P0A715 (KDSA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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 names

Name:	kdsA
Ordered Locus Names:	b1215, JW1206

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	284 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Synthesis of KDO 8-P which is required for lipid A maturation and cellular growth. HAMAP-Rule MF_00056
Catalytic activity	Phosphoenolpyruvate + D-arabinose 5-phosphate + H2O = 2-dehydro-3-deoxy-D-octonate 8-phosphate + phosphate. HAMAP-Rule MF_00056
Pathway	Carbohydrate biosynthesis; 3-deoxy-D-manno-octulosonate biosynthesis; 3-deoxy-D-manno-octulosonate from D-ribulose 5-phosphate: step 2/3. HAMAP-Rule MF_00056 Bacterial outer membrane biogenesis; lipopolysaccharide biosynthesis. HAMAP-Rule MF_00056
Subunit structure	Homotrimer.
Subcellular location	Cytoplasm HAMAP-Rule MF_00056.
Sequence similarities	Belongs to the KdsA family.
Mass spectrometry	Molecular mass is 30842±17 Da from positions 1 - 284. Determined by ESI. Ref.9

Ontologies

Keywords
Biological process	Lipopolysaccharide biosynthesis
Cellular component	Cytoplasm
Molecular function	Transferase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	keto-3-deoxy-D-manno-octulosonic acid biosynthetic process Inferred from electronic annotation. Source: HAMAP
Cellular_component	cytosol Inferred from direct assay PubMed 16858726. Source: UniProtKB
Molecular_function	3-deoxy-8-phosphooctulonate synthase activity Inferred from direct assay PubMed 8223657. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 284

284

2-dehydro-3-deoxyphosphooctonate aldolase HAMAP-Rule MF_00056

PRO_0000187124

Experimental info

Sequence conflict

22

1

F → L in CAA29067. Ref.1

Secondary structure

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284

Helix Strand Turn

Details...

Beta strand

6 – 8

3

Beta strand

11 – 13

3

Beta strand

15 – 17

3

Beta strand

20 – 22

3

Beta strand

24 – 27

4

Helix

31 – 48

18

Beta strand

55 – 58

4

Beta strand

64 – 68

5

Helix

74 – 88

15

Beta strand

93 – 95

3

Turn

99 – 101

3

Helix

102 – 108

7

Beta strand

110 – 114

5

Helix

116 – 119

4

Helix

122 – 131

10

Beta strand

134 – 139

6

Helix

145 – 147

3

Helix

148 – 156

9

Turn

157 – 159

3

Beta strand

163 – 167

5

Beta strand

173 – 175

3

Helix

183 – 190

8

Turn

191 – 193

3

Beta strand

196 – 199

4

Helix

201 – 204

4

Beta strand

211 – 213

3

Turn

219 – 222

4

Helix

223 – 231

9

Beta strand

234 – 237

4

Beta strand

240 – 242

3

Helix

244 – 247

4

Beta strand

250 – 252

3

Helix

257 – 259

3

Helix

260 – 275

16

Sequences

	Sequence		Length	Mass (Da)
	P0A715 [UniParc]. Last modified June 7, 2005. Version 1. Checksum: 35E79D692D134535	FASTA	284	30,833
	10 20 30 40 50 60 MKQKVVSIGD INVANDLPFV LFGGMNVLES RDLAMRICEH YVTVTQKLGI PYVFKASFDK 70 80 90 100 110 120 ANRSSIHSYR GPGLEEGMKI FQELKQTFGV KIITDVHEPS QAQPVADVVD VIQLPAFLAR 130 140 150 160 170 180 QTDLVEAMAK TGAVINVKKP QFVSPGQMGN IVDKFKEGGN EKVILCDRGA NFGYDNLVVD 190 200 210 220 230 240 MLGFSIMKKV SGNSPVIFDV THALQCRDPF GAASGGRRAQ VAELARAGMA VGLAGLFIEA 250 260 270 280 HPDPEHAKCD GPSALPLAKL EPFLKQMKAI DDLVKGFEEL DTSK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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]	"A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map." Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K., Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S., Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K. , Mori H., Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G., Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M., Horiuchi T. DNA Res. 3:137-155(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] 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.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X05552 Genomic DNA. Translation: CAA29067.1.
U18555 Genomic DNA. Translation: AAC43441.1.
U00096 Genomic DNA. Translation: AAC74299.1.
AP009048 Genomic DNA. Translation: BAA36073.1.

PIR

SYECOL. I83573.

RefSeq

NP_415733.1. NC_000913.2.
YP_489482.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1D9E	X-ray	2.40	A/B/C/D	1-284	[»]
1G7U	X-ray	2.80	A	1-284	[»]
1G7V	X-ray	2.40	A	1-284	[»]
1GG0	X-ray	3.00	A	1-284	[»]
1PHQ	X-ray	2.70	A	1-284	[»]
1PHW	X-ray	2.36	A	1-284	[»]
1PL9	X-ray	2.90	A	1-284	[»]
1Q3N	X-ray	2.70	A	1-284	[»]
1X6U	X-ray	2.70	A	1-284	[»]
1X8F	X-ray	2.40	A	1-284	[»]

ProteinModelPortal

P0A715.

SMR

P0A715. Positions 1-284.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-35940N.

IntAct

P0A715. 46 interactions.

MINT

MINT-1220797.

STRING

511145.b1215.

2D gel databases

SWISS-2DPAGE

P0A715.

Proteomic databases

PaxDb

P0A715.

PRIDE

P0A715.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC74299; AAC74299; b1215.
BAA36073; BAA36073; BAA36073.

GeneID

12931123.
945785.

KEGG

ecj:Y75_p1187.
eco:b1215.

PATRIC

32117682. VBIEscCol129921_1263.

Organism-specific databases

EchoBASE

EB0513.

EcoGene

EG10518. kdsA.

Phylogenomic databases

eggNOG

COG2877.

HOGENOM

HOG000023021.

KO

K01627.

OMA

FNVPLIT.

ProtClustDB

PRK05198.

Enzyme and pathway databases

BioCyc

EcoCyc:KDO-8PSYNTH-MONOMER.
ECOL316407:JW1206-MONOMER.
MetaCyc:KDO-8PSYNTH-MONOMER.

SABIO-RK

P0A715.

UniPathway

UPA00030.
UPA00357; UER00474.

Gene expression databases

Genevestigator

P0A715.

Family and domain databases

Gene3D

3.20.20.70. 1 hit.

HAMAP

MF_00056. KDO8P_synth.

InterPro

IPR013785. Aldolase_TIM.
IPR006218. DAHP1/KDSA.
IPR006269. KDO8P_synthase.
[Graphical view]

PANTHER

PTHR21057:SF2. PTHR21057:SF2. 1 hit.

Pfam

PF00793. DAHP_synth_1. 1 hit.
[Graphical view]

TIGRFAMs

TIGR01362. KDO8P_synth. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P0A715.

Entry information

Entry name

KDSA_ECOLI

Accession

Primary (citable) accession number: P0A715
Secondary accession number(s): P17579

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 7, 2005
Last sequence update:	June 7, 2005
Last modified:	May 1, 2013
This is version 81 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program