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11  structures 572  species 1  interaction 1339  sequences 14  architectures

Family: HEPN (PF05168)

Summary: HEPN domain

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HEPN domain Edit Wikipedia article

HEPN domain
PDB 1ufb EBI.jpg
crystal structure of tt1696 from thermus thermophilus hb8
Identifiers
Symbol HEPN
Pfam PF05168
Pfam clan CL0291
InterPro IPR007842
SCOP 1o3u
SUPERFAMILY 1o3u

In molecular biology, the HEPN domain (higher eukaryotes and prokaryotes nucleotide-binding domain) is a region of approximately 110 amino acids found in the C terminus of sacsin, a chaperonin implicated in an early-onset neurodegenerative disease in human, and in many bacterial and archaea proteins. There are three classes of proteins with HEPN domains:

  • Single-domain HEPN proteins found in many bacteria.
  • A multidomain sacsin protein in genomes of fish and mammals. The HEPN domain is located at the C terminus of the protein, directly after the DnaJ domain. The crystal structure of the HEPN domain from the TM0613 protein of Thermotoga maritima indicates that it is structurally similar to the C-terminal all-alpha-helical domain of kanamycin nucleotidyltransferases (KNTases). It is composed of five alpha helices, three of which form an up- and-down helical bundle, with a pair of short helices on the side. The distant structural similarity suggests that the HEPN domain might be involved in nucleotide binding.[1]

References[edit]

  1. ^ Grynberg M, Erlandsen H, Godzik A (May 2003). "HEPN: a common domain in bacterial drug resistance and human neurodegenerative proteins". Trends Biochem. Sci. 28 (5): 224–6. doi:10.1016/S0968-0004(03)00060-4. PMID 12765831. 

This article incorporates text from the public domain Pfam and InterPro IPR007842

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Literature references

  1. Grynberg M, Erlandsen H, Godzik A; , Trends Biochem Sci 2003;28:224-226.: HEPN: a common domain in bacterial drug resistance and human neurodegenerative proteins. PUBMED:12765831 EPMC:12765831


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007842

The HEPN (higher eukaryotes and prokaryotes nucleotide-binding) domain is a region of 110 residues found in the C terminus of sacsin, a chaperonin implicated in an early-onset neurodegenerative disease in human, and in many bacterial and archeabacterial proteins. There are three classes of proteins with HEPN domain:

  • Single-domain HEPN proteins found in many bacteria.
  • Two-domain proteins with N-terminal nucleotidyltransferase (NT) and C- terminal HEPN domains. This N-terminal NT domain belongs to a large family of NTs, which includes several classes of enzymes that are responsible for some types of bacterial resistance to aminoglycosides. These enzymes deactivate various antibiotics by transferring a nucleotidyl group to the drug.
  • A multidomain sacsin protein in genomes of fish and mammals. The HEPN domain is located at the C terminus of the protein, directly after the DnaJ domain (see PROSITEDOC).
  • The crystal structure of the HEPN domain from the TM0613 protein of Thermotoga maritima indicates that it is structurally similar to the C-terminal all- alpha-helical domain of kanamycin nucleotidyltransferases (KNTases). It is composed of five alpha helices, three of which form an up- and-down helical bundle, with a pair of short helices on the side. The distant structural similarity suggests that the HEPN domain might be involved in nucleotide binding [PUBMED:12765831].

    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 KNTase_C (CL0291), which has the following description:

    This alpha helical domain is found associated with a variety of nucleotidyltransferase domains.

    The clan contains the following 8 members:

    DUF294_C DUF4145 DUF86 GlnD_UR_UTase HEPN KNTase_C NTase_sub_bind PaREP1

    Alignments

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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
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    (1339)
    Representative proteomes NCBI
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    Meta
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    RP75
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    Format an alignment

      Seed
    (92)
    Full
    (1339)
    Representative proteomes NCBI
    (1274)
    Meta
    (106)
    RP15
    (263)
    RP35
    (417)
    RP55
    (547)
    RP75
    (648)
    Alignment:
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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
    (92)
    Full
    (1339)
    Representative proteomes NCBI
    (1274)
    Meta
    (106)
    RP15
    (263)
    RP35
    (417)
    RP55
    (547)
    RP75
    (648)
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    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: COG2250
    Previous IDs: DUF712;
    Type: Family
    Author: Bateman A
    Number in seed: 92
    Number in full: 1339
    Average length of the domain: 115.30 aa
    Average identity of full alignment: 18 %
    Average coverage of the sequence by the domain: 27.05 %

    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 21.0 21.0
    Trusted cut-off 21.0 21.0
    Noise cut-off 20.9 20.9
    Model length: 118
    Family (HMM) version: 9
    Download: download the raw HMM for this family

    Species distribution

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    Interactions

    There is 1 interaction for this family. More...

    HEPN

    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 HEPN domain has been found. There are 11 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 seqence.

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