Summary: Neutral/alkaline non-lysosomal ceramidase, N-terminal
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Neutral/alkaline non-lysosomal ceramidase, N-terminal Provide feedback
This family represents N-terminal domain of a group of neutral/alkaline ceramidases found in both bacteria and eukaryotes [1,2,3]. The EC classification is EC:3.5.1.23. The enzyme hydrolyses ceramide to generate sphingosine and fatty acid. The enzyme plays a regulatory role in a variety of physiological events in eukaryotes and also functions as an exotoxin in particular bacteria. This N-terminal domain carries two metal-binding sites, the first for Zn2+ residing within the domain, and the second, for Mg2+/Ca2+ lying at the interface between the two domains [4].
Literature references
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Tani M, Okino N, Mori K, Tanigawa T, Izu H, Ito M; , J Biol Chem 2000;275:11229-11234.: Molecular cloning of the full-length cDNA encoding mouse neutral ceramidase. A novel but highly conserved gene family of neutral/alkaline ceramidases. PUBMED:10753931 EPMC:10753931
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El Bawab S, Roddy P, Qian T, Bielawska A, Lemasters JJ, Hannun YA; , J Biol Chem 2000;275:21508-21513.: Molecular cloning and characterization of a human mitochondrial ceramidase. PUBMED:10781606 EPMC:10781606
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Okino N, Ichinose S, Omori A, Imayama S, Nakamura T, Ito M; , J Biol Chem 1999;274:36616-36622.: Molecular cloning, sequencing, and expression of the gene encoding alkaline ceramidase from Pseudomonas aeruginosa. Cloning of a ceramidase homologue from Mycobacterium tuberculosis. PUBMED:10593963 EPMC:10593963
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Inoue T, Okino N, Kakuta Y, Hijikata A, Okano H, Goda HM, Tani M, Sueyoshi N, Kambayashi K, Matsumura H, Kai Y, Ito M;, J Biol Chem. 2009;284:9566-9577.: Mechanistic insights into the hydrolysis and synthesis of ceramide by neutral ceramidase. PUBMED:19088069 EPMC:19088069
This tab holds annotation information from the InterPro database.
InterPro entry IPR031329
This entry represents the N-terminal domain of a group of neutral/alkaline ceramidases found in both bacteria and eukaryotes [ PUBMED:10753931 , PUBMED:10781606 , PUBMED:10593963 ]. The EC classification is ( EC ). The enzyme hydrolyses ceramide to generate sphingosine and fatty acid. The enzyme plays a regulatory role in a variety of physiological events in eukaryotes and also functions as an exotoxin in particular bacteria. This N-terminal domain carries two metal-binding sites, the first for Zn2+ residing within the domain, and the second, for Mg2+/Ca2+ lying at the interface between the two domains [ PUBMED:19088069 ].
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 DmpA_ArgJ (CL0635), which has the following description:
This superfamily includes the ArgJ protein and members of peptidase family S58. According to SCOP these proteins have a fold which resembles but is unrelated to that of the NTN hydrolases.
The clan contains the following 5 members:
ArgJ Ceramidase_alk MoCoBD_1 MoCoBD_2 Peptidase_S58Alignments
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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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 (113) |
Full (3497) |
Representative proteomes | UniProt (10015) |
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RP15 (652) |
RP35 (1719) |
RP55 (2997) |
RP75 (4343) |
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HTML | |||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
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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 (113) |
Full (3497) |
Representative proteomes | UniProt (10015) |
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RP15 (652) |
RP35 (1719) |
RP55 (2997) |
RP75 (4343) |
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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.
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
Seed source: | Pfam-B_3385 (release 7.5) |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Mifsud W |
Number in seed: | 113 |
Number in full: | 3497 |
Average length of the domain: | 387.5 aa |
Average identity of full alignment: | 33 % |
Average coverage of the sequence by the domain: | 65.02 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 509 | ||||||||||||
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 Ceramidase_alk 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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AlphaFold Structure Predictions
The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.