Protein structures are classified to generate overviews of structure types and detect evolutionary relationships. Major classification schemes include SCOP, CATH, and FSSP. SCOP classifies proteins into classes, folds, superfamilies, and families based on structural and sequence similarities. CATH also uses a hierarchical system of classes, architectures, topologies, and superfamilies. FSSP provides fully automated and updated structural alignments and classifications.

1. Protein structure Classification
Ole Lund,
Associate professor,
CBS, DTU.

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Why classify proteins
 Number of solved structures grow rapidly
 Generate overview of structure types
 Detect similarities (evolutionary relationships)
 Set up prediction benchmarks

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Classification schemes
 SCOP
– Manual classification (A Murzin)
 CATH
– Semi manual classification (C orengo)
 FSSP
– Automatic classification (L Holm)

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Levels in SCOP
1. Class 10
2. Folds 648
3. Superfamilies 1007
4. Families 1699
Murzin et al., 1995
http://scop.mrc-lmb.cam.ac.uk/scop/

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Major classes in scop
 Classes
– All alpha proteins
– Alpha and beta proteins (a/b)
– Alpha and beta proteins (a+b)
– Multi-domain proteins
– Membrane and cell surface proteins
– Small proteins

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All alpha: Hemoglobin (1bab)

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All beta: Immunoglobulin (8fab)

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Alpha/beta: Triosephosphate
isomerase (1hti)

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Alpha+beta: Lysozyme (1jsf)

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Folds*
 Each Class may be divided into one or more folds
 Proteins which have the same (>~50%) secondary
structure elements arranged the in the same order in
the protein chain and in three dimensions are
classified as having the same fold
*confusingly also called fold classes

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Superfamilies
 Superfamilies are a subdivisions of folds
 A superfamily contains proteins which are thought to
be evolutionarily related due to
– Sequence
– Function
– Special structural features
 Relationships between members of a superfamily
may not be readily recognizable from the sequence
alone

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Families
 Subdivision of supefamilies
 Contains members whose relationship is
readily recognizable from the sequence
(>~25% sequence identity)
 Families are further subdivided in to Proteins
 Proteins are divided into Species
– The same protein may be found in several
species

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Families

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CATH
 Levels
 Class
 Architecture
– This level is unique to CATH (~30 is defined)
 Topology
– ~Fold(/superfamily) in SCOP
 Homologous Superfamily
– ~Superfamily(/family) in SCOP
http://www.biochem.ucl.ac.uk/bsm/cath_new/index.html

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Architecture
 Same overall arrangement of secondary
structures
– Example: The architecture :Two layer beta sheet
proteins contains different folds each with a
distinct number and connectivity of strands

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FSSP
 Fully automated classification
 Automatic update
 Database contains structural alignments
 Tree of protein structures

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FSSP classification (MHC molecules)

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Links
 PDB
– www.rcsb.org/pdb/
 SCOP
– scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.html
 CATH
– www.biochem.ucl.ac.uk/bsm/cath_new/index.html
 FSSP
– http://www.bioinfo.biocenter.helsinki.fi:8080/dali/index.html