Kinesin
Types of Kinesins
There are over forty kinesins found in humans alone. The Kinesin superfamily has a high degree of sequence identity in their motor domains, and can be divided into three major groups depending upon the location of the motor domain, which can be positioned on the N-terminal (N-kinesins), C-terminal (C-kinesins) or internally (M-kinesins). These groups can be further subdivided based on phylogeny. Several subgroups are found only in higher plants, such as Arabidopsis, suggesting a broader range of functions in these organisms.
What InterPro Tells Us:
Below is the InterPro entry for human kinesin heavy chain, or kinesin I (conventional kinesin).
P33176 Human Kinesin Heavy Chain
(KIF5B)
InterPro Domain Architecture
|
InterPro Entry |
Method Accession |
Graphical Match |
Method Name |
|
IPR001752 |
PF00225 |
|
|
|
IPR001752 |
PR00380 |
|
|
|
IPR001752 |
PS00411 |
|
|
|
IPR001752 |
PS50067 |
|
|
|
IPR001752 |
SM00129 |
|
|
|
Classification |
PDB Chain/Domain ID |
PDB Chain/Structural Domains |
|
|
1mkj |
1mkja |
|
|
|
3.40.850.10.1 |
1mkjA0 |
|
|
|
c.37.1.9 |
d1mkja_ |
|
|
From the graphical match
above, you can see that the signatures (method accession) all fall into one
InterPro entry for human kinesin heavy chain, namely IPR001752, which represents
the kinesin motor domain. Five
signatures represent IPR001752: PF00225 from the PFAM database,
PR00380 from the PRINTS
database (derived from four well conserved motifs), PS00411 and PS50067 from the PROSITE
database, and SM00129 from the SMART
database. The human kinesin heavy chain
contains an N-terminal motor domain, followed by a short neck linker and a
coiled-coil dimerisation domain.
Neither the neck linker nor the coiled-coil domain are represented by
signatures in InterPro (as demonstrated by the absence of signatures in the
C-terminal region of the graphical match above).
The remaining three entries in the
table above are from the structural database PDB (green stripe), and
from the structural classification databases CATH (pink stripe) and SCOP (black
stripe) (the names such as 1mkjA0 are derived
from the PDB entry upon which they are based, here PDB entry 1mkj, chain A).
The graphical match for the PDB entry 1mkja displays the length
of the original PDB entry, here covering the entire motor domain. CATH and SCOP also cover the entire motor
domain and provide a structural classification of this domain as a P-loop
containing nucleoside triphosphate hydrolase (1mkjA0 in CATH and d1mkja_ in SCOP).
What the Structure Tells Us
Structures
associated with the kinesin motor domain can be viewed using AstexViewer®,
which is linked from the Match Table above via the logo 
on the
InterPro page (please note, there is no link directly from this page to the
AstexViewer®, therefore you need to go to the link on the InterPro page for P33176). The AstexViewer® displays the PDB structure
with the particular CATH or SCOP domain highlighted in yellow.
There are many structures associated with various kinesin proteins for several different species in the Protein Data Bank (PDB). A detailed description and visualisation of the structural features of kinesin motor domains can be found at the PDB ‘Molecule of the Month’. The crystallographic structures of different kinesin proteins have provided insight into how these molecules move in a cell.