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¤1¤ Crystal Structure of Allophycocyanin from Red AlgaePorphyra yezoensis at
2.2- Resolution[15]* ¤1¤
1. [16]Jin-Yu Liu,
2. [17]Tao Jiang,
3. [18]Ji-Ping Zhang and
4. [19]Dong-Cai Liang[20]à
1.
From the National Laboratory of Biomacromolecules, Institute of
Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing
100101, China
[21]Next Section
¤2¤ Abstract ¤2¤
The crystal structure of allophycocyanin from red algae Porphyra
yezoensis (APC-PY) at 2.2- resolution has been determined by the
molecular replacement method. The crystal belongs to space group R32
with cell parameters a = b = 105.3 , c = 189.4 , α = β = 90¡, γ =
120¡. After several cycles of refinement using program X-PLOR and model
building based on the electron density map, the crystallographic
R-factor converged to 19.3% (R-free factor is 26.9%) in the range of
10.0 to 2.2 . The r.m.s. deviations of bond length and angles are
0.015 and 2.9¡, respectively.
In the crystal, two APC-PY trimers associate face to face into a
hexamer. The assembly of two trimers within the hexamer is similar to
that of C-phycocyanin (C-PC) and R-phycoerythrin (R-PE) hexamers, but
the assembly tightness of the two trimers to the hexamer is not so high
as that in C-PC and R-PE hexamers.
The chromophore-protein interactions and possible pathway of energy
transfer were discussed. Phycocyanobilin 1α84 of APC-PY forms 5
hydrogen bonds with 3 residues in subunit 2β of another monomer. In
R-PE and C-PC, chromophore 1α84 only forms 1 hydrogen bond with 2β77
residue in subunit 2β. This result may support and explain great
spectrum difference exists between APC trimer and monomer.
Phycobilisomes are large supramolecular aggregates attached to the
stromal side of the thylakoid membrane in cyanobacteria, red algae, and
cryptomonads. These supramolecular aggregates are light-harvesting
protein pigment complexes that are composed of phycobiliproteins and
linker proteins. Based on the absorption of visible light, the
phycobiliproteins can be divided into three main groups: phycoerythrin
(PE)^1 or phycoerythrocyanin (PEC), phycocyanin (PC), and
allophycocyanin (APC). With the help of linker proteins,
phycobiliproteins form the two distinct structural domains of
phycobilisome, the core and the rods. The core, which is composed of
three or more core cylinders associated by APC discs, is in proximity
of the reaction centers, whereas the rods are attached on the core and
are composed of PC discs in the middle and PE or PEC discs on the tip.
Light energy is transferred from PE or PEC via PC to APC and finally to
the reaction centers ([22]1).
The crystal structures of several phycobiliproteins have been solved;
among them, three are PEs ([23]2-4), three are C-phycocyanins (C-PCs)
([24]5-7), one is PEC:PEC from Mastigocladus laminosus ([25]8), and one
is APC:APC from Spirulina platensis ([26]9). All these structures are
very similar. The basic building block is an αβ monomer composed of α
and β subunits (R-phycoerythrin (R-PE) and B-phycoerythrin (B-PE) have
a third subunit γ in the center of the molecule); three αβ monomers are
arranged around a 3-fold symmetry axis to form an (αβ)[3] trimer or two
(αβ)[3] trimers, which are assembled face to face into an (αβ)[6]
hexamer.
The crystal structure of APC is very special compared with other
phycobiliproteins. First, the spectrum difference between APC trimer
and its monomer is very large. When APC monomers aggregate to trimer,
the absorption spectrum has a 40-nm red shift; the CD spectrum also
changes a great deal, and exiton interaction in the trimer of APC was
suggested ([27]10), whereas the spectrum difference between C-PC
monomer and its trimer is not so large as in APC, although phycocyanin
has the same α84PCB and β84PCB as APC.
Second, the functional unit of APC was thought to be a trimer, whereas
the function unit of other phycobiliproteins were hexamer (αβ)[6] or
(αβ)[6]γ. Brejc and co-workers solved the structure of APC-SP from blue
alga S. platensis([28]9) in the unit cell of APC-SP crystal; two
trimers are associated in a Òback to backÓ manner that might represent
the assembly state of APC in nature. Red alga is higher than blue alga
in evolution, so it would be interesting to know the packing of APC
from red alga in the unit cell and in nature.
Third, in PE and PC, the two trimeric discs are superimposed along a
3-fold axis, but in PC and APC the two discs are connected
perpendicularly. The pathway of energy transfer between PC and APC is
still unknown.
The red algae Porphyra yezoensis is an algae that exists widely in
nature. Its phycobilisomes contain R-PE, C-PC, and APC. In this paper
we report the crystal structure of APC from P. yezoensis (APC-PY) at
2.2- resolution. The organization of APC trimers in the core cylinders
of phycobiliproteins and the pathway of energy transfer were discussed.
[29]Previous Section[30]Next Section
¤2¤ EXPERIMENTAL PROCEDURES ¤2¤
Crystallization and data collection of APC-PY was reported earlier
([31]11). The crystals of APC-PY belong to space group R32 with
parameters a = b = 105.3 , c = 189.4 , α = β = 90¡, and γ = 120¡.
Molecular replacement using program AMoRe ([32]12) was carried out
using the 2.3- structure of APC-SP as a model. Model cell parameters
were a = b = c = 150.0 , α = β = γ = 90¡, integrate radius was 30 ,
and rotation function calculation gave a rather high coefficient
solution, α = 60.07, β = 3.06, γ = 88.03, Cc = 20.0. The orientations
and positions of one αβ in the asymmetric unit were determined by the
translation function with a high correlation coefficient of 66.9%. The
R-factor in the range from 10 to 4 was 36.1%. After rigid-body
refinement, R-factor dropped to 33.1%, and the correlation coefficient
increased to 71.2%. The packing of molecules in the unit cell was
reasonable.
The structure was refined using X-PLOR ([33]13). The consensus sequence
was used for the initial model building. Fourier transform and electron
density were first calculated in the resolution range of 10 to 3.5 .
Residues that could not be fitted into the electron density map were
omitted from the phase calculation in the next refinement cycle. After
several cycles of rigid body, positional refinement, and manual model
adjustment, the R-factor dropped to 25.4%, and a 2Fo-Fc Fourier map
looked quite good. Then the resolution was extended to 2.2 . After the
chromophores were fitted in the map and followed by several cycles of
positional refinement and model adjustment, the electron density
improved further. At this stage almost all side chains were well
defined except those on the surface. Residue exchanges were carried out
at this stage according to the omit map. After several cycles of
positional refinement and model adjustment, the R-factor was converged
to 24.0%, the individual B-factors were then refined, and the R-factor
dropped to 21.5%. 169 water molecules were added to the model according
to the Fo-Fc and 2Fo-Fc maps, and the final R-factor of the model was
19.3% (R-free factor was 26.9%) in the range of 10 to 2.2 .
[34]Previous Section[35]Next Section
¤2¤ RESULTS AND DISCUSSION ¤2¤
¤5¤ Amino Acid Sequence ¤5¤
Because the amino acid sequence of APC from P. yezoensis is still
unknown, the following six APC amino acid sequences were used to get a
consensus sequence for model building. Among these sequences, four are
from cyanobacteria,Anabaena cylindrica ([36]14), Calotrix PCC7601
([37]15),Fischerella PCC7603 ([38]16), and SynechococcusPCC6301
([39]17), and two are from red algae, Aglaothamnion neglectum ([40]18)
and Cyanidium caldarium ([41]19). The alignment of these six sequences
is shown in Table[42]I.
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Table I
The sequence alignment of the APCs
¤5¤ Quality of the Model ¤5¤
The final crystallographic R-factor for APC-PY model is 19.3%, in the
range of 10.0 to 2.2 . The Luzzati plot gives a mean positional
error of 0.26 ([45]20). The r.m.s. deviations of bond lengths and
bond angles are 0.015 and 2.9¡, respectively. The quality of the
final model is summarized in Table[46]II. The Ramachandran plot shows
that all dihedral angles fall into most favored or allowed regions with
the only exception of β77Thr (Fig. [47]1) ([48]21), which has a
conserved unusual dihedral angle in all known phycobiliprotein
structures. In APC-PY, the N atom of β77Thr forms a hydrogen bond with
OD (the oxygen atom in the ring D of chromophore) oxygen atom of
α84PCB. The electron density of this residue is well defined in APC-PY.
The consensus amino acid sequence (Table [49]I) was used to build the
initial model and later modified according to the electron density map.
In the 2.3--resolution crystal structure of APC-SP ([50]9), 28
residues were not well defined with 102 atoms of zero occupancy; these
residues are α25 Asp, α35Glu, α36Arg, α49Glu, α50Arg, α53Lys, α54 Gln,
α76 Tyr, α79 Asp, α120Lys, α127Glu, β2 Gln, β10Asn, β17Lys, β20 Asp,
β25 Gln, β35Glu, β36Leu, β39Arg, β50Asn, β58Lys, β65 Asp, β68Arg,
β116Lys, β117Glu, β131 Gln, β138Glu, β150Lys. The fit of these residues
to our electron density map is better in APC-PY; most of them behave
well at 1ς density level (Fig. [51]2); others behave well at 0.7ς
density level except α76 in the loop, which has a density at 0.5ς
density level.
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Table II
Parameters of refined APC-PY model
[54]Figure 1
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Figure 1
Ramachandran plot of the APC-PY residues. Glycine residues are marked
as squares. Nonglycine residues are marked as crosses. β77 (277) is in
an unusual region. PSI and PHI are dihedral angles ψ and φ.
[58]Figure 2
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Figure 2
Omit electron density map of residues β35Glu and β36Leu in APC-PY .
Comparing the crystallographic sequences of the final model of APC-PY
and APC-SP, there are 37 nonidentical residues, 25 in the α subunit and
12 in the β subunit (Table [62]III). In comparison with other APC
sequences, the 37 residues of APC-PY are more conserved than those of
APC-SP. For example, α52Val and α61Gln of APC-PY are identical to other
known sequences. The electron density of these two residues in APC-PY
are well defined.
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Table III
Sequence comparison of APC-PY and APC-SP
¤5¤ Molecular Structure ¤5¤
The asymmetric unit of APC-PY contains α and β subunit. The α subunit
is composed of 160 residues, and the β subunit contains 161 residues.
Three αβ monomers are arranged around a 3-fold axis to form a disc
shaped (αβ)[3] trimer of 30 in thickness and 110 in diameter with a
cave in the center. The α and β subunits in the αβ monomer have similar
structures, with nine α-helices (X, Y, A, B, E, F, FÕ, G, H) separated
by irregular loops (Fig.[65]3).
[66]Figure 3
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Figure 3
Ribbon representation of APC α subunit (a), APC β subunit (b).
The three-dimensional structure of APC-PY α and β subunits are very
similar to the known structure of APC-SP. The intersubunit interactions
within the (αβ) monomer and the (αβ)[3] trimer are also very similar to
these of APC-SP and other phycobiliproteins. In the (αβ) monomer of
APC-PY, the ionic- and polar-interacting residues between the two
subunits are α3 Ser-β3 Asp, α13 Asp-β94 Tyr, α13 Asp-β110Arg,
α17Arg-β97 Tyr, α18 Tyr-β93Arg, β13 Asp-α93Arg, β13 Asp-α97 Tyr, β18
Tyr-α89 Asp.
In the APC-PY crystal, two trimers associate face to face into the
(αβ)[6] hexamer through a crystallographic dyad perpendicular to the
triad. There are three (αβ)[6]hexamers in a unit cell, locating at
(0,0,0), (2/3, 1/3, 1/3), and (1/3, 2/3, 2/3) (Fig. [70]4 a). The
assembly of two trimers in this hexamer is completely different from
that of APC-SP. In APC-SP crystal, the two trimers are associated
loosely through β subunits in a Òback to backÓ manner (Fig. [71]4 b) in
the hexamer ([72]9), but in APC-PY crystal, the two trimers in the
hexamer contact through α subunits, and the assembly of the two trimers
is much tighter than that in APC-SP.
[73]Figure 4
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Figure 4
a, packing of APC-PY in the unit cell.b, packing of APC-SP in the unit
cell.
The assembly of the hexamer in the APC-PY crystal is similar to that of
C-PC from Fremylla diplosiphon (C-PC-FR) and R-PE fromPolysiphonia
urceolata (R-PE-PU) hexamers; two (αβ)[3] trimers associate face to
face in the hexamer. The α subunits provide the contacting surface, and
the two trimers fit complementarily in the hexamer.
Despite the similarity in assembly in APC-PY, C-PC-FR, and R-PE-PU
hexamers, the superposition of the C[α] atoms of APC-PY and C-PC-FR
hexamers shows that the assembly of the two trimers in APC-PY hexamer
is obviously looser than that in C-PC-FR and R-PE-PU hexamers. The
calculated accessible areas between the trimers in C-PC-FR and R-PE-PU
hexamers are about 5900 and 6900 ^2. In APC-PY hexamer, this value is
about 3200 ^2, which is much bigger than that in APC-SP (600 ^2);
thus, the APC-PY hexamer can be described as a Òloose hexamer.Ó The
interactions between the trimers in APC-PY hexamer are different from
those in C-PC-FR and R-PE-PU hexamers.
First, the number of the residues involved in the interactions between
the two trimers in APC-PY hexamer is smaller than that in C-PC-FR and
R-PE-PU hexamers, indicating a weaker association. This is consistent
with the calculated accessible areas between the two trimers in
C-PC-FR, R-PE-PU, and APC-PY hexamers. The special polar network
present in C-PC of Agmenellum quadruplaticum (C-PC-AQ), formed by
residues 1β46 Asn-6α164 Asn-1α21 Asn-6α161 Glu-6α33 Glu-6α30 Arg
([77]6) is not conserved in APC-PY hexamer. In addition, the
electrostatic interactions between 1α2Lys-6α23Glu, 1α17Arg-6α108 Asp,
and 1α120Arg-4α174 C-terminal carboxyl group, which were suggested to
be involved in the hexamer formation in C-PC-FR ([78]22), are also not
present in APC-PY hexamer. Furthermore, the comparison of APC-PY with
C-PC-FR and R-PE-PU reveals that all the conserved polar and ionic
interactions between the two trimers in C-PC-FR and R-PE-PU hexamers
are not present in APC-PY hexamer.
Despite the above difference, the interactions that maintain APC-PY as
a loose hexamer seem still to be the polar and charged interactions
between the two trimers. In APC-PY hexamer, the polar and charged
interactions are 1α25 Asp-6α37Arg, 1α22 Gly-6α26Arg, 1α25 Asp-6α161Glu,
1α25 Asp-6α165 Tyr, and 1α28Lys-6α147 Asp. In APC-SP, only a few polar
and charged interactions (<4 ) exist between the two trimers, such as
1β65 Asp-6β131 Gln and 1β120AsnÐ6β120Asn, indicating a very loose
packing.
Second, in C-PC-FR and R-PE-PU hexamers, the trimer-trimer association
is mediated almost exclusively by polar and charged residues ([79]6),
but in the APC-PY hexamer, some hydrophobic residues are also involved,
such as α21 Pro, α22 Gly, α104 Val, α164 Phe, β42 Ala, and β46 Ala.
¤5¤ Chromophores α84PCB and β84PCB ¤5¤
In APC, two phycocyanobilins are covalently bound to cysteine residues
at position α84 and β84 (Fig. [80]5). Both chromophores are well
defined in APC-PY (Fig.[81]6). The geometry and protein environment of
these two chromophores resemble those of APC-SP. The α84 PCB
chromophores have a protein environment similar to that of β84PCB. The
polar and ionic protein-chromophore interactions in α84PCB and β84PCB
are shown in Table [82]IV.
[83]Figure 5
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Figure 5
Chemical structure of PCB .
[87]Figure 6
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Figure 6
The coincidence of chromophores in APC-PY with 2Fo-Fc electron density
map α84PCB (a), β84PCB (b).
View this table:
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Table IV
The polar and ionic protein-chromophore interactions in APC-PY ()
Chromophores α84PCB and β84PCB have similar hydrophobic environment;
there are three aromatic residues close to α84, such as α90 Tyr, α91
Tyr, and α119 Tyr, and three close to β84, such as β90 Tyr, β91 Tyr,
and β119 Tyr. In C-PC-FR, α90 and α91 are all Tyr, and β90 and β91 are
all Ile. In R-PE-PU, α90 and α91 are His and Tyr, respectively, and β90
and β91 are all Ile. But in all known APCs, α90, α91, β90, and β91 are
all Tyr. So the microenvironment of α84 and β84 in APC-PY is similar to
that in C-PC-FR and R-PE-PU, indicating that α84PCB and β84PCB have
similar conformation and spectrum character. β90 Tyr and β91 Tyr
stabilize the β84PCB ring D conformation, which may make PCB have
different spectrum characteristics in APC and C-PC.
¤5¤ Energy Transfer ¤5¤
There are 12 PCBs in APC-PY hexamer; the arrangement of these
chromophores is shown in Fig.[93]7. The theory of shot-distance exiton
interaction ([94]23) and long distance dipole-dipole resonance
mechanism ([95]24) has been used to explain the energy transfer rate
between chromophores.
[96]Figure 7
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Figure 7
The chromophores of APC-PY hexamer.
Inside trimer of APC-PY, the distance between 1β84PCB and 2β84PCB in
APC-PY is about 34 and that between 1α84PCB and 2β84PCB is about 21
. These values are similar to those in C-PCs. The chromophores are too
far away to have exiton interaction. It is also difficult to explain
why exiton interaction exists in APC but not in C-PC. Our study of
chromophore-protein interactions and comparison of microenvironments in
R-PE-PU, C-PC-FR, and APC-PY show that almost all the
chromophore-protein interactions exist within the same monomer (αβ),
the only exception being α84PEB in R-PE-PU, which forms a hydrogen bond
with β77 Thr in another monomer. In C-PC-FR, the situation is the same
as in R-PE-PU. However, it is different in APC-PY; its α84PCB forms
five hydrogen bonds with the residues in other monomer, such as α84PCB
O2B-2β62 Tyr OH, O1C-2β62 Tyr N, O1C-2β67 Thr OG1, O2C-2β67 Thr OG1,
and OD-2β77 Thr N (see Table[100]IV). We believe this difference may
explain why the spectrum of APC changes greatly when its monomers
associate to trimer. In APC-SP, distances of α84PCB O2B-2β62 Tyr OH,
O1C-2β62 Tyr N, O1C-2β67 Thr OG1, O2C-2β67 Thr OG1, and OD-2β77 Thr N
are all within the distance of hydrogen bond formation. As we know, β62
Tyr and β67 Thr are close to chromophore β84PCB and may control the
conformation of chromophore and bridge between α84 PCB and β84 PCB to
make the exiton interaction occur.
The distances of chromophores between the two trimers in APC-PY hexamer
are similar to those in C-PC-FR and R-PE-PU hexamers. Based on the
1.9- resolution crystal structure, the possible pathway of energy
transfer within and between the two trimers of R-PE-PU were discussed
([101]25). There are three pairs of short distance interactions between
two trimers, such as 1α84 → 4α84,1α140a →6β155, and 1β155 → 6β155.
α84PEB is on the inner surface of R-PE-PU, and 1α84PEB → 4α84PEB may be
the dominant energy transfer pathway between the two trimers. Similar
energy pathways (1α84PCB → 4α84PCB) also exists in C-PC-FR hexamers
([102]26). In C-PC-FR, R-PE-PU, and APC-PY hexamers, the distances
between 1α84 (C10 atom) and 4α84 (C10 atom) are 27.5, 28.7, and 30.3 ,
respectively, which are comparable. Therefore, the distance between the
two chromophores of APC-PY seems adequate for effective energy
transfer.
In addition to the energy pathway composed of chromophores, the
aromatic pathway formed by aromatic residues may play an important role
in energy transfer. The energy transfer from chromophores to aromatic
residues vice versa can be explained by exiton interaction mechanism,
because the distances between some chromophores and aromatic residues,
such as α84PCB-α90 Tyr, α84PCB-α91 Tyr, β84PCB-β90 Tyr, β84PCB-β91 Tyr
are very short (∼4 ). FrsterÕs dipole-dipole resonance transfer can
occur between different aromatic residues rather than between
chromophores and aromatic residues, because the overlap integral
between chromophore absorption (λ[max] ≅ 650 nm for fluorescence
spectrum) and aromatic residue emission (λ[max] ≅ 300 nm for
fluorescence spectrum and λ[max] ≅ 400 nm for phosphorescence spectrum)
is quite small. In APC-PY there are two areas abundant in aromatic
residues as shown in Fig.[103]8. One is close to chromophore α84PCB and
composed of α164 Phe, α165 Tyr, α166 Phe, α168 Tyr, α90 Tyr, α91 Tyr,
α97 Tyr, α119 Tyr, and β18 Tyr. Another is close to chromophore β84 and
composed of β165 Tyr, β166 Phe, β168 Tyr, β90 Tyr, β91 Tyr, β94 Tyr,
β97 Tyr, β119 Tyr, and α18 Tyr. α164 Phe is involved in the hydrophobic
interactions between the two trimers. The aromatic residues in the α
subunit and the β subunit have high homology and similar locations.
Other aromatic residues are on the periphery of the disc, such as α76
Tyr, α60 Phe, β76 Tyr, β62 Tyr, β30 Tyr, β31 Phe, α30 Phe, and β81 Tyr;
among them α76 Tyr and β62 Tyr may mediate the energy transfer between
1α84PCB and 2β84PCB. Because PC and APC are connected perpendicularly
in vivo, aromatic residues on the periphery may mediate the energy
transfer from the chromophores of PC to those of APC.
[104]Figure 8
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Figure 8
The location of aromatic residues in APC-PY .
¤5¤ Functional Unit ¤5¤
In the core cylinders of phycobilisomes, several APC trimers are close
together, but the association manner of these APC trimers is still
unknown. Based on dissociation experiments, it was suggested that
allophycocyanin does not form hexamers ([108]27), because almost all
the residues involved in the trimer-trimer aggregation in C-PC-AQ and
C-PC-FR hexamers are not conserved in APC. Similar conclusions were
reported later ([109]6, [110]9). In the APC-PY hexamer, all the
interactions involved in the formation of C-PC-AQ and C-PC-FR hexamers
and all the conserved polar and charged interactions in C-PC-FR and
R-PE-PU hexamers are not present, but APC-PY can still associate face
to face to form a hexamer, which is maintained by some polar and
charged interactions, different from those in C-PC-FR and R-PE-PU.
Because the distances of chromophores between the two trimers in this
hexamer are also adequate for effective energy transfer, we assume that
the loose hexamer may represent the basic unit of APC in physiological
conditions. It is possible that linker proteins may help to stabilize
the loose hexamers.
[111]Previous Section[112]Next Section
¤2¤ ACKNOWLEDGEMENT ¤2¤
We thank Professor Lu-Lu Gui, Institute of Biophysics, Chinese Academy
of Sciences and Professor You-Shang Zhang, Institute of Biochemistry,
Chinese Academy of Sciences for their support and concern.
[113]Previous Section[114]Next Section
¤2¤ Footnotes ¤2¤
* [115]↵* This work was supported by Chinese Academy of Sciences
(KJ85-04-40) and the National Natural Science Foundation of China
(39630090).The costs of publication of this article were defrayed
in part by the payment of page charges. The article must therefore
be hereby marked ÒadvertisementÓ in accordance with 18 U.S.C.
Section 1734 solely to indicate this fact.
* [116]↵à To whom correspondence should be addressed: National
Laboratory of Biomacromolecules, Institute of Biophysics, Chinese
Academy of Sciences, 15 Datun Rd., Chaoyang District, Beijing
100101, China. Tel.: 86-10-64889867; Fax: 86-10-64889867;
E-mail:dcliang{at}sun5.ibp.ac.cn.
* Abbreviations:
PE
phycoerythrin
APC
allophycocyanin
PC
phycocyanin
C-PC
C-phycocyanin
PEC
phycoerythrocyanin
APC-PY
allophycocyanin from P. yezoensis
APC-SP
APC from S. platensis
C-PC-AQ
C-PC from A. quadruplaticum
C-PC-FR
C-PC from F. diplosiphon
R-PE-PU
R-PE from Polysiphonia urceolata
PCB
phycocyanobilin
α
1β, 2α, 2β,  É 6β stand for the individual subunits of
different monomers within the hexamer (according to
Schirmer et al. ([117]6))
r.m.s.
root mean square
*
+ Received December 16, 1998.
+ Revision received March 31, 1999.
* The American Society for Biochemistry and Molecular Biology, Inc.
[118]Previous Section
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