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Protein

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

Gene

kdsC

Organism
Yersinia pestis
Status
Reviewed-Annotation score: -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 (AU253_04860), 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

Keywordsi

Molecular functionHydrolase
Biological processLipopolysaccharide biosynthesis
LigandMagnesium, 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

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002017021 – 1873-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsCAdd BLAST187

Proteomic databases

PaxDbiQ8ZB47

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
OMAiCVGDDYN

Family and domain databases

Gene3Di3.40.50.1000, 1 hit
InterProiView protein in InterPro
IPR036412 HAD-like_sf
IPR023214 HAD_sf
IPR010023 KdsC_fam
PIRSFiPIRSF006118 KDO8-P_Ptase, 1 hit
SFLDiSFLDG01138 C1.6.2:_Deoxy-d-mannose-octulo, 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_PDBR01000029.1
YP_002348465.1, NC_003143.1

Genome annotation databases

EnsemblBacteriaiAAM83744; AAM83744; y0150
AAS63980; AAS63980; YP_3833
GeneIDi1176398
KEGGiype:YPO3578
ypk:y0150
ypm:YP_3833
PATRICifig|214092.21.peg.4072

Entry informationi

Entry nameiKDSC_YERPE
AccessioniPrimary (citable) accession number: Q8ZB47
Secondary accession number(s): Q0WB73
Entry historyiIntegrated into UniProtKB/Swiss-Prot: September 26, 2003
Last sequence update: March 1, 2002
Last modified: May 23, 2018
This is version 109 of the entry and version 1 of the sequence. See 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

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