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0  structures 2354  species 0  interactions 2446  sequences 6  architectures

Family: LpxB (PF02684)

Summary: Lipid-A-disaccharide synthetase

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Lipid-A-disaccharide synthetase Provide feedback

This is a family of lipid-A-disaccharide synthetases, EC:2.4.2.128. These enzymes catalyse the reaction: UDP-2,3-bis(3-hydroxytetradecanoyl) glucosamine + 2,3-bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl 1-phosphate <=> UDP + 2,3-bis(3-hydroxytetradecanoyl)-D-glucosaminyl-1,6 -beta-D-2,3-bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl 1-phosphate. These enzymes catalyse the fist disaccharide step in the synthesis of lipid-A-disaccharide.

Literature references

  1. Servos S, Khan S, Maskell D; , Gene 1996;175:137-141.: Cloning and expression of genes encoding lipid A biosynthesis from Haemophilus influenzae type b. PUBMED:8917090 EPMC:8917090

  2. Crowell DN, Reznikoff WS, Raetz CR; , J Bacteriol 1987;169:5727-5734.: Nucleotide sequence of the Escherichia coli gene for lipid A disaccharide synthase. PUBMED:2824445 EPMC:2824445


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003835

The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (EC) and related proteins into distinct sequence based families has been described [PUBMED:9334165]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'.

These enzymes belong to the glycosyltransferase family 19 CAZY. Lipid-A-disaccharide synthetase EC is involved with acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase EC and tetraacyldisaccharide 4'-kinase EC in the biosynthesis of the phosphorylated glycolipid, lipid A, in the outer membrane of Escherichia coli and other bacteria. These enzymes catalyse the first disaccharide step in the synthesis of lipid-A-disaccharide.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

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Alignments

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(8)
Full
(2446)
Representative proteomes NCBI
(1902)
Meta
(2953)
RP15
(184)
RP35
(368)
RP55
(488)
RP75
(585)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(8)
Full
(2446)
Representative proteomes NCBI
(1902)
Meta
(2953)
RP15
(184)
RP35
(368)
RP55
(488)
RP75
(585)
Alignment:
Format:
Order:
Sequence:
Gaps:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(8)
Full
(2446)
Representative proteomes NCBI
(1902)
Meta
(2953)
RP15
(184)
RP35
(368)
RP55
(488)
RP75
(585)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

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 View help on the curation process

Seed source: COG0763
Previous IDs: none
Type: Family
Author: Bashton M, Bateman A
Number in seed: 8
Number in full: 2446
Average length of the domain: 358.50 aa
Average identity of full alignment: 35 %
Average coverage of the sequence by the domain: 93.79 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.0 20.0
Trusted cut-off 20.0 20.0
Noise cut-off 19.9 19.9
Model length: 373
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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