Protein folds and functions.
BACKGROUND
The recent rapid increase in the number of available three-dimensional protein structures has further highlighted the necessity to understand the relationship between biological function and structure. Using structural classification schemes such as SCOP, CATH and DALI, it is now possible to explore global relationships between protein fold and function, something which was previously impractical.


RESULTS
Using a relational database of CATH data we have generated fold distributions for arbitrary selections of proteins automatically. These distributions have been examined in the light of protein function and bound ligand. Different enzyme classes are not clearly reflected in distributions of protein class and architecture, whereas the type of bound ligand has a much more dramatic effect.


CONCLUSIONS
The availability of structural classification data has enabled this novel overview analysis. We conclude that function at the top level of the EC number enzyme classification is not related to fold, as only a very few specific residues are actually responsible for enzyme activity. Conversely, the fold is much more closely related to ligand type.
Martin
A C
AC
Department of Biochemistry and Molecular Biology, University College, London, UK.
Orengo
C A
CA
Hutchinson
E G
EG
Jones
S
S
Karmirantzou
M
M
Laskowski
R A
RA
Mitchell
J B
JB
Taroni
C
C
Thornton
J M
JM
D001665:Binding Sites; D050260:Carbohydrate Metabolism; D002241:Carbohydrates / Q000737:chemistry; D004247:DNA / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000145:classification / Q000378:metabolism; D004798:Enzymes / Q000737:chemistry / Q000378:metabolism; D006418:Heme / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D008962:Models, Theoretical; D009711:Nucleotides / Q000378:metabolism; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry / Q000145:classification* / Q000378:metabolism*; D012984:Software; D013329:Structure-Activity Relationship
D002241:Carbohydrates; D004268:DNA-Binding Proteins; D004798:Enzymes; D009711:Nucleotides; D011506:Proteins; D006418:Heme; D004247:DNA