Q8ZB47 (KDSC_YERPE) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC
EC=3.1.3.45

Alternative name(s):
KDO 8-P phosphatase

Gene names

Name:	kdsC
Ordered Locus Names:	YPO3578, y0150, YP_3833

Organism

Yersinia pestis

Taxonomic identifier

632 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Yersinia

Protein attributes

Sequence length	187 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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.
Catalytic activity	3-deoxy-D-manno-octulosonate 8-phosphate + H2O = 3-deoxy-D-manno-octulosonate + phosphate.
Cofactor	Magnesium Probable.
Pathway	Carbohydrate biosynthesis; 3-deoxy-D-manno-octulosonate biosynthesis; 3-deoxy-D-manno-octulosonate from D-ribulose 5-phosphate: step 3/3. Bacterial outer membrane biogenesis; lipopolysaccharide biosynthesis.
Subunit structure	Homotetramer By similarity. Ref.4
Sequence similarities	Belongs to the kdsC family.

Ontologies

Keywords
Biological process	Lipopolysaccharide biosynthesis
Ligand	Magnesium Metal-binding
Molecular function	Hydrolase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	lipopolysaccharide biosynthetic process Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	3-deoxy-manno-octulosonate-8-phosphatase activity Inferred from electronic annotation. Source: EC metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 187

187

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

PRO_0000201702

Regions

Region

31 – 33

3

Substrate binding By similarity

Region

54 – 58

5

Substrate binding By similarity

Region

75 – 76

2

Substrate binding By similarity

Sites

Metal binding

31

1

Magnesium By similarity

Metal binding

33

1

Magnesium; via carbonyl oxygen By similarity

Metal binding

124

1

Magnesium By similarity

Binding site

33

1

Substrate By similarity

Binding site

62

1

Substrate By similarity

Binding site

77

1

Substrate By similarity

Binding site

85

1

Substrate By similarity

Binding site

101

1

Substrate By similarity

Binding site

186

1

Substrate; via carbonyl oxygen By similarity

Secondary structure

1

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187

Helix Strand Turn

Details...

Helix

16 – 22

7

Beta strand

26 – 30

5

Beta strand

41 – 43

3

Beta strand

50 – 53

4

Helix

62 – 66

5

Beta strand

70 – 74

5

Helix

80 – 88

9

Beta strand

93 – 95

3

Helix

101 – 112

12

Helix

116 – 118

3

Beta strand

119 – 122

4

Helix

126 – 128

3

Helix

129 – 132

4

Beta strand

138 – 140

3

Turn

146 – 148

3

Helix

149 – 151

3

Beta strand

152 – 155

4

Helix

165 – 175

11

Sequences

	Sequence		Length	Mass (Da)
	Q8ZB47 [UniParc]. Last modified March 1, 2002. Version 1. Checksum: 299EA75C7DEA7878	FASTA	187	20,299
	10 20 30 40 50 60 MSNTAYIDTC YGPVADDVIQ RAANIRLLIC DVDGVMSDGL IYMGNQGEEL KAFNVRDGYG 70 80 90 100 110 120 IRCLITSDID VAIITGRRAK LLEDRANTLG ITHLYQGQSD KLVAYHELLA TLQCQPEQVA 130 140 150 160 170 180 YIGDDLIDWP VMAQVGLSVA VADAHPLLLP KAHYVTRIKG GRGAVREVCD LILLAQDKLE GATGLSI

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Genome sequence of Yersinia pestis, the causative agent of plague." Parkhill J., Wren B.W., Thomson N.R., Titball R.W., Holden M.T.G., Prentice M.B., Sebaihia M., James K.D., Churcher C.M., Mungall K.L., Baker S., Basham D., Bentley S.D., Brooks K., Cerdeno-Tarraga A.-M., Chillingworth T., Cronin A., Davies R.M. , Davis P., Dougan G., Feltwell T., Hamlin N., Holroyd S., Jagels K., Karlyshev A.V., Leather S., Moule S., Oyston P.C.F., Quail M.A., Rutherford K.M., Simmonds M., Skelton J., Stevens K., Whitehead S., Barrell B.G. Nature 413:523-527(2001) [PubMed: 11586360] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: CO-92 / Biovar Orientalis.
[2]	"Genome sequence of Yersinia pestis KIM." Deng W., Burland V., Plunkett G. III, Boutin A., Mayhew G.F., Liss P., Perna N.T., Rose D.J., Mau B., Zhou S., Schwartz D.C., Fetherston J.D., Lindler L.E., Brubaker R.R., Plano G.V., Straley S.C., McDonough K.A., Nilles M.L. , Matson J.S., Blattner F.R., Perry R.D. J. Bacteriol. 184:4601-4611(2002) [PubMed: 12142430] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: KIM5 / Biovar Mediaevalis.
[3]	"Complete genome sequence of Yersinia pestis strain 91001, an isolate avirulent to humans." Song Y., Tong Z., Wang J., Wang L., Guo Z., Han Y., Zhang J., Pei D., Zhou D., Qin H., Pang X., Han Y., Zhai J., Li M., Cui B., Qi Z., Jin L., Dai R. , Chen F., Li S., Ye C., Du Z., Lin W., Wang J., Yu J., Yang H., Wang J., Huang P., Yang R. DNA Res. 11:179-197(2004) [PubMed: 15368893] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: 91001 / Biovar Mediaevalis.
[4]	"1.95 angstrom resolution crystal structure of 3-deoxy-d- manno-octulosonate 8-phosphate phosphatase from Yersinia pestis." Papazisi L., Anderson W.F. Submitted (AUG-2009) to the PDB data bank Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS), SUBUNIT.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AL590842 Genomic DNA. Translation: CAL22166.1.
AE009952 Genomic DNA. Translation: AAM83744.1.
AE017042 Genomic DNA. Translation: AAS63980.1.

PIR

AC0435.

RefSeq

NP_667493.1. NC_004088.1.
NP_995103.1. NC_005810.1.
YP_002348465.1. NC_003143.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3IJ5	X-ray	1.95	A/B/C/D	1-187	[»]

ProteinModelPortal

Q8ZB47.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

1145097.
1176398.
2764371.

GenomeReviews

Gene locus y0150 in contig AE009952_GR.
Gene locus YP_3833 in contig AE017042_GR.
Gene locus YPO3578 in contig AL590842_GR.

KEGG

ype:YPO3578.
ypk:y0150.
ypm:YP_3833.

Phylogenomic databases

HOGENOM

HBG471796.

OMA

KTFNTLD.

ProtClustDB

PRK09484.

Enzyme and pathway databases

BioCyc

YPES187410:Y0150-MONOMER.
YPES214092:YPO3578-MONOMER.

Family and domain databases

InterPro

IPR023214. HAD-like_dom.
IPR013200. HAD-SF_hydro-like_3.
IPR010023. KDO_8-P_phosphatase.
[Graphical view]

Gene3D

G3DSA:3.40.50.1000. HAD-like_dom. 1 hit.

KO

K03270.

PANTHER

PTHR26053. PTHR26053. 1 hit.

Pfam

PF08282. Hydrolase_3. 1 hit.
[Graphical view]

PIRSF

PIRSF006118. KDO8-P_Ptase. 1 hit.

SUPFAM

SSF56784. HAD-like_dom. 1 hit.

TIGRFAMs

TIGR01670. YrbI-phosphatas. 1 hit.

ProtoNet

Search...

Entry information

Entry name

KDSC_YERPE

Accession

Primary (citable) accession number: Q8ZB47
Secondary accession number(s): Q0WB73

Entry history

Integrated into UniProtKB/Swiss-Prot:	September 26, 2003
Last sequence update:	March 1, 2002
Last modified:	November 16, 2011
This is version 69 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program