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IDENTIFICATION OF CONSERVED
CORE STRUCTURES AND ACTIVE SITE RESIDUES IN KINESINS. |
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ABSTRACT |
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The kinesin molecular
motor protein has been previously identified as a member
of the P-loop nucleotide triphosphate containing hydrolysing
superfamily of enzymes, based on the conservation of nucleotide
binding site residues (SCOP release 1.57; Murzin et al,
1995). |
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Structural alignments of the
14 currently available kinesin motor domain structures
confirmed that these enzymes have a common core structure
and revealed extensive similarity located outside the
conserved nucleotide binding site residues. |
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| A model structure composed of
the structurally invariant core residues was constructed.
This model was subsequently used to scan the entire RCSB
PDB for structurally similar proteins. |
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| The results of this procedure
were analysed with respect to their suitability for future
use in sequence profiles for the identification of structurally
homologous sequences. |
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The initial alignment of the
18 kinesin structures.
Variant regions such as the helical tails, the switch
II region and the loop-5 are present in all motor domain
structures. |
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| The resulted structurally
invariable kinesin core domain and the alignment used
for its production are illustrated with thick ribbons.
The regions of the alignment that were not included in
the core are shown in various colours. |
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| REFERENCES: |
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| Gerstein M and Altman RB. (1995).
"Average Core Structures and Variability measures
for Protein Families: Application to Immunoglobins",
J.Mol.Biol. 251:161-175 |
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| Artymiuk PJ, Poirrette AR, Grindley
HM, Rice DW, Willett P. (1994). "A graph-theoretic
approach to the identification of three-dimensional patterns
of amino-acid side-chains in protein structures",
J.Mol.Biol. 243:327-344 |
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| Yun M, Zhang X, Park CG, Park
HW, Endow SA (2001). "A Structural Pathway for Activation
of the Kinesin Motor ATPase", Embo J. 20:2611-2618 |
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| Lo Conte L., Brenner S E., Hubbard
TJP, Chothia C., Murzin A. (2002). "SCOP database
in 2002: refinements accommodate structural genomics",
Nucl. Acid Res. 30(1), 264-267. |
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| PREVIOUS PROJECTS: |
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| SNP
Viewer |
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| Kinesins
Structural Bioinformatics |
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| Microarray
Data Analysis |
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| Methylation
Studies in Cancer |
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