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Expression|

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Standard Name	kdsB
Gene Synonym(s)	ECK0909, b0918, JW0901^[1], JW0901
Product Desc.	CPM- 3-deoxy-manno-octulosonate cytidylyltransferase; LPS biosynthesis^[2]
Product Synonyms(s)	3-deoxy-manno-octulosonate cytidylyltransferase^[1], B0918^[3]^[1], KdsB^[3]^[1] , ECK0909, JW0901, b0918
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ycaR^[3]
Regulation/Activity
Quick Links
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Notes

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Also known as CMP-KDO synthase(CKS). E. coli K-12 only has the L-CKS isozyme involved in LPS biosynthesis. The K-CKS isozyme KpsU is specific for K5 group II capsule biosynthesis , is 45% identical to KdsB, and has been characterized from E. coli K5 isolate #2980 (Genbank:X74567, UniProtKB:P42216; PDB:1H7E).^[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	kdsB
Mnemonic	KDO synthesis
Synonyms	ECK0909, b0918, JW0901^[1], JW0901
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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	20.91 minutes	MG1655: 970075..970821 <gbrowseImage> name=NC_000913:970075..970821 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 987944..988690 <gbrowseImage> name=NC_012967:987944..988690 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 873043..873789 <gbrowseImage> name=NC_012759:873043..873789 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 971274..972020 <gbrowseImage> name=NC_007779:971274..972020 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1024003..1024749 <gbrowseImage> name=NC_010473:1024003..1024749 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	970078	Edman degradation	PMID:3023327
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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
JW0901	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAGTTTTGTGGTCATTATTCC Primer 2:CCGCGCATTTCAGCGCGAACGCG
E1D1	Kohara Phage	Genobase	PMID:3038334
zca-1230::Tn10	Linked marker	CAG18478 = CGSC7356^[4]	est. P1 cotransduction: 41% ^[5] Synonyms:zbj-1230::Tn10
zcb-3059::Tn10	Linked marker	CAG12094 = CGSC7358^[4]	est. P1 cotransduction: 28% ^[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:EG10519	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10519	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000512	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945539	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0514	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003122	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	KdsB
Synonyms	3-deoxy-manno-octulosonate cytidylyltransferase^[1], B0918^[3]^[1], KdsB^[3]^[1] , ECK0909, JW0901, b0918
Product description	CPM- 3-deoxy-manno-octulosonate cytidylyltransferase; LPS biosynthesis^[2]
EC number (for enzymes)	2.7.7.38^[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: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:0000287	magnesium ion binding	PMID:19815542	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00057	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004528	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:0008690	3-deoxy-manno-octulosonate cytidylyltransferase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00057	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008690	3-deoxy-manno-octulosonate cytidylyltransferase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004528	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008690	3-deoxy-manno-octulosonate cytidylyltransferase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.7.7.38	F	Seeded from EcoCyc (v14.0)	complete
	GO:0019294	keto-3-deoxy-D-manno-octulosonic acid biosynthetic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00057	P	Seeded from EcoCyc (v14.0)	complete
	GO:0019294	keto-3-deoxy-D-manno-octulosonic acid biosynthetic process	PMID:2989246	IDA: Inferred from Direct Assay		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	tufA	PMID:15690043	Experiment(s):EBI-881333
Protein	dnaJ	PMID:15690043	Experiment(s):EBI-888863
Protein	dnaK	PMID:15690043	Experiment(s):EBI-888863
Protein	hupB	PMID:15690043	Experiment(s):EBI-888863
Protein	pepB	PMID:15690043	Experiment(s):EBI-888863
Protein	rplD	PMID:15690043	Experiment(s):EBI-888863
Protein	rplK	PMID:15690043	Experiment(s):EBI-888863
Protein	rplL	PMID:15690043	Experiment(s):EBI-888863
Protein	rpsA	PMID:15690043	Experiment(s):EBI-888863
Protein	yfbS	PMID:15690043	Experiment(s):EBI-888863
Protein	yjaH	PMID:15690043	Experiment(s):EBI-888863
Protein	dcuR	PMID:15690043	Experiment(s):EBI-888863
Protein	nadE	PMID:16606699	Experiment(s):EBI-1138355
Protein	sdhA	PMID:16606699	Experiment(s):EBI-1138355
Protein	dcuR	PMID:19402753	LCMS(ID Probability):99.0
Protein	yfbS	PMID:19402753	LCMS(ID Probability):99.0
Protein	yjaH	PMID:19402753	LCMS(ID Probability):99.0
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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 MSFVVIIPAR YASTRLPGKP LVDINGKPMI VHVLERARES GAERIIVATD HEDVARAVEA AGGEVCMTRA DHQSGTERLA EVVEKCAFSD DTVIVNVQGD EPMIPATIIR QVADNLAQRQ VGMATLAVPI HNAEEAFNPN AVKVVLDAEG YALYFSRATI PWDRDRFAEG LETVGDNFLR HLGIYGYRAG FIRRYVNWQP SPLEHIEMLE QLRVLWYGEK IHVAVAQEVP GTGVDTPEDL ERVRAEMR
Length	248
Mol. Wt	27.613 kDa
pI	5.1 (calculated)
Extinction coefficient	26,930 - 27,180 (calc based on 7 Y, 3 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
Initiator Methionine	1	Removed	UniProt:P04951
Domain	4..221	PF02348 Cytidylyltransferase		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=kdsB 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:16128885	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945539	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003122	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P04951	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10519	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10519	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945539	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000512	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0514	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	6.13E+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	35.914+/-0.123	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.091152815	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	3374	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	899	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	1321	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)
ycaR
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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_000913:970055..970095 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:b0918 (EcoliWiki Page)	NCBI GEO profiles for kdsB
microarray	GenExpDB:b0918 (EcoliWiki Page)	Summary of data for kdsB 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 kdsB Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10519	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0514	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0918
EcoGene	EcoGene:EG10519	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000512	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003122	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	ENSANGP00000028620 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT1G53000 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Oryza gramene	Q688Y2 (score: 1.000; bootstrap: 100%) Q9M4G3 (score: 0.852) Q9M4D3 (score: 0.669)	From Inparanoid:20070104
Shigella flexneri	KDSB	From SHIGELLACYC
E. coli O157	KDSB	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)	PF02348 Cytidylyltransferase
Panther (EcoliWiki Page)	PTHR21485:SF4
Superfamily (EcoliWiki Page)	SUPERFAMILY:53448
EcoCyc	EcoCyc:EG10519	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10519	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000512	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0514	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003122	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 ^1.7 ^1.8 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 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 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

kdsB: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 kdsB Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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