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44  structures 564  species 0  interactions 4087  sequences 1407  architectures

Family: Dockerin_1 (PF00404)

Summary: Dockerin type I domain

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This is the Wikipedia entry entitled "Dockerin". More...

Dockerin Edit Wikipedia article

Dockerin is a protein domain found in the Cellulosome cellular structure. It is part of endoglucanase enzymes. The dockerin's binding partner is the cohesin domain. This interaction is essential to the construction of the Cellulosome complex (also know as Scaffoldin). The Dockerin domain has two in-tandem repeats of a non-EF hand calcium binding motif. Each motif is charactrized by a loop-helix structure [1].The three dimensional structure of dockerin has been determined in solution[2] as well as in complex with Cohesin [3]. There are two types of Dockerin domains: I and II which bind to Cohesin Type I and Cohesin Type II respectively. A type I dockering domain is 65-70 residues long. [4]. The binding specificity of Type I interaction was well studied by structural and mutagenesis studies. Type II interaction is less well characterized [5].

External links

Protein Structure:

  • Lytle BL, Volkman BF, Westler WM, Heckman MP, Wu JH (2001). "Solution structure of a type I dockerin domain, a novel prokaryotic, extracellular calcium-binding domain". J Mol Biol. 307: 745–753. PMID 11273698.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  • Bayer EA, Shimon LJ, Shoham Y, Lamed R (1998). "Cellulosomes-structure and ultrastructure". J Struct Biol. 124 (2–3): 221–234. PMID 10049808.{{cite journal}}: CS1 maint: multiple names: authors list (link)

Specificity Characterization:

  • Haimovitz R, Barak Y, Morag E, Voronov-Goldman M, Shoham Y, Lamed R, Bayer EA (2008). "Cohesin-dockerin microarray: Diverse specificities between two complementary families of interacting protein modules". Proteomics. 8 (5): 968–979. PMID 18219699.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  • Adams JJ, Webb BA, Spencer HL, Smith SP (2005). "Structural characterization of type II dockerin module from the cellulosome of Clostridium thermocellum: calcium-induced effects on conformation and target recognition". Biochemistry. 44 (6): 2173–2182. PMID 15697243.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  • Jindou S, Soda A, Karita S, Kajino T, Béguin P, Wu JH, Inagaki M, Kimura T, Sakka K, Ohmiya K (2004). "Cohesin-dockerin interactions within and between Clostridium josui and Clostridium thermocellum: binding selectivity between cognate dockerin and cohesin domains and species specificity". J Biol Chem. 279 (11): 9867–9874. PMID 14688277.{{cite journal}}: CS1 maint: multiple names: authors list (link)

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.

Dockerin type I domain Provide feedback

The dockerin repeat is the binding partner of the cohesin domain PF00963. The cohesin-dockerin interaction is the crucial interaction for complex formation in the cellulosome [1]. The dockerin repeats, each bearing homology to the EF-hand calcium-binding loop bind calcium [2]. This family contains two copies of the repeat.

Literature references

  1. Shoham Y, Lamed R, Bayer EA; , Trends Microbiol 1999;7:275-281.: The cellulosome concept as an efficient microbial strategy for the degradation of insoluble polysaccharides [In Process Citation] PUBMED:10390637 EPMC:10390637

  2. Lytle BL, Volkman BF, Westler WM, Wu JH; , Arch Biochem Biophys 2000;379:237-244.: Secondary structure and calcium-induced folding of the Clostridium thermocellum dockerin domain determined by NMR spectroscopy. PUBMED:10898940 EPMC:10898940

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002105

Gram-positive, thermophilic anaerobes such as Clostridium thermocellum or Clostridium cellulolyticum secretes a highly active and thermostable cellulase complex (cellulosome) responsible for the degradation of crystalline cellulose [ PUBMED:2252383 , PUBMED:1478480 ]. The cellulosome contains at least 30 polypeptides, the majority of the enzymes are endoglucanases ( EC ), but there are also some xylanases ( EC ), beta-glucosidases ( EC ) and endo-beta-1,3-1,4-glucanases ( EC ).

Complete sequence data for many of these enzymes has been obtained. A majority of these proteins contain a highly conserved type I dockerin domain of about 65 to 70 residues, which is generally (but not always) located in the C terminus. The dockerin domain is the binding partner of the cohesin domain (see INTERPRO ). The cohesin-dockerin interaction is the crucial interaction for complex formation in the cellulosome [ PUBMED:10390637 ]. The dockerin domain contains a tandem repeat of two calcium-binding loop-helix motifs (distinct from EF-hand Ca-binding motifs). These motifs are about 24 amino acids in length. This entry represents these repeated Ca-binding motifs.

Gene Ontology

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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


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.

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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...


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.

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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 View help on the curation process

Seed source: Prosite
Previous IDs: celCC;
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD , Bateman A
Number in seed: 78
Number in full: 4087
Average length of the domain: 57.6 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 5.23 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.9 22.9
Trusted cut-off 22.9 22.9
Noise cut-off 22.8 22.8
Model length: 58
Family (HMM) version: 21
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence


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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 Dockerin_1 domain has been found. There are 44 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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