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Protein

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

Gene

kdsC

Organism
Yersinia pestis
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the biosynthesis of lipopolysaccharides (LPSs). 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 similarity).By similarity

Catalytic activityi

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

Cofactori

Mg2+Curated

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), 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 bindingi31 – 311MagnesiumBy similarity
Metal bindingi33 – 331Magnesium; via carbonyl oxygenBy similarity
Binding sitei33 – 331SubstrateBy similarity
Binding sitei62 – 621SubstrateBy similarity
Binding sitei77 – 771SubstrateBy similarity
Binding sitei85 – 851SubstrateBy similarity
Binding sitei101 – 1011SubstrateBy similarity
Metal bindingi124 – 1241MagnesiumBy similarity
Binding sitei186 – 1861Substrate; via carbonyl oxygenBy similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Lipopolysaccharide biosynthesis

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciYPES214092:GKDD-3535-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:YPO3578, y0150, YP_3833
OrganismiYersinia pestis
Taxonomic identifieri632 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeYersinia
Proteomesi
  • UP000000815 Componenti: Chromosome
  • UP000001019 Componenti: Chromosome
  • UP000002490 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 1871873-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsCPRO_0000201702Add
BLAST

Interactioni

Subunit structurei

Homotetramer.By similarity

Protein-protein interaction databases

STRINGi187410.y0150.

Structurei

Secondary structure

1
187
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi16 – 227Combined sources
Beta strandi26 – 305Combined sources
Turni33 – 353Combined sources
Beta strandi36 – 449Combined sources
Beta strandi49 – 546Combined sources
Helixi55 – 6612Combined sources
Beta strandi70 – 745Combined sources
Helixi80 – 8910Combined sources
Beta strandi93 – 953Combined sources
Helixi101 – 11212Combined sources
Helixi116 – 1183Combined sources
Beta strandi119 – 1235Combined sources
Helixi126 – 1283Combined sources
Helixi129 – 1324Combined sources
Beta strandi135 – 1406Combined sources
Turni146 – 1483Combined sources
Helixi149 – 1513Combined sources
Beta strandi152 – 1554Combined sources
Turni160 – 1634Combined sources
Helixi164 – 17512Combined sources
Turni179 – 1813Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3IJ5X-ray1.95A/B/C/D1-187[»]
ProteinModelPortaliQ8ZB47.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ8ZB47.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni31 – 333Substrate bindingBy similarity
Regioni54 – 585Substrate bindingBy similarity
Regioni75 – 762Substrate bindingBy similarity

Sequence similaritiesi

Belongs to the KdsC family.Curated

Phylogenomic databases

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

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.

Q8ZB47-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSNTAYIDTC YGPVADDVIQ RAANIRLLIC DVDGVMSDGL IYMGNQGEEL
60 70 80 90 100
KAFNVRDGYG IRCLITSDID VAIITGRRAK LLEDRANTLG ITHLYQGQSD
110 120 130 140 150
KLVAYHELLA TLQCQPEQVA YIGDDLIDWP VMAQVGLSVA VADAHPLLLP
160 170 180
KAHYVTRIKG GRGAVREVCD LILLAQDKLE GATGLSI
Length:187
Mass (Da):20,299
Last modified:March 1, 2002 - v1
Checksum:i299EA75C7DEA7878
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL590842 Genomic DNA. Translation: CAL22166.1.
AE009952 Genomic DNA. Translation: AAM83744.1.
AE017042 Genomic DNA. Translation: AAS63980.1.
PIRiAC0435.
RefSeqiWP_002228203.1. NZ_LQAY01000029.1.
YP_002348465.1. NC_003143.1.

Genome annotation databases

EnsemblBacteriaiAAM83744; AAM83744; y0150.
AAS63980; AAS63980; YP_3833.
GeneIDi1176398.
KEGGiype:YPO3578.
ypj:CH55_2490.
ypk:y0150.
ypl:CH46_1512.
ypm:YP_3833.
ypv:BZ15_4157.
ypw:CH59_2469.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL590842 Genomic DNA. Translation: CAL22166.1.
AE009952 Genomic DNA. Translation: AAM83744.1.
AE017042 Genomic DNA. Translation: AAS63980.1.
PIRiAC0435.
RefSeqiWP_002228203.1. NZ_LQAY01000029.1.
YP_002348465.1. NC_003143.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3IJ5X-ray1.95A/B/C/D1-187[»]
ProteinModelPortaliQ8ZB47.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi187410.y0150.

Protocols and materials databases

DNASUi1145097.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAM83744; AAM83744; y0150.
AAS63980; AAS63980; YP_3833.
GeneIDi1176398.
KEGGiype:YPO3578.
ypj:CH55_2490.
ypk:y0150.
ypl:CH46_1512.
ypm:YP_3833.
ypv:BZ15_4157.
ypw:CH59_2469.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayiUPA00030.
UPA00357; UER00475.
BioCyciYPES214092:GKDD-3535-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ8ZB47.

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...

Entry informationi

Entry nameiKDSC_YERPE
AccessioniPrimary (citable) accession number: Q8ZB47
Secondary accession number(s): Q0WB73
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 26, 2003
Last sequence update: March 1, 2002
Last modified: September 7, 2016
This is version 100 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, Reference 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.