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Protein

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

Gene

kdsC

Organism
Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the biosynthesis of lipopolysaccharides (LPSs) (By similarity). Catalyzes the hydrolysis of 3-deoxy-D-manno-octulosonate 8-phosphate (KDO 8-P) to 3-deoxy-D-manno-octulosonate (KDO) and inorganic phosphate.By similarity1 Publication

Catalytic activityi

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

Cofactori

Mg2+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 – 321Magnesium
Metal bindingi34 – 341Magnesium; via carbonyl oxygen
Binding sitei34 – 341Substrate1 Publication
Binding sitei63 – 631Substrate1 Publication
Binding sitei78 – 781Substrate1 Publication
Binding sitei86 – 861Substrate1 Publication
Binding sitei102 – 1021Substrate1 Publication
Metal bindingi125 – 1251Magnesium
Binding sitei187 – 1871Substrate; via carbonyl oxygen1 Publication

GO - Molecular functioni

  • 3-deoxy-manno-octulosonate-8-phosphatase activity Source: UniProtKB
  • metal ion binding Source: UniProtKB-KW

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

BioCyciECOL199310:C3958-MONOMER.
UniPathwayiUPA00030.
UPA00357; UER00475.

Names & Taxonomyi

Protein namesi
Recommended name:
3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC (EC:3.1.3.45)
Alternative name(s):
KDO 8-P phosphatase
Gene namesi
Name:kdsC
Ordered Locus Names:c3958
OrganismiEscherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)
Taxonomic identifieri199310 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000001410 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 1881883-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsCPRO_0000201698Add
BLAST

Interactioni

Subunit structurei

Homotetramer.1 Publication

Protein-protein interaction databases

STRINGi199310.c3958.

Structurei

Secondary structure

1
188
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi17 – 248Combined sources
Beta strandi27 – 315Combined sources
Helixi33 – 375Combined sources
Beta strandi40 – 456Combined sources
Beta strandi50 – 556Combined sources
Helixi56 – 6611Combined sources
Turni67 – 693Combined sources
Beta strandi71 – 755Combined sources
Helixi81 – 9010Combined sources
Beta strandi94 – 963Combined sources
Helixi103 – 11311Combined sources
Helixi117 – 1193Combined sources
Beta strandi120 – 1267Combined sources
Helixi127 – 1293Combined sources
Helixi130 – 1334Combined sources
Beta strandi136 – 1416Combined sources
Turni147 – 1493Combined sources
Helixi150 – 1523Combined sources
Beta strandi153 – 1564Combined sources
Turni161 – 1644Combined sources
Helixi165 – 17612Combined sources
Turni180 – 1823Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2R8EX-ray1.40A/B/C/D/E/F/G/H1-188[»]
2R8XX-ray2.60A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P1-188[»]
2R8YX-ray1.85A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P1-188[»]
2R8ZX-ray2.10A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P1-188[»]
3HYCX-ray3.06A/B/C/D/E/F/G/H1-188[»]
3I6BX-ray2.49A/B/C/D1-180[»]
ProteinModelPortaliP67653.
SMRiP67653. Positions 8-188.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP67653.

Family & Domainsi

Region

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

Sequence similaritiesi

Belongs to the KdsC family.Curated

Phylogenomic databases

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

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.

P67653-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSKAGASLAT CYGPVSADVM 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):20,015
Last modified:October 11, 2004 - v1
Checksum:i6A40ED8C20B1E3A7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE014075 Genomic DNA. Translation: AAN82398.1.
RefSeqiWP_000030016.1. NC_004431.1.

Genome annotation databases

EnsemblBacteriaiAAN82398; AAN82398; c3958.
KEGGiecc:c3958.
PATRICi18285690. VBIEscCol75197_3725.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE014075 Genomic DNA. Translation: AAN82398.1.
RefSeqiWP_000030016.1. NC_004431.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2R8EX-ray1.40A/B/C/D/E/F/G/H1-188[»]
2R8XX-ray2.60A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P1-188[»]
2R8YX-ray1.85A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P1-188[»]
2R8ZX-ray2.10A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P1-188[»]
3HYCX-ray3.06A/B/C/D/E/F/G/H1-188[»]
3I6BX-ray2.49A/B/C/D1-180[»]
ProteinModelPortaliP67653.
SMRiP67653. Positions 8-188.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi199310.c3958.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAN82398; AAN82398; c3958.
KEGGiecc:c3958.
PATRICi18285690. VBIEscCol75197_3725.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayiUPA00030.
UPA00357; UER00475.
BioCyciECOL199310:C3958-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP67653.

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: CFT073 / ATCC 700928 / UPEC.
  2. "The tail of KdsC: conformational changes control the activity of a haloacid dehalogenase superfamily phosphatase."
    Biswas T., Yi L., Aggarwal P., Wu J., Rubin J.R., Stuckey J.A., Woodard R.W., Tsodikov O.V.
    J. Biol. Chem. 284:30594-30603(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN COMPLEX WITH SUBSTRATE AND DIVALENT METALS, FUNCTION AS A KDO 8-P PHOSPHATASE, REACTION MECHANISM, COFACTOR, SUBUNIT.

Entry informationi

Entry nameiKDSC_ECOL6
AccessioniPrimary (citable) accession number: P67653
Secondary accession number(s): Q83JF3, Q8FD72
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 11, 2004
Last sequence update: October 11, 2004
Last modified: November 11, 2015
This is version 77 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

3D-structure, Complete proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  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.