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24  structures 55  species 2  interactions 1647  sequences 223  architectures

Family: Dockerin_1 (PF00404)

Summary: Dockerin type I repeat

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Dockerin Edit Wikipedia article

Dockerin domain
PDB 1daq EBI.jpg
Structure of the Dockerin type I domain from C. thermocellum cellulosome.
Identifiers
Symbol Dockerin_1
Pfam PF00404
InterPro IPR018242
PROSITE PDOC00416
SCOP 1daq
SUPERFAMILY 1daq

Dockerin is a protein domain found in the cellulosome cellular structure. It is found on many endoglucanase enzymes. The dockerin's binding partner is the cohesin domain, located on the scaffoldin protein. This interaction between the dockerin domains of the enzyme constituents of the cellulosome and the cohesin domains of the scaffoldin protein is essential to the construction of the cellulosome complex.[1] The Dockerin domain has two in-tandem repeats of a non-EF hand calcium binding motif. Each motif is characterized by a loop-helix structure.[2] The three dimensional structure of dockerin has been determined in solution,[3] as well as in complex with Cohesin.[4]

There are three types of Dockerin domains: I, II and III which bind to Cohesin Type I, Cohesin Type II and Cohesin Type III respectively. A type I dockerin domain is 65-70 residues long.[5] The binding specificity of Type I interaction was well studied by structural and mutagenesis studies. Type II interaction is less well characterized.[6]

See also

References

  1. ^ Ding SY, Rincon MT, Lamed R, Martin JC, McCrae SI, Aurilia V et al. (2001). "Cellulosomal scaffoldin-like proteins from Ruminococcus flavefaciens.". J Bacteriol 183 (6): 1945–53. doi:10.1128/JB.183.6.1945-1953.2001. PMC 95089. PMID 11222592. 
  2. ^ SCOP 63447
  3. ^ PDB 1DAQ; Lytle BL, Volkman BF, Westler WM, Heckman MP, Wu JH (March 2001). "Solution structure of a type I dockerin domain, a novel prokaryotic, extracellular calcium-binding domain". J. Mol. Biol. 307 (3): 745–53. doi:10.1006/jmbi.2001.4522. PMID 11273698. 
  4. ^ PDB 1OHZ; Carvalho AL, Dias FM, Prates JA, Nagy T, Gilbert HJ, Davies GJ, Ferreira LM, Romão MJ, Fontes CM (November 2003). "Cellulosome assembly revealed by the crystal structure of the cohesin–dockerin complex". Proc. Natl. Acad. Sci. U.S.A. 100 (24): 13809–14. doi:10.1073/pnas.1936124100. PMC 283503. PMID 14623971. 
  5. ^ InterPro: IPR016134
  6. ^ Adams JJ, Webb BA, Spencer HL, Smith SP (February 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): 2173–82. doi:10.1021/bi048039u. PMID 15697243. 

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 (3): 745–753. doi:10.1006/jmbi.2001.4522. PMID 11273698. 
  • Bayer EA, Shimon LJ, Shoham Y, Lamed R (1998). "Cellulosomes-structure and ultrastructure". J Struct Biol 124 (2–3): 221–234. doi:10.1006/jsbi.1998.4065. PMID 10049808. 

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. doi:10.1002/pmic.200700486. PMID 18219699. 
  • 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. doi:10.1021/bi048039u. PMID 15697243. 
  • 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. doi:10.1074/jbc.M308673200. PMID 14688277. 

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Dockerin type I repeat 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].

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


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR018242

The dockerin repeat 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 repeats are present as a tandem repeat of a calcium-binding motif bearing homology to the EF-hand calcium-binding loop [PUBMED:10898940].

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

This family is a member of clan EF_hand (CL0220), which has the following description:

The EF hand is a calcium binding domain found in a wide variety of proteins [1].

The clan contains the following 16 members:

Caleosin Dockerin_1 EF-hand_1 EF-hand_10 EF-hand_2 EF-hand_3 EF-hand_4 EF-hand_5 EF-hand_6 EF-hand_7 EF-hand_8 EF-hand_9 EF-hand_like EFhand_Ca_insen S_100 SPARC_Ca_bdg

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
(130)
Full
(1647)
Representative proteomes NCBI
(1211)
Meta
(47)
RP15
(294)
RP35
(503)
RP55
(504)
RP75
(504)
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  Seed
(130)
Full
(1647)
Representative proteomes NCBI
(1211)
Meta
(47)
RP15
(294)
RP35
(503)
RP55
(504)
RP75
(504)
Alignment:
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  Seed
(130)
Full
(1647)
Representative proteomes NCBI
(1211)
Meta
(47)
RP15
(294)
RP35
(503)
RP55
(504)
RP75
(504)
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.

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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.

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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
Author: Finn RD
Number in seed: 130
Number in full: 1647
Average length of the domain: 21.00 aa
Average identity of full alignment: 49 %
Average coverage of the sequence by the domain: 5.22 %

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 20.5 20.5
Trusted cut-off 20.5 20.5
Noise cut-off 20.4 20.4
Model length: 21
Family (HMM) version: 13
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Species distribution

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Interactions

There are 2 interactions for this family. More...

Dockerin_1 Cohesin

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 Dockerin_1 domain has been found. There are 24 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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