{PDOC51766}
{PS51766; DOCKERIN}
{BEGIN}
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* Dockerin domain profile *
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Plant cell  wall  polysaccharides  comprise  the  most  abundant  reservoir of
organic carbon  in  the  biosphere.  The  cellulosomne  is a large multienzyme
complex used  by  many  anaerobic  bacteria  for  the efficient degradation of
plant-cell wall polysaccharides. The principal component of the cellulosome is
a scaffoldin  subunit,  a  large  enzyme-integrating  protein,  that  contains
cohesin modules   (usually  in  multiple  copies)  for  incorporation  of  the
different enzymes  and  other  cellulosomal  components. The enzymes contain a
complementary type  of  module, the dockerin domain, that binds tenaciously to
the cohesin modules of the scaffoldin subunit [1,2,3,4].

The dockerin  domains  consist of about 70 amino acid residues and contain two
duplicated segments,  each  of  about  22  amino  acid  residues. The first 12
residues of  these  duplicated  sequences  bear  remarkable resemblance to the
calcium-binding loop  of the EF-hand motif (see <PDOC00018>), in which all the
calcium-binding residues  (i.e.,  aspartic  acids  and asparagines) are highly
conserved. The  second halves of the duplicated sequences appear to form alpha
helices. These  helices would be analogous to the F helix of the EF-hand motif
[1,2,3,4].

The dockerin domain comprises three alpha-helices (see <PDB:2MTE>). Helices H1
and H3,  which  are  antiparallel  to one another, and the two calcium-binding
loops (Ca1  and  Ca2)  correspond to the tandem duplicated sequences that form
the two  F-hand  motifs.  A  short loop region and helix H2 connect the F-hand
motifs. The  12-residue  Ca(2+)-binding  loop  of  each  motif coordinates one
Ca(2+) ion  in  the  typical  pentagonal  bipyramid  configuration  of EF-hand
Ca(2+)-binding proteins [3,4].

The profile we developed covers the entire dockerin domain.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: July 2015 / First entry.

[ 1] Pages S., Belaich A., Belaich J.-P., Morag E., Lamed R., Shoham Y.,
     Bayer E.A.
     "Species-specificity of the cohesin-dockerin interaction between
     Clostridium thermocellum and Clostridium cellulolyticum: prediction of
     specificity determinants of the dockerin domain."
     Proteins 29:517-527(1997).
     PubMed=9408948
[ 2] Bayer E.A., Belaich J.-P., Shoham Y., Lamed R.
     "The cellulosomes: multienzyme machines for degradation of plant cell
     wall polysaccharides."
     Annu. Rev. Microbiol. 58:521-554(2004).
     PubMed=15487947; DOI=10.1146/annurev.micro.57.030502.091022
[ 3] Adams J.J., Pal G., Jia Z., Smith S.P.
     "Mechanism of bacterial cell-surface attachment revealed by the
     structure of cellulosomal type II cohesin-dockerin complex."
     Proc. Natl. Acad. Sci. U.S.A. 103:305-310(2006).
     PubMed=16384918; DOI=10.1073/pnas.0507109103
[ 4] Chen C., Cui Z., Xiao Y., Cui Q., Smith S.P., Lamed R., Bayer E.A.,
     Feng Y.
     "Revisiting the NMR solution structure of the Cel48S type-I dockerin
     module from Clostridium thermocellum reveals a cohesin-primed
     conformation."
     J. Struct. Biol. 188:188-193(2014).
     PubMed=25270376; DOI=10.1016/j.jsb.2014.09.006

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