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Protein

3-deoxy-manno-octulosonate cytidylyltransferase

Gene

kdsB

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

Functioni

Activates KDO (a required 8-carbon sugar) for incorporation into bacterial lipopolysaccharide in Gram-negative bacteria.By similarity

Catalytic activityi

CTP + 3-deoxy-D-manno-octulosonate = diphosphate + CMP-3-deoxy-D-manno-octulosonate.

Cofactori

Pathwayi: CMP-3-deoxy-D-manno-octulosonate biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes CMP-3-deoxy-D-manno-octulosonate from 3-deoxy-D-manno-octulosonate and CTP.
Proteins known to be involved in this subpathway in this organism are:
  1. 3-deoxy-manno-octulosonate cytidylyltransferase (kdsB)
This subpathway is part of the pathway CMP-3-deoxy-D-manno-octulosonate biosynthesis, which is itself part of Nucleotide-sugar biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes CMP-3-deoxy-D-manno-octulosonate from 3-deoxy-D-manno-octulosonate and CTP, the pathway CMP-3-deoxy-D-manno-octulosonate biosynthesis and in Nucleotide-sugar 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.

GO - Molecular functioni

  • 3-deoxy-manno-octulosonate cytidylyltransferase activity Source: EcoCyc
  • magnesium ion binding Source: EcoCyc

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Nucleotidyltransferase, Transferase

Keywords - Biological processi

Lipopolysaccharide biosynthesis

Keywords - Ligandi

Magnesium

Enzyme and pathway databases

BioCyciEcoCyc:CPM-KDOSYNTH-MONOMER.
ECOL316407:JW0901-MONOMER.
MetaCyc:CPM-KDOSYNTH-MONOMER.
UniPathwayiUPA00030.
UPA00358; UER00476.

Names & Taxonomyi

Protein namesi
Recommended name:
3-deoxy-manno-octulosonate cytidylyltransferase (EC:2.7.7.38)
Alternative name(s):
CMP-2-keto-3-deoxyoctulosonic acid synthase
Short name:
CKS
Short name:
CMP-KDO synthase
Gene namesi
Name:kdsB
Ordered Locus Names:b0918, JW0901
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10519. kdsB.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved
Chaini2 – 2482473-deoxy-manno-octulosonate cytidylyltransferasePRO_0000188501Add
BLAST

Proteomic databases

EPDiP04951.
PaxDbiP04951.
PRIDEiP04951.

2D gel databases

SWISS-2DPAGEP04951.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
nemRP674302EBI-544810,EBI-544803
rutRP0ACU22EBI-544810,EBI-1121539

Protein-protein interaction databases

BioGridi4260010. 206 interactions.
DIPiDIP-10066N.
IntActiP04951. 19 interactions.
MINTiMINT-1224838.
STRINGi511145.b0918.

Structurei

Secondary structure

1
248
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 85Combined sources
Beta strandi14 – 163Combined sources
Helixi19 – 213Combined sources
Beta strandi23 – 286Combined sources
Helixi29 – 3911Combined sources
Beta strandi43 – 508Combined sources
Helixi52 – 609Combined sources
Beta strandi64 – 674Combined sources
Helixi75 – 8612Combined sources
Beta strandi93 – 975Combined sources
Helixi106 – 11712Combined sources
Beta strandi122 – 1298Combined sources
Helixi133 – 1364Combined sources
Beta strandi143 – 1464Combined sources
Beta strandi150 – 1589Combined sources
Helixi164 – 1696Combined sources
Beta strandi179 – 1813Combined sources
Beta strandi183 – 1886Combined sources
Helixi189 – 1979Combined sources
Helixi202 – 2076Combined sources
Helixi212 – 2165Combined sources
Beta strandi221 – 2255Combined sources
Helixi237 – 24610Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1VH1X-ray2.60A/B/C/D2-248[»]
3K8DX-ray1.90A/B/C/D1-248[»]
3K8EX-ray2.51A/B/C/D1-248[»]
ProteinModelPortaliP04951.
SMRiP04951. Positions 2-247.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP04951.

Family & Domainsi

Sequence similaritiesi

Belongs to the KdsB family.Curated

Phylogenomic databases

eggNOGiENOG4105CET. Bacteria.
COG1212. LUCA.
HOGENOMiHOG000007602.
InParanoidiP04951.
KOiK00979.
OMAiNSGTERC.
OrthoDBiEOG6KT2SK.
PhylomeDBiP04951.

Family and domain databases

Gene3Di3.90.550.10. 1 hit.
HAMAPiMF_00057. CMP_KDO_synth.
InterProiIPR003329. Cytidylyl_trans.
IPR004528. KdsB.
IPR029044. Nucleotide-diphossugar_trans.
[Graphical view]
PANTHERiPTHR21485:SF4. PTHR21485:SF4. 1 hit.
PfamiPF02348. CTP_transf_3. 1 hit.
[Graphical view]
SUPFAMiSSF53448. SSF53448. 1 hit.
TIGRFAMsiTIGR00466. kdsB. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P04951-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSFVVIIPAR YASTRLPGKP LVDINGKPMI VHVLERARES GAERIIVATD
60 70 80 90 100
HEDVARAVEA AGGEVCMTRA DHQSGTERLA EVVEKCAFSD DTVIVNVQGD
110 120 130 140 150
EPMIPATIIR QVADNLAQRQ VGMATLAVPI HNAEEAFNPN AVKVVLDAEG
160 170 180 190 200
YALYFSRATI PWDRDRFAEG LETVGDNFLR HLGIYGYRAG FIRRYVNWQP
210 220 230 240
SPLEHIEMLE QLRVLWYGEK IHVAVAQEVP GTGVDTPEDL ERVRAEMR
Length:248
Mass (Da):27,614
Last modified:January 23, 2007 - v2
Checksum:iAAB3CFDF4841FE7A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J02614 Genomic DNA. Translation: AAA83877.1.
U00096 Genomic DNA. Translation: AAC74004.1.
AP009048 Genomic DNA. Translation: BAA35664.1.
PIRiA26322.
RefSeqiNP_415438.1. NC_000913.3.
WP_000011603.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC74004; AAC74004; b0918.
BAA35664; BAA35664; BAA35664.
GeneIDi945539.
KEGGiecj:JW0901.
eco:b0918.
PATRICi32117049. VBIEscCol129921_0949.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J02614 Genomic DNA. Translation: AAA83877.1.
U00096 Genomic DNA. Translation: AAC74004.1.
AP009048 Genomic DNA. Translation: BAA35664.1.
PIRiA26322.
RefSeqiNP_415438.1. NC_000913.3.
WP_000011603.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1VH1X-ray2.60A/B/C/D2-248[»]
3K8DX-ray1.90A/B/C/D1-248[»]
3K8EX-ray2.51A/B/C/D1-248[»]
ProteinModelPortaliP04951.
SMRiP04951. Positions 2-247.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260010. 206 interactions.
DIPiDIP-10066N.
IntActiP04951. 19 interactions.
MINTiMINT-1224838.
STRINGi511145.b0918.

2D gel databases

SWISS-2DPAGEP04951.

Proteomic databases

EPDiP04951.
PaxDbiP04951.
PRIDEiP04951.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74004; AAC74004; b0918.
BAA35664; BAA35664; BAA35664.
GeneIDi945539.
KEGGiecj:JW0901.
eco:b0918.
PATRICi32117049. VBIEscCol129921_0949.

Organism-specific databases

EchoBASEiEB0514.
EcoGeneiEG10519. kdsB.

Phylogenomic databases

eggNOGiENOG4105CET. Bacteria.
COG1212. LUCA.
HOGENOMiHOG000007602.
InParanoidiP04951.
KOiK00979.
OMAiNSGTERC.
OrthoDBiEOG6KT2SK.
PhylomeDBiP04951.

Enzyme and pathway databases

UniPathwayiUPA00030.
UPA00358; UER00476.
BioCyciEcoCyc:CPM-KDOSYNTH-MONOMER.
ECOL316407:JW0901-MONOMER.
MetaCyc:CPM-KDOSYNTH-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP04951.
PROiP04951.

Family and domain databases

Gene3Di3.90.550.10. 1 hit.
HAMAPiMF_00057. CMP_KDO_synth.
InterProiIPR003329. Cytidylyl_trans.
IPR004528. KdsB.
IPR029044. Nucleotide-diphossugar_trans.
[Graphical view]
PANTHERiPTHR21485:SF4. PTHR21485:SF4. 1 hit.
PfamiPF02348. CTP_transf_3. 1 hit.
[Graphical view]
SUPFAMiSSF53448. SSF53448. 1 hit.
TIGRFAMsiTIGR00466. kdsB. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Primary structure of CTP:CMP-3-deoxy-D-manno-octulosonate cytidylyltransferase (CMP-KDO synthetase) from Escherichia coli."
    Goldman R.C., Bolling T.J., Kohlbrenner W.E., Kim Y., Fox J.L.
    J. Biol. Chem. 261:15831-15835(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE.
    Strain: K12.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "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.
  5. "Escherichia coli proteome analysis using the gene-protein database."
    VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
    Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY 2D-GEL.

Entry informationi

Entry nameiKDSB_ECOLI
AccessioniPrimary (citable) accession number: P04951
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: January 23, 2007
Last modified: March 16, 2016
This is version 150 of the entry and version 2 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

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.