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MOLECULE OF THE MONTH:
CONCANAVALIN A AND
CIRCULAR PERMUTATION
doi: 10.2210/rcsb_pdb/mom_2010_4
Evolution is a great tinkerer:
once a successful plan is found,
it is used again and again,
often with many changes and
improvements. This is easily
seen in the living things around
us. Most mammals have four
limbs, which have evolved into
all manner of arms and legs,
and even into flippers and
wings. Most plants are covered
with leaves, which range from
spiny needles to huge jungle
fronds. Looking at protein
sequences and structures, we see
the same diversity generated
through variation. Proteins
evolve by slow mutation of
individual amino acids, but
they also evolve through larger
piece-wise changes, where the
genes for successful proteins are
clipped and reassembled in
new combinations.
About the
RCSB PDB Molecule of the Month
Using selected molecules from the PDB
archive, each feature includes an
introduction to the structure and function of
the molecule, a discussion of its relevance to
human health and welfare, and
suggestions for viewing and
accessing further details.
The RCSB PDB Molecule of the Month is
read by students, teachers, and scientists
worldwide at www.pdb.org.
This April 2010 edition was written and
illustrated by David S. Goodsell
(RCSB PDB and The Scripps
Research Institute).
Circular Reasoning
Circular permutation is one of the most unusual
changes found in protein evolution. To understand
where the name "circular permutation"
comes from, imagine a folded protein that has the
two ends of the chain near to one another. Now,
chemically link these two ends. This would form
a circular protein chain, with no ends. Then, clip
the circularized chain in a different place. The
folded protein would look the same, except that
the two ends would be in a different place.
Permuted Proteins
This is exactly what happens with the protein
concanavalin A, a carbohydrate-binding protein
found in jack beans, shown on the top of the page
from PDB entry 1cvn. When the amino acid
sequence of this protein was determined in the
seventies (by actually studying the amino acids in
the protein, not looking at the gene), it was found
to have a similar sequence to favin, a protein from
fava beans. However, the sequence was permuted,
as if the protein chain had been cut in the middle
and the two halves swapped. Further study
showed that in cells, concanavalin A is synthesized
similarly to favin, but then a circular permutation
is performed, as shown on the right using PDB
entry 3cna. The precursor protein made by ribosomes
has an extra tail and an extra loop, both
shown here with dotted lines. The mature form is
produced by clipping off the loop to create the
1cvn
new ends of the chain, and sealing up the two
original ends of the chain into a new loop.
Permuting Genes
Since the discovery of circular permutation in
concanavalin A, many other examples have been
discovered. In most cases, however, the circular
permutation occurs in the genome, not by the
more laborious cutting and pasting of the actual
protein. In these cases, a rearrangement of the
gene occurs: a portion at the front of the gene is
removed and then replaced at the end. Sometimes
only a single helix at one end is moved (as in the
proteins in PDB entries 1ui9 and 1h0r) and in
other cases, entire domains are switched. As
described on the next page, scientists have also
gotten in on the action, and they have done their
own circular permutations.
3cna

CONCANAVALIN A AND
CIRCULAR PERMUTATION
RCSB Protein Data Bank
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& Digestive & Kidney Diseases.
References:
The RCSB PDB is a member of
the worldwide PDB
(wwPDB; www.wwpdb.org).
1cvn: J.H. Naismith, R.A. Field (1996) Structural
basis of trimannoside recognition by concanavalin A.
J.Biol.Chem. 271: 972-976
3cna: K.D. Hardman, C.F. Ainsworth (1972)
Structure of concanavalin A at 2.4-A resolution.
Biochemistry 11: 4910-4919
1ui9: E. Inagaki, S. Kuramitsu, S. Yokoyama, M.
Miyano, T.H. Tahirov; The crystal structure of chorismate
mutase from thermus thermophilus. To be
Published
1h0r: D.A. Robinson, A.W. Roszak, M. Frederickson,
C. Abell, J.R. Coggins, A.J.Lapthorn; Structural Basis
for Selectivity of Oxime Based Inhibitors Towards
Type II Dehydroquinase from Mycobacterium
Tuberculosis. To be Published
2ayh: M. Hahn, T. Keitel, U. Heinemann (1995)
Crystal and molecular structure at 0.16-nm resolution
of the hybrid Bacillus endo-1,3-1,4-beta-D-glucan
4-glucanohydrolase H(A16-M). Eur.J.Biochem.
232: 849-858
1ajk, 1ajo: J. Ay, M. Hahn., K. Decanniere, K.
Piotukh, R. Borriss, U. Heinemann (1998) Crystal
structures and properties of de novo circularly permuted
1,3-1,4-beta-glucanases. Proteins 30: 155-167
1cpm: M. Hahn, K. Piotukh, R. Borriss, U.
Heinemann (1994) Native-like in vivo folding of a
circularly permuted jellyroll protein shown by crystal
structure analysis. Proc.Natl.Acad.Sci.USA 91:
10417-10421
2pel: R. Banerjee, K. Das, R. Ravishankar, K. Suguna,
A. Surolia, M. Vijayan (1996) Conformation, protein-carbohydrate
interactions and a novel subunit
association in the refined structure of peanut lectinlactose
complex. J.Mol.Biol. 259: 281-296
2ayh 1ajk 1ajo 1cpm
Permutation on Purpose
Scientists are also great tinkerers. As soon as they
discovered the process of circular permutation, they
had to try it out themselves. The glucanase protein
shown above (PDB entries 2ayh, 1ajk, 1ajo and
1cpm) has been permuted in several different ways,
by cutting the gene in different places and reassembling
the two pieces. In this picture, each protein
chain is colored blue at one end, red at the other,
and rainbow colors in between. Notice that the
overall protein fold is the same in each one, except
that the ends are in a different place. This demonstrates
that protein folding is a robust process, and
that the protein fold is determined by the sequence,
even if it's shuffled around a bit.
Exploring the Structure
3cna
2pel
Circular permutation was originally discovered by
comparing the amino acid sequences of concanavalin
A (PDB entry 3cna) with the sequences
of other lectins, such as the peanut lectin shown
here (PDB entry 2pel). When the structures were
solved years later, as expected, they showed very
similar three-dimensional structures, in spite of
the permutation of the chain. The Protein
Comparison Tool available in the "Compare
Structures" section of the RCSB WWW site was
used to overlap the proteins in this Molecule of
the Month. When you use this tool, you'll find
that it gets a bit confused by circularly-permuted
proteins, and ends up using only part of the
chain for the overlap. Fortunately, this works well
enough for comparing proteins like concanavalin
A and peanut lectin that have similar folds.
Topics for Further Exploration
1. Can you find other examples of circularlypermuted
proteins in the PDB? Several
databases are available to help with this,
including CPDB and SISYPHUS.
2. Can you think of any ways that circular
permutation would improve the function
of a protein?
Additional reading about
circular permutation
U. Heinemann and M. Hahn (1995)
Circular permutation of polypeptide chains:
implications for protein folding and stability.
Progress in Biophysics and Molecular Biology
64, 121-143.
D. J. Bowles and D. J. Pappin (1988) Traffic
and assembly of concanavalin A. Trends in
Biochemical Sciences 13, 60-64.
B. A. Cunningham, J. J. Hemperly, T. P.
Hopp and G. M. Edelman (1979) Favin versus
concanavalin A: circularly permuted amino
acid sequences. Proceedings of the National
Academy of Sciences USA 76, 3218-3222.