SCOP Definitions for
b-Propeller Proteins
with other than 5-fold Symmetry
Structural Classification of Proteins
<http://scop.mrc-lmb.cam.ac.uk/scop/index.html>
<http://scop.mrc-lmb.cam.ac.uk/scop/mail.cgi>
<http://scop.mrc-lmb.cam.ac.uk/scop/help.html>
<http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.html>
<http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.c.hd.b.html>
<http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.c.hd.b.b.A.html>
Family: Hemopexin-like domain
Lineage:
1. Root: <http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.html>
scop
2. Class: <http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.c.html>
All beta proteins
3. Fold: <http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.c.hd.A.A.html>
4-bladed beta-propeller
consists of four 4-stranded beta-sheet motifs; meander
4. Superfamily: <http://scop.mrc- lmb.cam.ac.uk/scop/data/scop.b.c.hd.b.A.html>
Hemopexin-like domain
5. Family: <http://scop.mrc- lmb.cam.ac.uk/scop/data/scop.b.c.hd.b.b.html>
Hemopexin-like domain
Protein Domains:
1. Hemopexin duplication: consists of two domains of this fold
1. <http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.c.hd.b.b.b.html>
Rabbit (Oryctolagus cuniculus) (3) <http://scop.mrclmb.cam.ac.uk/scop/rsgen.cgi?pd=1hxn>
<http://scop.mrc-lmb.cam.ac.uk/scop/rsgen.cgi?chime=1;pd=1hxn>
2. Gelatinase A (MMP-2), C-terminal domain
1. <http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.c.hd.b.b.c.html>
Human (Homo sapiens) (3) <http://scop.mrclmb.cam.ac.uk/scop/rsgen.cgi?pd=1gen>
<http://scop.mrc-lmb.cam.ac.uk/scop/rsgen.cgi?chime=1;pd=1gen>
3. Collagenase, C-terminal domain
1. <http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.c.hd.b.b.d.html>
Pig (Sus scrofa) (1)
<http://scop.mrc-lmb.cam.ac.uk/scop/rsgen.cgi?pd=1fbl;pr=272-466>
<http://scop.mrc-lmb.cam.ac.uk/scop/rsgen.cgi?chime=1;pd=1fbl;pr=272-466>
4. Collagenase-3 (MMP-13), C-terminal domain
1. <http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.c.hd.b.b.e.html>
Human (Homo sapiens) (1)
<http://scop.mrc-lmb.cam.ac.uk/scop/rsgen.cgi?pd=1pex>
<http://scop.mrc-lmb.cam.ac.uk/scop/rsgen.cgi?chime=1;pd=1pex>
Generated from scop database 1.57 with scopm 1.096 on Tue Jan 22 23:13:23
2002
<http://scop.mrc-lmb.cam.ac.uk/scop/lic/copy.html>
Structural Classification of Proteins
<http://scop.mrc-lmb.cam.ac.uk/scop/index.html>
<http://scop.mrc-lmb.cam.ac.uk/scop/mail.cgi>
<http://scop.mrc-lmb.cam.ac.uk/scop/help.html>
<http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.html>
<http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.c.html>
<http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.c.hf.A.html>
Fold: 6-bladed beta-propeller
consists of six 4-stranded beta-sheet motifs; meander
Lineage:
1. Root: <http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.html>
scop
2. Class: <http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.c.html>
All beta proteins
3. Fold: <http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.c.hf.html>
6-bladed beta-propeller
consists of six 4-stranded beta-sheet motifs; meander
Superfamilies:
1. <http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.c.hf.b.A.html>
Sialidases (neuraminidases) (1)
<http://scop.mrc-lmb.cam.ac.uk/scop/rsgen.cgi?pd=3sil>
<http://scop.mrc-lmb.cam.ac.uk/scop/rsgen.cgi?chime=1;pd=3sil>
2. <http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.c.hf.c.A.A.html>
Soluble quinoprotein glucose dehydrogenase (1)
<http://scop.mrc-lmb.cam.ac.uk/scop/rsgen.cgi?pd=1cru;pc=a>
<http://scop.mrc-lmb.cam.ac.uk/scop/rsgen.cgi?chime=1;pd=1cru;pc=a>
3. <http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.c.hf.d.A.A.html>
Thermostable phytase (3-phytase) (1)
<http://scop.mrc-lmb.cam.ac.uk/scop/rsgen.cgi?pd=1h6l;pc=a>
<http://scop.mrc-lmb.cam.ac.uk/scop/rsgen.cgi?chime=1;pd=1h6l;pc=a>
4. <http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.c.hf.e.A.A.html>
TolB, C-terminal domain (1)
<http://scop.mrc-lmb.cam.ac.uk/scop/rsgen.cgi?pd=1crz;pr=a:141-409>
<http://scop.mrc-lmb.cam.ac.uk/scop/rsgen.cgi?chime=1;pd=1crz;pr=a:141-409>
5. <http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.c.hf.f.A.A.html>
Low density lipoprotein (LDL) reseptor YWTD domain (1)
<http://scop.mrc-lmb.cam.ac.uk/scop/rsgen.cgi?pd=1ijq;pr=a:377-642>
<http://scop.mrc-lmb.cam.ac.uk/scop/rsgen.cgi?chime=1;pd=1ijq;pr=a:377-642>
6. <http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.c.hf.g.A.A.html>
Diisopropylfluorophosphatase (phosphotriesterase, DFP) (1)
<http://scop.mrc-lmb.cam.ac.uk/scop/rsgen.cgi?pd=1e1a;pc=a>
<http://scop.mrc-lmb.cam.ac.uk/scop/rsgen.cgi?chime=1;pd=1e1a;pc=a>
Generated from scop database 1.57 with scopm 1.096 on Tue Jan 22 23:13:23
2002
<http://scop.mrc-lmb.cam.ac.uk/scop/lic/copy.html>
Structural Classification of Proteins
<http://scop.mrc-lmb.cam.ac.uk/scop/index.html>
<http://scop.mrc-lmb.cam.ac.uk/scop/mail.cgi>
<http://scop.mrc-lmb.cam.ac.uk/scop/help.html>
<http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.html>
<http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.c.html>
<http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.c.hg.A.html>
Fold: 7-bladed beta-propeller
consists of seven 4-stranded beta-sheet motifs;
meander
Lineage:
1. Root: <http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.html>
scop
2. Class: <http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.c.html>
All beta proteins
3. Fold: <http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.c.hg.html>
7-bladed beta-propeller
consists of seven 4-stranded beta-sheet motifs; meander
Superfamilies:
1. <http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.c.hg.b.A.A.html>
Galactose oxidase, central domain (1)
<http://scop.mrc-lmb.cam.ac.uk/scop/rsgen.cgi?pd=1gof;pr=151-537>
<http://scop.mrc-lmb.cam.ac.uk/scop/rsgen.cgi?chime=1;pd=1gof;pr=151-537>
2. <http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.c.hg.c.A.html>
Methylamine dehydrogenase, H-chain (1)
<http://scop.mrc-lmb.cam.ac.uk/scop/rsgen.cgi?pd=2bbk;pc=h>
<http://scop.mrc-lmb.cam.ac.uk/scop/rsgen.cgi?chime=1;pd=2bbk;pc=h>
3. <http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.c.hg.d.A.html>
Nitrous oxide reductase, N-terminal domain (1)
<http://scop.mrc-lmb.cam.ac.uk/scop/rsgen.cgi?pd=1qni;pr=a:10-450>
<http://scop.mrc-lmb.cam.ac.uk/scop/rsgen.cgi?chime=1;pd=1qni;pr=a:10-450>
4. <http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.c.hg.e.A.html>
Trp-Asp repeat (WD-repeat) (1)
<http://scop.mrc-lmb.cam.ac.uk/scop/rsgen.cgi?pd=1tbg;pc=a>
<http://scop.mrc-lmb.cam.ac.uk/scop/rsgen.cgi?chime=1;pd=1tbg;pc=a>
5. <http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.c.hg.f.A.A.html>
Regulator of chromosome condensation RCC1 (1)
<http://scop.mrc-lmb.cam.ac.uk/scop/rsgen.cgi?pd=1a12;pc=a>
<http://scop.mrc-lmb.cam.ac.uk/scop/rsgen.cgi?chime=1;pd=1a12;pc=a>
6. <http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.c.hg.g.A.A.html>
Clathrin heavy-chain terminal domain (1)
<http://scop.mrc-lmb.cam.ac.uk/scop/rsgen.cgi?pd=1c9l;pr=a:3-330>
<http://scop.mrc-lmb.cam.ac.uk/scop/rsgen.cgi?chime=1;pd=1c9l;pr=a:3-330>
7. <http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.c.hg.h.A.A.html>
Prolyl oligopeptidase, N-terminal domain (1)
<http://scop.mrc-lmb.cam.ac.uk/scop/rsgen.cgi?pd=1qfm;pr=a:1-430>
<http://scop.mrc-lmb.cam.ac.uk/scop/rsgen.cgi?chime=1;pd=1qfm;pr=a:1-430>
<http://scop.mrc-lmb.cam.ac.uk/scop/index.html>
<http://scop.mrc-lmb.cam.ac.uk/scop/mail.cgi>
<http://scop.mrc-lmb.cam.ac.uk/scop/help.html>
<http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.html>
<http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.c.html>
<http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.c.hh.A.html>
Fold: 8-bladed beta-propeller
consists of eight 4-stranded beta-sheet motifs;
meander
Lineage:
1. Root: <http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.html>
scop
2. Class: <http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.c.html>
All beta proteins
3. Fold: <http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.c.hh.html>
8-bladed beta-propeller
consists of eight 4-stranded beta-sheet motifs; meander
Superfamilies:
1. <http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.c.hh.b.A.html>
Quinoprotein alcohol dehydrogenase (1)
<http://scop.mrc-lmb.cam.ac.uk/scop/rsgen.cgi?pd=4aah;pc=a>
<http://scop.mrc-lmb.cam.ac.uk/scop/rsgen.cgi?chime=1;pd=4aah;pc=a>
2. <http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.c.hh.c.A.html>
C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase (1)
<http://scop.mrc-lmb.cam.ac.uk/scop/rsgen.cgi?pd=1hj5;pr=a:134-567>
<http://scop.mrc-lmb.cam.ac.uk/scop/rsgen.cgi?chime=1;pd=1hj5;pr=a:134-567>
Generated from scop database 1.57 with scopm 1.096 on Tue Jan 22 23:13:23
2002
<http://scop.mrc-lmb.cam.ac.uk/scop/lic/copy.html>
Several Examples for Ligand Binding Sites in
b-Propeller Proteins
other than Tachylectin-2
The b propeller proteins
can be divided into several families. It has been estimated that the b
propeller
fold has participated in the formation of new proteins for the last
three billion years of evolution
(Neer and Smith, Proc. Natl. Acad. Sci. 97, 960 -962, 2000).
The largest single family within the b
propeller proteins, currently comprising more than 160 members,
is characterized by repeats of a motif consisting of the two amino
acids WD.
The WD repeat consists of a pattern of amino acids typically bracketed
by the dipeptide sequences
WD and GH (Smith TF, Gaitatzes C, Saxena K, Neer EJ, Trends Biochem.
Sci.24, 181 - 185, 1999);
this sequence pattern is of constant length and corresponds to the
strands 1, 2 and 3 of a propeller blade.
Strand 4 is defined by a region of variable length; its sequence defines
the functional subfamily of WD
repeat proteins to which the individual protein belongs.Few residues
are truly conserved, and the
detailed structures of the presumed b
sheets are not yet well defined. In the b
subunit
of heterotrimeric G proteins (the only "canonical" WD repeat protein
for which the crystallographic
structure has been solved), a highly conserved ASP residue located
six positions upstream from the WD
motif forms the tight turn between strands 2 and 3.
There seems to be a remarkable functional correlation with the presence
of a WD domain in any given
b propeller protein:
none of the WD-containing proteins has been identified as having enzymatic
activity,
whereas numerous b
propeller proteins without WD repeats are recognized as enzymes.In agreement
with this definition, the non-enzymatic lectin Tachylectin-2 does not
contain a WD repeat
The topography of the ligand binding domain in tachylectin-2 is loosely
conserved in two other proteins
without WD repeats, hemopexin and clathrin.
Hemopexin is characterized by two four-bladed propellers per chain;
by dimerization, it can form a
highly symmetrical superstructure of four four-bladed propellers
(Faber et al, Structure 3, 551 - 559, 1995).The ligand heme
is bound by a groove formed by surface
residues between the blades III and IV of each individual propeller.
Clathrin is characterized by a seven-bladed propeller in its N-terminal
domain.Clathrin-coated vesicles
are of great significance in cell biology,because they are the site
of receptor-mediated uptake of ligands
and other molecular payloads. Clathrin connects to transmembrane receptors
by way of adaptor proteins,
such as b-arrestin-2
and AP-3. (Scheme Fig.4 from ter Haar/PNAS).
Recent analysis of the crystal structure of the clathrin N-terminus
in complex with peptides derived
from the adaptor proteins b-arrestin-2
or AP-3 (ter Haar E, Harrison SC, Kirchhausen T, Proc Nat.
Acad. Sci. 97, 1096 - 1100) has revealed a peptide binding site
formed by strand 4 of blade I and
residues at the upper surface of blade II.(Fig 1 and 3 from ter Haar/PNAS).
In some propeller proteins with enzymatic activity, the central tunnel
seems to play a prominent role in
binding of prosthetic groups. For example, in the enzyme cytochrome
cd1/nitrate reductase, a heme
group is coordinated at the entrance of the central tunnel, and in
the enzyme methanol dehydrogenase, a
noncovalently bound quinone molecule and a Ca2+
ion are coordinated to the central tunnel.
The tunnel is an important interaction site for WD-containig propeller
proteins as well: the seven-bladed
propeller forming the G protein b
subunit utilizes the top of the central tunnel to coordinate a histidine
provided by the binding partner G protein a
subunit.
Undoubtedly, b propeller
proteins employ a vast combinatorial array of permutations and variations
to define binding sites for small and large interaction partners.