T he o/B
barreli s a commonlyo ccurringm otifc onstructefdro m repetitionosf
theB -a-B loop motif fhis a/B barreli s a domaino f pyruvatek inase( a
glycolytice nzymef)r omr abbit( derivedfr omp DB lD l pKN).
(Fig. 4-20). In ttus structure, each parallel B segment
is attachedt o its neighborb y an a-helicals egment.A ll
connectionsa rer ight-handedT. he o,lpbarrelisf oundi n
many enzyrnes, often with a binding site (for a cofactor
or substrate)in the form of a pocketn earo ne end of the
barrel. Note that domains with similar folding patterns
are said to have the same motif even though their constituent
a helices and B sheets may differ in length.
ProteMino tifAs reth eB asfiso rP rotein
StructuI Cral assciafit ion
$ ProteinA rchitecture-TertiarSy tructureo f LargeG lobularp roteins,
lV.S tructuralC lassificationo f proteinsA s we have seen,
understandingth e complexitieso f tertiary structurei s
made easierb y considerings ubstructuresT. akingt his
FIGURE4- 21 Organizationo f proteinsb asedo n motifs. Shown
herea rej usta few of the hundredso f knowns tablem otifsT. heya re
divided into four classesa: ll a, all B, a/B, anda * p. Structural
classificatiodna taf rom the SCOp( StructuraCl lassificatioonf pro_
teins)d atabase(h ttp://scomp rc-lmbc am.acu k/scop)a re alsop ro_
idea further, researihers have organized the complete
contentso fprotein databasesa ccordingt o hierarchical
Ievelso f structure.A ll of these databasesre ly on data
and information deposited in the Protein Data Bank.
The Structural Classificationo f Proteins (SCOP)d atabase
is a good example of this important trend in biochemistry.
At the highest level of classification, the
SCO P database( http ://scop.mrc-lmbc.a m.a c.u k/scop)
borrows a scheme already in common use, with four
classes of protein structure: all c, all F, qlg (with a
and B segmentsin terspersedo r alternating),a nd c +
p (with a andB regionss omewhats egregated)E. ach
class includes tens to hundreds of different folding
arrangements (motifs), built up from increasingly
identifiable substructures. Some of the substructure
arrangements are very common, others have been
found in just one protein. Figure 4-21 shows a variety
of motifs arrayed among the four classes of protein
structure; this is just a minute sample of the hundreds
of known motifs. The number of folding patterns is not
infinite, however. As the rate at which new protein
structuresa re elucidatedh asi ncreasedt,h e fraction of
those structures containing a new motif has steadily
declined. Fewer than 1,000 different folds or motifs
may exist in all. Figure 4-21 also shows how proteins
can be organizedb asedo n the presenceo f the various
motifs. The top two levels of organization,c lass and
fold, are purely structural. Below the fold level (see
color key in Fig. 4-21), categorizationis basedo n evolutionary
relationships.
Many examples of recurring domain or motif structures
are availablea, nd theser evealt hat protein tertiary
structure is more reliably conserved than amino
acid sequence. The comparison of protein structures
can thus provide much information about evolution.
vided (seet he color key).T he PDB identifier( listedf irst for each
structure)i s the unique accessionc ode given to each structure
archivedi n the ProteinD ata Bank( www.rcsb.orgf)h. e a/B bArrel
(seeF ig.4 -2O)i s anotherp articularlyc ommona /B motil.
(Figure continues on facing page.)