IMLHSVSVGE TLAAIPLVRA LRHRYPDLPI TVTTMTPTGS ERVQSAFGKD VQHVYLPYDL PDALNRFLNK VDPKLVLIME TELWPNLIAA LHKRKIPLVI ANARLSARSA AGYAKLGKFV RRLLRRITLI AAQNEEDGAR FVALGAKNNQ VTVTGSLKFD ISVTPQLAAK AVTLRRQWAP HRPVWIATST HEGEESVVIA AHQALLQQFP NLLLILVPRH PERFPDAINL VRQAGLSYIT RSSGEVPSTS TQVVVGDTMG ELMLLYGIAD LAFVGGSLVE RGGHNPLEAA AHAIPVLMGP HTFNFKDICA RLEQASGLIT VTDATTLAKE VSSLLTDADY RSFYGRHAVE VLYQNQGALQ RLLQLLEPYL PPKTH
Length	425
Mol. Wt	47.291 kDa
pI	10.2 (calculated)
Extinction coefficient	55,350 - 55,475 (calc based on 15 Y, 6 W, and 1 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	231..401	PF00534 Glycosyl transferases group 1	PMID:19920124
Domain	31..213	PF04413 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase)	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=waaA taxon=562,83333 </beststructure>

Models

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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:16131504	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:949048	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011873	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AC75	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10520	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10520	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:949048	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000513	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0515	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 MC4100	1.53E+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	Ecoli K-12	10.62+/-0.115	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.023492561	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	593	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	144	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	193	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)
kdtA
kdtA-coaD
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File:.jpg

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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_000913:3806543..3806583 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:b3633 (EcoliWiki Page)	NCBI GEO profiles for waaA
microarray	GenExpDB:b3633 (EcoliWiki Page)	Summary of data for waaA 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 (3805641..3806242) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ08; Well:H4^[5]
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Notes

Accessions Related to waaA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10520	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0515	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3633
EcoGene	EcoGene:EG10520	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000513	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011873	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
Arabidopsis thaliana	AT5G03770 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	KDTA	From SHIGELLACYC
E. coli O157	KDTA	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)	PF04413 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase)
Pfam (EcoliWiki Page)	PF00534 Glycosyl transferases group 1
Panther (EcoliWiki Page)	PTHR23417:SF2
Superfamily (EcoliWiki Page)	SUPERFAMILY:53756
EcoCyc	EcoCyc:EG10520	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10520	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000513	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0515	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011873	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)
↑ ^2.0 ^2.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^4.0 ^4.1 ^4.2 ^4.3 ^4.4 ^4.5 ^4.6 ^4.7 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

waaA: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 waaA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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