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* Residue conservation analysis
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Enzyme class:
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Chain A:
E.C.5.2.1.8
- peptidylprolyl isomerase.
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Reaction:
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[protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0)
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Peptidylproline (omega=180)
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=
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peptidylproline (omega=0)
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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DOI no:
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J Mol Biol
283:435-449
(1998)
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PubMed id:
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X-ray structures and analysis of 11 cyclosporin derivatives complexed with cyclophilin A.
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J.Kallen,
V.Mikol,
P.Taylor,
M.D.Walkinshaw.
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ABSTRACT
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Eight new X-ray structures of different cyclophilin A/cyclosporin-derivative
complexes are presented. These structures, combined with the existing three
published cyclosporin complexes, provide a useful structural database for the
analysis of protein-ligand interactions. The effect of small chemical
differences on protein-ligand hydrogen-bonding, van der Waals interactions and
water structure is presented.
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Selected figure(s)
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Figure 1.
Figure 1. Residue labelling scheme for CsA-analogues
(see also Table 1). Atom labelling is according to the
IUPAC convention. CN is the methyl carbon atom of
the N-methylated amino acids. MLE for MeLeu; MVA
for MeVal; BMT for MeBmt; ABU for Abu; SAR for Sar;
VAL for Val; ALA for Ala; DAL for D-Ala. All amino
acid residues with the exception of D-Ala8 (and Sar3)
are in the L-configuration.
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Figure 5.
Figure 5. Stereo picture of CsA/CypA with the most conserved water molecules. CsA is coloured magenta, CypA
is coloured cyan and the 11 water molecules which occur in 10 or 11 of the 11 structures discussed in this paper are
shown as labelled yellow spheres. The label corresponds to the number in Table 5 and also to the label of the water
molecule in the deposited PDB file. The position of the sphere is the average position of the water molecules from
the different structures which all refine to within 0.2 Å of each other.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1998,
283,
435-449)
copyright 1998.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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A.Kuglstatter,
F.Mueller,
E.Kusznir,
B.Gsell,
M.Stihle,
R.Thoma,
J.Benz,
L.Aspeslet,
D.Freitag,
and
M.Hennig
(2011).
Structural basis for the cyclophilin A binding affinity and immunosuppressive potency of E-ISA247 (voclosporin).
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Acta Crystallogr D Biol Crystallogr,
67,
119-123.
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PDB codes:
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T.L.Davis,
J.R.Walker,
V.Campagna-Slater,
P.J.Finerty,
R.Paramanathan,
G.Bernstein,
F.MacKenzie,
W.Tempel,
H.Ouyang,
W.H.Lee,
E.Z.Eisenmesser,
and
S.Dhe-Paganon
(2010).
Structural and biochemical characterization of the human cyclophilin family of peptidyl-prolyl isomerases.
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PLoS Biol,
8,
e1000439.
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PDB codes:
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K.S.Keating,
S.C.Flores,
M.B.Gerstein,
and
L.A.Kuhn
(2009).
StoneHinge: hinge prediction by network analysis of individual protein structures.
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Protein Sci,
18,
359-371.
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V.Venugopal,
A.K.Datta,
D.Bhattacharyya,
D.Dasgupta,
and
R.Banerjee
(2009).
Structure of cyclophilin from Leishmania donovani bound to cyclosporin at 2.6 A resolution: correlation between structure and thermodynamic data.
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Acta Crystallogr D Biol Crystallogr,
65,
1187-1195.
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PDB code:
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P.Mark,
and
L.Nilsson
(2007).
A molecular dynamics study of Cyclophilin A free and in complex with the Ala-Pro dipeptide.
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Eur Biophys J,
36,
213-224.
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V.Venugopal,
B.Sen,
A.K.Datta,
and
R.Banerjee
(2007).
Structure of cyclophilin from Leishmania donovani at 1.97 A resolution.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
63,
60-64.
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PDB code:
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O.Yasuda,
K.Fukuo,
X.Sun,
M.Nishitani,
T.Yotsui,
M.Higuchi,
T.Suzuki,
H.Rakugi,
O.Smithies,
N.Maeda,
and
T.Ogihara
(2006).
Apop-1, a novel protein inducing cyclophilin D-dependent but Bax/Bak-related channel-independent apoptosis.
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J Biol Chem,
281,
23899-23907.
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D.Schlatter,
R.Thoma,
E.Küng,
M.Stihle,
F.Müller,
E.Borroni,
A.Cesura,
and
M.Hennig
(2005).
Crystal engineering yields crystals of cyclophilin D diffracting to 1.7 A resolution.
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Acta Crystallogr D Biol Crystallogr,
61,
513-519.
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PDB codes:
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K.Levitsky,
M.D.Boersma,
C.J.Ciolli,
and
P.J.Belshaw
(2005).
Exo-mechanism proximity-accelerated alkylations: investigations of linkers, electrophiles and surface mutations in engineered cyclophilin-cyclosporin systems.
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Chembiochem,
6,
890-899.
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G.Kontopidis,
P.Taylor,
and
M.D.Walkinshaw
(2004).
Enzymatic and structural characterization of non-peptide ligand-cyclophilin complexes.
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Acta Crystallogr D Biol Crystallogr,
60,
479-485.
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PDB codes:
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M.I.Zavodszky,
M.Lei,
M.F.Thorpe,
A.R.Day,
and
L.A.Kuhn
(2004).
Modeling correlated main-chain motions in proteins for flexible molecular recognition.
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Proteins,
57,
243-261.
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R.Banerjee,
M.Dutta,
M.Sen,
and
A.K.Datta
(2002).
Crystallization and preliminary X-ray analysis of cyclophilin from Leishmania donovani.
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Acta Crystallogr D Biol Crystallogr,
58,
1846-1847.
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P.Taylor,
J.Dornan,
A.Carrello,
R.F.Minchin,
T.Ratajczak,
and
M.D.Walkinshaw
(2001).
Two structures of cyclophilin 40: folding and fidelity in the TPR domains.
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Structure,
9,
431-438.
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PDB codes:
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Wu Sy,
J.Dornan,
G.Kontopidis,
P.Taylor,
and
M.D.Walkinshaw
(2001).
The First Direct Determination of a Ligand Binding Constant in Protein Crystals.
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Angew Chem Int Ed Engl,
40,
582-586.
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PDB code:
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C.Schiene,
and
G.Fischer
(2000).
Enzymes that catalyse the restructuring of proteins.
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Curr Opin Struct Biol,
10,
40-45.
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M.T.Ivery
(2000).
Immunophilins: switched on protein binding domains?
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Med Res Rev,
20,
452-484.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
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Links
