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Protein

3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC

Gene

kdsC

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the biosynthesis of lipopolysaccharides (LPSs), but is not essential (PubMed:16765569). Catalyzes the hydrolysis of 3-deoxy-D-manno-octulosonate 8-phosphate (KDO 8-P) to 3-deoxy-D-manno-octulosonate (KDO) and inorganic phosphate (PubMed:12639950, PubMed:16765569).2 Publications

Catalytic activityi

3-deoxy-D-manno-octulosonate 8-phosphate + H2O = 3-deoxy-D-manno-octulosonate + phosphate.1 Publication

Cofactori

Mg2+1 Publication, Co2+1 PublicationNote: Mg2+. The phosphatase activity is also stimulated by cobalt ions, whereas baryum, zinc, and manganese ions are less effective stimulators.1 Publication

Enzyme regulationi

Inhibited by calcium, cadmium, mercury, and copper ions.1 Publication

pH dependencei

Optimum pH is 5.5 (at pH 7.5 and 37 degrees Celsius).1 Publication

Pathwayi: 3-deoxy-D-manno-octulosonate biosynthesis

This protein is involved in step 3 of the subpathway that synthesizes 3-deoxy-D-manno-octulosonate from D-ribulose 5-phosphate.
Proteins known to be involved in the 3 steps of the subpathway in this organism are:
  1. Arabinose 5-phosphate isomerase KdsD (kdsD)
  2. 2-dehydro-3-deoxyphosphooctonate aldolase (kdsA)
  3. 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC (kdsC)
This subpathway is part of the pathway 3-deoxy-D-manno-octulosonate biosynthesis, which is itself part of Carbohydrate biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes 3-deoxy-D-manno-octulosonate from D-ribulose 5-phosphate, the pathway 3-deoxy-D-manno-octulosonate biosynthesis and in Carbohydrate biosynthesis.

Pathwayi: lipopolysaccharide biosynthesis

This protein is involved in the pathway lipopolysaccharide biosynthesis, which is part of Bacterial outer membrane biogenesis.
View all proteins of this organism that are known to be involved in the pathway lipopolysaccharide biosynthesis and in Bacterial outer membrane biogenesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi32 – 321MagnesiumBy similarity
Metal bindingi34 – 341Magnesium; via carbonyl oxygenBy similarity
Binding sitei34 – 341SubstrateBy similarity
Binding sitei63 – 631SubstrateBy similarity
Binding sitei78 – 781SubstrateBy similarity
Binding sitei86 – 861SubstrateBy similarity
Binding sitei102 – 1021SubstrateBy similarity
Metal bindingi125 – 1251MagnesiumBy similarity
Binding sitei187 – 1871Substrate; via carbonyl oxygenBy similarity

GO - Molecular functioni

GO - Biological processi

  • dephosphorylation Source: GOC
  • lipopolysaccharide biosynthetic process Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Lipopolysaccharide biosynthesis

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:G7663-MONOMER.
ECOL316407:JW3165-MONOMER.
UniPathwayiUPA00030.
UPA00357; UER00475.

Names & Taxonomyi

Protein namesi
Recommended name:
3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC (EC:3.1.3.451 Publication)
Alternative name(s):
KDO 8-P phosphatase
Gene namesi
Name:kdsC
Synonyms:yrbI, yrbJ
Ordered Locus Names:b3198, JW3165
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG12804. kdsC.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved
Chaini2 – 1881873-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsCPRO_0000201696Add
BLAST

Proteomic databases

EPDiP0ABZ4.
PaxDbiP0ABZ4.
PRIDEiP0ABZ4.

Interactioni

Subunit structurei

Homotetramer.1 Publication

Protein-protein interaction databases

BioGridi4261882. 244 interactions.
DIPiDIP-48034N.
IntActiP0ABZ4. 2 interactions.
STRINGi511145.b3198.

Structurei

3D structure databases

ProteinModelPortaliP0ABZ4.
SMRiP0ABZ4. Positions 8-188.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni32 – 343Substrate bindingBy similarity
Regioni55 – 595Substrate bindingBy similarity
Regioni76 – 772Substrate bindingBy similarity

Sequence similaritiesi

Belongs to the KdsC family.Curated

Phylogenomic databases

eggNOGiENOG4108Z4R. Bacteria.
COG1778. LUCA.
HOGENOMiHOG000264740.
InParanoidiP0ABZ4.
KOiK03270.
OMAiFDENFHE.
OrthoDBiEOG62C9JR.
PhylomeDBiP0ABZ4.

Family and domain databases

Gene3Di3.40.50.1000. 1 hit.
InterProiIPR023214. HAD-like_dom.
IPR010023. KDO_8-P_phosphatase.
[Graphical view]
PfamiPF08282. Hydrolase_3. 1 hit.
[Graphical view]
PIRSFiPIRSF006118. KDO8-P_Ptase. 1 hit.
SUPFAMiSSF56784. SSF56784. 1 hit.
TIGRFAMsiTIGR01670. KdsC-phosphatas. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P0ABZ4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSKAGASLAT CYGPVSADVI AKAENIRLLI LDVDGVLSDG LIYMGNNGEE
60 70 80 90 100
LKAFNVRDGY GIRCALTSDI EVAIITGRKA KLVEDRCATL GITHLYQGQS
110 120 130 140 150
NKLIAFSDLL EKLAIAPENV AYVGDDLIDW PVMEKVGLSV AVADAHPLLI
160 170 180
PRADYVTRIA GGRGAVREVC DLLLLAQGKL DEAKGQSI
Length:188
Mass (Da):19,997
Last modified:November 8, 2005 - v1
Checksum:i75AF512CF4E5E6E2
GO

Sequence cautioni

The sequence AAA57999.1 differs from that shown. Reason: Frameshift at position 116. Curated
The sequence AAA58000.1 differs from that shown. Reason: Frameshift at position 116. Curated
The sequence AAA58000.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Mass spectrometryi

Molecular mass is 19881 Da from positions 2 - 188. Determined by ESI. 1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U18997 Genomic DNA. Translation: AAA57999.1. Frameshift.
U18997 Genomic DNA. Translation: AAA58000.1. Sequence problems.
U00096 Genomic DNA. Translation: AAC76230.1.
AP009048 Genomic DNA. Translation: BAE77242.1.
PIRiH65110.
RefSeqiNP_417665.1. NC_000913.3.
WP_000030005.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC76230; AAC76230; b3198.
BAE77242; BAE77242; BAE77242.
GeneIDi947717.
KEGGiecj:JW3165.
eco:b3198.
PATRICi32121816. VBIEscCol129921_3292.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U18997 Genomic DNA. Translation: AAA57999.1. Frameshift.
U18997 Genomic DNA. Translation: AAA58000.1. Sequence problems.
U00096 Genomic DNA. Translation: AAC76230.1.
AP009048 Genomic DNA. Translation: BAE77242.1.
PIRiH65110.
RefSeqiNP_417665.1. NC_000913.3.
WP_000030005.1. NZ_LN832404.1.

3D structure databases

ProteinModelPortaliP0ABZ4.
SMRiP0ABZ4. Positions 8-188.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261882. 244 interactions.
DIPiDIP-48034N.
IntActiP0ABZ4. 2 interactions.
STRINGi511145.b3198.

Proteomic databases

EPDiP0ABZ4.
PaxDbiP0ABZ4.
PRIDEiP0ABZ4.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76230; AAC76230; b3198.
BAE77242; BAE77242; BAE77242.
GeneIDi947717.
KEGGiecj:JW3165.
eco:b3198.
PATRICi32121816. VBIEscCol129921_3292.

Organism-specific databases

EchoBASEiEB2656.
EcoGeneiEG12804. kdsC.

Phylogenomic databases

eggNOGiENOG4108Z4R. Bacteria.
COG1778. LUCA.
HOGENOMiHOG000264740.
InParanoidiP0ABZ4.
KOiK03270.
OMAiFDENFHE.
OrthoDBiEOG62C9JR.
PhylomeDBiP0ABZ4.

Enzyme and pathway databases

UniPathwayiUPA00030.
UPA00357; UER00475.
BioCyciEcoCyc:G7663-MONOMER.
ECOL316407:JW3165-MONOMER.

Miscellaneous databases

PROiP0ABZ4.

Family and domain databases

Gene3Di3.40.50.1000. 1 hit.
InterProiIPR023214. HAD-like_dom.
IPR010023. KDO_8-P_phosphatase.
[Graphical view]
PfamiPF08282. Hydrolase_3. 1 hit.
[Graphical view]
PIRSFiPIRSF006118. KDO8-P_Ptase. 1 hit.
SUPFAMiSSF56784. SSF56784. 1 hit.
TIGRFAMsiTIGR01670. KdsC-phosphatas. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  2. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. "Escherichia coli YrbI is 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase."
    Wu J., Woodard R.W.
    J. Biol. Chem. 278:18117-18123(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION, MASS SPECTROMETRY, SUBUNIT.
    Strain: B.
  4. "Non-essential KDO biosynthesis and new essential cell envelope biogenesis genes in the Escherichia coli yrbG-yhbG locus."
    Sperandeo P., Pozzi C., Deho G., Polissi A.
    Res. Microbiol. 157:547-558(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.

Entry informationi

Entry nameiKDSC_ECOLI
AccessioniPrimary (citable) accession number: P0ABZ4
Secondary accession number(s): P45396, P45398, Q2M914
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 8, 2005
Last sequence update: November 8, 2005
Last modified: March 16, 2016
This is version 91 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.