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PDBsum entry 1fc7
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Crystal structures of the photosystem ii d1 c-Terminal processing protease.
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Authors
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D.I.Liao,
J.Qian,
D.A.Chisholm,
D.B.Jordan,
B.A.Diner.
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Ref.
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Nat Struct Biol, 2000,
7,
749-753.
[DOI no: ]
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PubMed id
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Abstract
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We report here the first three-dimensional structure of the D1 C-terminal
processing protease (D1P), which is encoded by the ctpA gene. This enzyme
removes the C-terminal extension of the D1 polypeptide of photosystem II of
oxygenic photosynthesis. Proteolytic processing is necessary to allow the light
driven assembly of the tetranuclear manganese cluster, which is responsible for
photosynthetic water oxidation. The X-ray structure of the Scenedesmus obliquus
enzyme has been determined at 1.8 A resolution using the multiwavelength
anomalous dispersion method. The enzyme is monomeric and is composed of three
folding domains. The middle domain is topologically homologous to known PDZ
motifs and is proposed to be the site at which the substrate C-terminus binds.
The remainder of the substrate likely extends across the face of the enzyme,
interacting at its scissile bond with the enzyme active site Ser 372 / Lys 397
catalytic dyad, which lies at the center of the protein at the interface of the
three domains.
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Figure 1.
Figure 1. Structure of D1 protease. a, Ribbon drawing of D1P.
The A domain is in red, the B domain in yellow and the C domain
in blue. The extended  -hairpin
loop from the C domain forms an integral part of the folding
domain A and is regarded as part of that domain. The loops that
connect domains A to B and B to C have very high temperature
factors and are colored in green. The side chains of the
residues involved in catalysis or substrate binding, K397, S372
and R247, are shown in ball-and-stick representation. The GVGL
loop in the B domain, highlighted in magenta, has been shown to
be involved in the binding of the C-terminal residues of the
peptide ligand in the structurally homologous third PDZ domain
of synaptic protein PSD-95^25. b, Stereo view of the C  trace
of D1P. Every 10^th residue and the N-terminus and C-terminus
are labeled. The disulfide bond between Cys 260 and Cys 451 is
shown in yellow. The orientation of the molecule is the same as
the standard orientation in (a).
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Figure 4.
Figure 4. The PDZ domain. a, Schematic diagram of the
secondary structures of the B domain of D1P (upper) and the
third PDZ domain of human D1gA (PDB accession code 1PDR,
residues 463 -544)24, the third PDZ domain of the synaptic
protein PSD-95 (1KWA, residues 487 -570)25 and the PDZ domain of
neuronal nitric oxide synthase (1QAU, residues 14 -101)26. The
location of the conserved Arg/Lys (Arg 247 in D1P, Arg 471 in
1PDR, Lys 495 in 1KWA and Arg 23 in 1QAU) is marked by a red
circle. The location of the GLGF repeat of the carboxylate
binding loop in 1PDR and 1QAU (GVGL in D1P and PMGL in 1KWA) is
labeled by a yellow circle. Their three-dimensional structures
are also very similar. The r.m.s.d. for C atoms
between D1P and 1PDR is 1.5 Å using 76 matching residues for the
alignment. The r.m.s.d. is 1.79 Å for 81 matching pairs of C
atoms
between D1P and 1QAU. For D1P and 1KWA, the r.m.s.d. is 1.9 Å
for 71 matching pairs. b, The conserved Arg 247 in the B domain
of D1P. The side chain of Arg 247 is partially buried with a
solvent accessible area of 23 Å2.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Biol
(2000,
7,
749-753)
copyright 2000.
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