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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)DescriptionActionsGraphical viewLength
Metal bindingi31MagnesiumBy similarity1
Metal bindingi33Magnesium; via carbonyl oxygenBy similarity1
Binding sitei33SubstrateBy similarity1
Binding sitei62SubstrateBy similarity1
Binding sitei77SubstrateBy similarity1
Binding sitei85SubstrateBy similarity1
Binding sitei101SubstrateBy similarity1
Metal bindingi124MagnesiumBy similarity1
Binding sitei186Substrate; via carbonyl oxygenBy similarity1

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

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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesYersiniaceaeYersinia
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)DescriptionActionsGraphical viewLength
ChainiPRO_00002017021 – 1873-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsCAdd BLAST187

Interactioni

Subunit structurei

Homotetramer.By similarity

Protein-protein interaction databases

STRINGi187410.y0150.

Structurei

Secondary structure

1187
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi16 – 22Combined sources7
Beta strandi26 – 30Combined sources5
Turni33 – 35Combined sources3
Beta strandi36 – 44Combined sources9
Beta strandi49 – 54Combined sources6
Helixi55 – 66Combined sources12
Beta strandi70 – 74Combined sources5
Helixi80 – 89Combined sources10
Beta strandi93 – 95Combined sources3
Helixi101 – 112Combined sources12
Helixi116 – 118Combined sources3
Beta strandi119 – 123Combined sources5
Helixi126 – 128Combined sources3
Helixi129 – 132Combined sources4
Beta strandi135 – 140Combined sources6
Turni146 – 148Combined sources3
Helixi149 – 151Combined sources3
Beta strandi152 – 155Combined sources4
Turni160 – 163Combined sources4
Helixi164 – 175Combined sources12
Turni179 – 181Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3IJ5X-ray1.95A/B/C/D1-187[»]
ProteinModelPortaliQ8ZB47.
SMRiQ8ZB47.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ8ZB47.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni31 – 33Substrate bindingBy similarity3
Regioni54 – 58Substrate bindingBy similarity5
Regioni75 – 76Substrate bindingBy similarity2

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_LQBA01000026.1.
YP_002348465.1. NC_003143.1.

Genome annotation databases

EnsemblBacteriaiAAM83744; AAM83744; y0150.
AAS63980; AAS63980; YP_3833.
GeneIDi1176398.
KEGGiype:YPO3578.
ypk:y0150.
ypm:YP_3833.

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_LQBA01000026.1.
YP_002348465.1. NC_003143.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3IJ5X-ray1.95A/B/C/D1-187[»]
ProteinModelPortaliQ8ZB47.
SMRiQ8ZB47.
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.
ypk:y0150.
ypm:YP_3833.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayiUPA00030.
UPA00357; UER00475.

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: November 2, 2016
This is version 102 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.