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Protein

2-dehydro-3-deoxyphosphooctonate aldolase

Gene

kdsA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Synthesis of KDO 8-P which is required for lipid A maturation and cellular growth.

Catalytic activityi

Phosphoenolpyruvate + D-arabinose 5-phosphate + H2O = 2-dehydro-3-deoxy-D-octonate 8-phosphate + phosphate.

Pathway:i3-deoxy-D-manno-octulosonate biosynthesis

This protein is involved in step 2 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.

Pathway:ilipopolysaccharide 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.

GO - Molecular functioni

  • 3-deoxy-8-phosphooctulonate synthase activity Source: EcoCyc

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

Lipopolysaccharide biosynthesis

Enzyme and pathway databases

BioCyciEcoCyc:KDO-8PSYNTH-MONOMER.
ECOL316407:JW1206-MONOMER.
MetaCyc:KDO-8PSYNTH-MONOMER.
BRENDAi2.5.1.55. 2026.
SABIO-RKP0A715.
UniPathwayiUPA00030.
UPA00357; UER00474.

Names & Taxonomyi

Protein namesi
Recommended name:
2-dehydro-3-deoxyphosphooctonate aldolase (EC:2.5.1.55)
Alternative name(s):
3-deoxy-D-manno-octulosonic acid 8-phosphate synthase
KDO-8-phosphate synthase
Short name:
KDO 8-P synthase
Short name:
KDOPS
Phospho-2-dehydro-3-deoxyoctonate aldolase
Gene namesi
Name:kdsA
Ordered Locus Names:b1215, JW1206
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10518. kdsA.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 2842842-dehydro-3-deoxyphosphooctonate aldolasePRO_0000187124Add
BLAST

Proteomic databases

PaxDbiP0A715.
PRIDEiP0A715.

2D gel databases

SWISS-2DPAGEP0A715.

Interactioni

Subunit structurei

Homotrimer.

Protein-protein interaction databases

DIPiDIP-35940N.
IntActiP0A715. 46 interactions.
MINTiMINT-1220797.
STRINGi511145.b1215.

Structurei

Secondary structure

1
284
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi6 – 83Combined sources
Beta strandi11 – 133Combined sources
Beta strandi15 – 173Combined sources
Beta strandi20 – 223Combined sources
Beta strandi24 – 274Combined sources
Helixi31 – 4818Combined sources
Beta strandi55 – 584Combined sources
Beta strandi64 – 685Combined sources
Helixi74 – 8815Combined sources
Beta strandi93 – 953Combined sources
Turni99 – 1013Combined sources
Helixi102 – 1087Combined sources
Beta strandi110 – 1145Combined sources
Helixi116 – 1194Combined sources
Helixi122 – 13110Combined sources
Beta strandi134 – 1396Combined sources
Helixi145 – 1473Combined sources
Helixi148 – 1569Combined sources
Turni157 – 1593Combined sources
Beta strandi163 – 1675Combined sources
Beta strandi173 – 1753Combined sources
Helixi183 – 1908Combined sources
Turni191 – 1933Combined sources
Beta strandi196 – 1994Combined sources
Helixi201 – 2044Combined sources
Beta strandi211 – 2133Combined sources
Turni219 – 2224Combined sources
Helixi223 – 2319Combined sources
Beta strandi234 – 2374Combined sources
Beta strandi240 – 2423Combined sources
Helixi244 – 2474Combined sources
Beta strandi250 – 2523Combined sources
Helixi257 – 2593Combined sources
Helixi260 – 27516Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1D9EX-ray2.40A/B/C/D1-284[»]
1G7UX-ray2.80A1-284[»]
1G7VX-ray2.40A1-284[»]
1GG0X-ray3.00A1-284[»]
1PHQX-ray2.70A1-284[»]
1PHWX-ray2.36A1-284[»]
1PL9X-ray2.90A1-284[»]
1Q3NX-ray2.70A1-284[»]
1X6UX-ray2.70A1-284[»]
1X8FX-ray2.40A1-284[»]
ProteinModelPortaliP0A715.
SMRiP0A715. Positions 1-284.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A715.

Family & Domainsi

Sequence similaritiesi

Belongs to the KdsA family.Curated

Phylogenomic databases

eggNOGiCOG2877.
HOGENOMiHOG000023021.
InParanoidiP0A715.
KOiK01627.
OMAiFRGIPTM.
OrthoDBiEOG680X4R.
PhylomeDBiP0A715.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_00056. KDO8P_synth.
InterProiIPR013785. Aldolase_TIM.
IPR006218. DAHP1/KDSA.
IPR006269. KDO8P_synthase.
[Graphical view]
PANTHERiPTHR21057:SF2. PTHR21057:SF2. 1 hit.
PfamiPF00793. DAHP_synth_1. 1 hit.
[Graphical view]
TIGRFAMsiTIGR01362. KDO8P_synth. 1 hit.

Sequencei

Sequence statusi: Complete.

P0A715-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKQKVVSIGD INVANDLPFV LFGGMNVLES RDLAMRICEH YVTVTQKLGI
60 70 80 90 100
PYVFKASFDK ANRSSIHSYR GPGLEEGMKI FQELKQTFGV KIITDVHEPS
110 120 130 140 150
QAQPVADVVD VIQLPAFLAR QTDLVEAMAK TGAVINVKKP QFVSPGQMGN
160 170 180 190 200
IVDKFKEGGN EKVILCDRGA NFGYDNLVVD MLGFSIMKKV SGNSPVIFDV
210 220 230 240 250
THALQCRDPF GAASGGRRAQ VAELARAGMA VGLAGLFIEA HPDPEHAKCD
260 270 280
GPSALPLAKL EPFLKQMKAI DDLVKGFEEL DTSK
Length:284
Mass (Da):30,833
Last modified:June 7, 2005 - v1
Checksum:i35E79D692D134535
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti22 – 221F → L in CAA29067 (PubMed:3039295).Curated

Mass spectrometryi

Molecular mass is 30842±17 Da from positions 1 - 284. Determined by ESI. 1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X05552 Genomic DNA. Translation: CAA29067.1.
U18555 Genomic DNA. Translation: AAC43441.1.
U00096 Genomic DNA. Translation: AAC74299.1.
AP009048 Genomic DNA. Translation: BAA36073.1.
PIRiI83573. SYECOL.
RefSeqiNP_415733.1. NC_000913.3.
WP_000811065.1. NZ_CP010445.1.

Genome annotation databases

EnsemblBacteriaiAAC74299; AAC74299; b1215.
BAA36073; BAA36073; BAA36073.
GeneIDi945785.
KEGGieco:b1215.
PATRICi32117682. VBIEscCol129921_1263.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X05552 Genomic DNA. Translation: CAA29067.1.
U18555 Genomic DNA. Translation: AAC43441.1.
U00096 Genomic DNA. Translation: AAC74299.1.
AP009048 Genomic DNA. Translation: BAA36073.1.
PIRiI83573. SYECOL.
RefSeqiNP_415733.1. NC_000913.3.
WP_000811065.1. NZ_CP010445.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1D9EX-ray2.40A/B/C/D1-284[»]
1G7UX-ray2.80A1-284[»]
1G7VX-ray2.40A1-284[»]
1GG0X-ray3.00A1-284[»]
1PHQX-ray2.70A1-284[»]
1PHWX-ray2.36A1-284[»]
1PL9X-ray2.90A1-284[»]
1Q3NX-ray2.70A1-284[»]
1X6UX-ray2.70A1-284[»]
1X8FX-ray2.40A1-284[»]
ProteinModelPortaliP0A715.
SMRiP0A715. Positions 1-284.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-35940N.
IntActiP0A715. 46 interactions.
MINTiMINT-1220797.
STRINGi511145.b1215.

2D gel databases

SWISS-2DPAGEP0A715.

Proteomic databases

PaxDbiP0A715.
PRIDEiP0A715.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74299; AAC74299; b1215.
BAA36073; BAA36073; BAA36073.
GeneIDi945785.
KEGGieco:b1215.
PATRICi32117682. VBIEscCol129921_1263.

Organism-specific databases

EchoBASEiEB0513.
EcoGeneiEG10518. kdsA.

Phylogenomic databases

eggNOGiCOG2877.
HOGENOMiHOG000023021.
InParanoidiP0A715.
KOiK01627.
OMAiFRGIPTM.
OrthoDBiEOG680X4R.
PhylomeDBiP0A715.

Enzyme and pathway databases

UniPathwayiUPA00030.
UPA00357; UER00474.
BioCyciEcoCyc:KDO-8PSYNTH-MONOMER.
ECOL316407:JW1206-MONOMER.
MetaCyc:KDO-8PSYNTH-MONOMER.
BRENDAi2.5.1.55. 2026.
SABIO-RKP0A715.

Miscellaneous databases

EvolutionaryTraceiP0A715.
PROiP0A715.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_00056. KDO8P_synth.
InterProiIPR013785. Aldolase_TIM.
IPR006218. DAHP1/KDSA.
IPR006269. KDO8P_synthase.
[Graphical view]
PANTHERiPTHR21057:SF2. PTHR21057:SF2. 1 hit.
PfamiPF00793. DAHP_synth_1. 1 hit.
[Graphical view]
TIGRFAMsiTIGR01362. KDO8P_synth. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The kdsA gene coding for 3-deoxy-D-manno-octulosonic acid 8-phosphate synthetase is part of an operon in Escherichia coli."
    Woisetschlaeger M., Hoegenauer G.
    Mol. Gen. Genet. 207:369-373(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  2. "Expression of genes kdsA and kdsB involved in 3-deoxy-D-manno-octulosonic acid metabolism and biosynthesis of enterobacterial lipopolysaccharide is growth phase regulated primarily at the transcriptional level in Escherichia coli K-12."
    Strohmaier H., Remler P., Renner W., Hoegenauer G.
    J. Bacteriol. 177:4488-4500(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  5. "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.
  6. "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12."
    Link A.J., Robison K., Church G.M.
    Electrophoresis 18:1259-1313(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 1-12.
    Strain: K12 / EMG2.
  7. "Overproduction and one-step purification of Escherichia coli 3-deoxy-D-manno-octulosonic acid 8-phosphate synthase and oxygen transfer studies during catalysis using isotopic-shifted heteronuclear NMR."
    Dotson G.D., Dua R.K., Clemens J.C., Wooten E.W., Woodard R.W.
    J. Biol. Chem. 270:13698-13705(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION, PROTEIN SEQUENCE OF 1-10.
  8. "3-deoxy-D-manno-octulosonate-8-phosphate synthase from Escherichia coli. Model of binding of phosphoenolpyruvate and D-arabinose-5-phosphate."
    Wagner T., Kretsinger R.H., Bauerle R., Tolbert W.D.
    J. Mol. Biol. 301:233-238(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
  9. "Crystal structures of KDOP synthase in its binary complexes with the substrate phosphoenolpyruvate and with a mechanism-based inhibitor."
    Asojo O., Friedman J., Adir N., Belakhov V., Shoham Y., Baasov T.
    Biochemistry 40:6326-6334(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS), MASS SPECTROMETRY.

Entry informationi

Entry nameiKDSA_ECOLI
AccessioniPrimary (citable) accession number: P0A715
Secondary accession number(s): P17579
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 7, 2005
Last sequence update: June 7, 2005
Last modified: July 22, 2015
This is version 96 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, Direct protein sequencing, 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.