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Expression|

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Standard Name	kdsC
Gene Synonym(s)	ECK3187, b3198, JW3165, yrbI, yrbJ^[1], yrbJ
Product Desc.	3-deoxy-D-manno-octulosonate 8-phosphate phosphatase^[2]^[3]; Component of [[:Category:Complex:3-deoxy-D-manno-octulosonate 8-phosphate phosphatase\|3-deoxy-D-manno-octulosonate 8-phosphate phosphatase]]^[2]^[3] 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase; KDO 8-P phosphatase; LPS biosynthesis; HAD22^[4]
Product Synonyms(s)	3-deoxy-D-manno-octulosonate 8-phosphate phosphatase^[1], B3198^[2]^[1], YrbJ^[2]^[1], KdsC^[2]^[1], YrbI^[2]^[1] , ECK3187, JW3165, yrbI, yrbJ, b3198
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s):
Regulation/Activity
Quick Links
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Notes

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YrbI is renamed as KdsC (personal comm., R.W. Woodard, Univ. of Mich.). KdsC native N-terminal sequence is from E. coli B. Cloned kdsC is from BL21. KdsC is tetrameric and requires a divalent metal cofactor. HAD superfamily.^[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	kdsC
Mnemonic	KDO synthesis
Synonyms	ECK3187, b3198, JW3165, yrbI, yrbJ^[1], yrbJ
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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	71.99 minutes	MG1655: 3340295..3340861 <gbrowseImage> name=NC_000913:3340295..3340861 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3277508..3278074 <gbrowseImage> name=NC_012967:3277508..3278074 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3227443..3228009 <gbrowseImage> name=NC_012759:3227443..3228009 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3342128..3342694 <gbrowseImage> name=NC_007779:3342128..3342694 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3438040..3438606 <gbrowseImage> name=NC_010473:3438040..3438606 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	3340298	Edman degradation	PMID:12639950
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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
ΔkdsC (Keio:JW3165)	deletion	deletion	PMID:16738554	Shigen CGSC10402^[5]
ΔkdsC728::kan			PMID:16738554	CGSC:101618
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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
JW3165	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAGCAAAGCAGGTGCGTCGCT Primer 2:CCTATCGATTGCCCTTTGGCTTC
7E3	Kohara Phage	Genobase	PMID:3038334
sfsB203::Tn10	Linked marker	CAG12072 = CGSC7440^[5]	est. P1 cotransduction: 74% ^[6] Synonyms:zgj-203::Tn10, zha-203::Tn10
zhc-6::Tn10	Linked marker	CAG12153 = CGSC7442^[5]	est. P1 cotransduction: 42% ^[6] Synonyms:zha-6::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:G7663	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12804	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004211	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947717	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2656	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010506	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	KdsC
Synonyms	3-deoxy-D-manno-octulosonate 8-phosphate phosphatase^[1], B3198^[2]^[1], YrbJ^[2]^[1], KdsC^[2]^[1], YrbI^[2]^[1] , ECK3187, JW3165, yrbI, yrbJ, b3198
Product description	3-deoxy-D-manno-octulosonate 8-phosphate phosphatase^[2]^[3]; Component of [[:Category:Complex:3-deoxy-D-manno-octulosonate 8-phosphate phosphatase\|3-deoxy-D-manno-octulosonate 8-phosphate phosphatase]]^[2]^[3] 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase; KDO 8-P phosphatase; LPS biosynthesis; HAD22^[4]
EC number (for enzymes)	3.1.3.45^[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:0030288	outer membrane-bounded periplasmic space				C	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	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:0019143	3-deoxy-manno-octulosonate-8-phosphatase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR010023	F	Seeded from EcoCyc (v14.0)	complete
	GO:0019143	3-deoxy-manno-octulosonate-8-phosphatase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:3.1.3.45	F	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	Notes	References	Evidence
Protein	Subunits of [[:Category:Complex:3-deoxy-D-manno-octulosonate 8-phosphate phosphatase\|3-deoxy-D-manno-octulosonate 8-phosphate phosphatase]]	could be indirect
Protein	plsB		PMID:16606699	Experiment(s):EBI-1145130
Protein	sapF		PMID:16606699	Experiment(s):EBI-1145130
Protein	rplM		PMID:19402753	LCMS(ID Probability):99.6
Protein	rplA		PMID:19402753	LCMS(ID Probability):99.6
Protein	rplP		PMID:19402753	LCMS(ID Probability):99.6
Protein	slyD		PMID:19402753	LCMS(ID Probability):99.6
Protein	ycgF		PMID:19402753	LCMS(ID Probability):99.6
Protein	rfaD		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		PMID:12639950	EchoLocation:kdsC
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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 MSKAGASLAT CYGPVSADVI AKAENIRLLI LDVDGVLSDG LIYMGNNGEE LKAFNVRDGY GIRCALTSDI EVAIITGRKA KLVEDRCATL GITHLYQGQS NKLIAFSDLL EKLAIAPENV AYVGDDLIDW PVMEKVGLSV AVADAHPLLI PRADYVTRIA GGRGAVREVC DLLLLAQGKL DEAKGQSI
Length	188
Mol. Wt	19.997 kDa
pI	5.0 (calculated)
Extinction coefficient	14,440 - 14,940 (calc based on 6 Y, 1 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	88..167	PF08282 haloacid dehalogenase-like hydrolase		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=kdsC 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:16131088	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947717	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010506	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0ABZ4	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7663	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12804	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947717	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004211	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2656	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	4.53E+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	36.695+/-0.627	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	997	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	313	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	714	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)
kdsC-lptC
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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_000913:3340275..3340315 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:b3198 (EcoliWiki Page)	NCBI GEO profiles for kdsC
microarray	GenExpDB:b3198 (EcoliWiki Page)	Summary of data for kdsC 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 kdsC Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7663	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2656	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3198
EcoGene	EcoGene:EG12804	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004211	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010506	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
Bos taurus	ENSBTAP00000013373 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000017456 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-050420-277 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000021574 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000229329 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000027392 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000022125 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Mus musculus	MGI:1337124 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000008135 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000018734 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000153995 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000042665 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	YRBI	From SHIGELLACYC
E. coli O157	YRBI	From ECOO157CYC
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Notes

Families

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<protect> See Help:Evolution_families for help entering or editing information in this section of EcoliWiki.

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF08282 haloacid dehalogenase-like hydrolase
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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)
↑ ^2.00 ^2.01 ^2.02 ^2.03 ^2.04 ^2.05 ^2.06 ^2.07 ^2.08 ^2.09 ^2.10 ^2.11 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).

kdsC: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 kdsC Expression

Notes

Links

Evolution

Homologs in Other Organisms

Notes

Families

Notes

Links

References

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