Summary: Lipopolysaccharide kinase (Kdo/WaaP) family
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This is the Wikipedia entry entitled "Lipopolysaccharide kinase (Kdo/WaaP) family". More...
Lipopolysaccharide kinase (Kdo/WaaP) family Edit Wikipedia article
Kdo | |||||||||
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Identifiers | |||||||||
Symbol | Kdo | ||||||||
Pfam | PF06293 | ||||||||
Pfam clan | CL0016 | ||||||||
InterPro | IPR010440 | ||||||||
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In molecular biology, the lipopolysaccharide kinase (Kdo/WaaP) family is a family of kinases.
The family consists of lipopolysaccharide kinases including lipopolysaccharide core heptose(I) kinase rfaP (encoded by the waaP (rfaP) gene). Lipopolysaccharide core heptose(I) kinase rfaP is required for the addition of phosphate to O-4 of the first heptose residue of the lipopolysaccharide (LPS) inner core region. It has previously been shown that it is necessary for resistance to hydrophobic and polycationic antimicrobials in E. coli and that it is required for virulence in invasive strains of Salmonella enterica.[1] The family also includes 3-deoxy-D-manno-octulosonic acid kinase (KDO kinase) from Haemophilus influenzae, which phosphorylates Kdo-lipid IV(A), a lipopolysaccharide precursor, and is involved in virulence.[2]
References
- ^ Yethon JA, Whitfield C (February 2001). "Purification and characterization of WaaP from Escherichia coli, a lipopolysaccharide kinase essential for outer membrane stability". J. Biol. Chem. 276 (8): 5498–504. doi:10.1074/jbc.M008255200. PMID 11069912.
- ^ White KA, Lin S, Cotter RJ, Raetz CR (1999). "A Haemophilus influenzae gene that encodes a membrane bound 3-deoxy-D-manno-octulosonic acid (Kdo) kinase. Possible involvement of kdo phosphorylation in bacterial virulence.". J Biol Chem. 274 (44): 31391–400. doi:10.1074/jbc.274.44.31391. PMID 10531340.
Further reading
- Krupa A, Srinivasan N (2002). "Lipopolysaccharide phosphorylating enzymes encoded in the genomes of Gram-negative bacteria are related to the eukaryotic protein kinases.". Protein Sci. 11 (6): 1580–4. doi:10.1110/ps.3560102. PMC 2373617
. PMID 12021457.
This article incorporates text from the public domain Pfam and InterPro IPR010440
This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.
This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
Lipopolysaccharide kinase (Kdo/WaaP) family Provide feedback
These lipopolysaccharide kinases are related to protein kinases PF00069. This family includes waaP (rfaP) gene product is required for the addition of phosphate to O-4 of the first heptose residue of the lipopolysaccharide (LPS) inner core region. It has previously been shown that WaaP is necessary for resistance to hydrophobic and polycationic antimicrobials in E. coli and that it is required for virulence in invasive strains of S. enterica [1].
Literature references
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Yethon JA, Whitfield C; , J Biol Chem 2001;276:5498-5504.: Purification and characterization of WaaP from Escherichia coli, a lipopolysaccharide kinase essential for outer membrane stability. PUBMED:11069912 EPMC:11069912
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Krupa A, Srinivasan N; , Protein Sci 2002;11:1580-1584.: Lipopolysaccharide phosphorylating enzymes encoded in the genomes of Gram-negative bacteria are related to the eukaryotic protein kinases. PUBMED:12021457 EPMC:12021457
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White KA, Lin S, Cotter RJ, Raetz CR; , J Biol Chem 1999;274:31391-31400.: A Haemophilus influenzae gene that encodes a membrane bound 3-deoxy-D-manno-octulosonic acid (Kdo) kinase. Possible involvement of kdo phosphorylation in bacterial virulence. PUBMED:10531340 EPMC:10531340
Internal database links
SCOOP: | ABC1 APH Choline_kinase DUF1679 DUF5898 EcKL FTA2 Haspin_kinase Kinase-like PK_Tyr_Ser-Thr Pkinase Pkinase_fungal RIO1 Seadorna_VP7 TCAD9 WaaY YrbL-PhoP_reg |
Similarity to PfamA using HHSearch: | Pkinase RIO1 APH PK_Tyr_Ser-Thr TCAD9 |
This tab holds annotation information from the InterPro database.
No InterPro data for this Pfam family.
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
This family is a member of clan PKinase (CL0016), which has the following description:
This superfamily includes the Serine/Threonine- and Tyrosine- protein kinases as well as related kinases that act on non-protein substrates.
The clan contains the following 40 members:
ABC1 AceK Act-Frag_cataly Alpha_kinase APH APH_6_hur Choline_kinase CotH DUF1679 DUF2252 DUF4135 DUF5898 EcKL Fam20C Fructosamin_kin FTA2 Haspin_kinase HipA_C Ins_P5_2-kin IPK IucA_IucC Kdo Kinase-like Kinase-PolyVal KIND Pan3_PK PI3_PI4_kinase PIP49_C PIP5K PK_Tyr_Ser-Thr Pkinase Pkinase_fungal Pox_ser-thr_kin RIO1 Seadorna_VP7 TCAD9 UL97 WaaY YrbL-PhoP_reg YukCAlignments
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...
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Seed (10) |
Full (4188) |
Representative proteomes | UniProt (22488) |
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RP15 (597) |
RP35 (1751) |
RP55 (3820) |
RP75 (7214) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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Seed (10) |
Full (4188) |
Representative proteomes | UniProt (22488) |
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RP15 (597) |
RP35 (1751) |
RP55 (3820) |
RP75 (7214) |
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Raw Stockholm | |||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
Curation
Seed source: | Krupa A, Srinivasan N |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Studholme DJ |
Number in seed: | 10 |
Number in full: | 4188 |
Average length of the domain: | 158.70 aa |
Average identity of full alignment: | 17 % |
Average coverage of the sequence by the domain: | 46.79 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 207 | ||||||||||||
Family (HMM) version: | 16 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Structures
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Kdo domain has been found. There are 5 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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