aminoglycoside antibiotics - color plates
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COLOR PLATES
Unkn
own
rela
tion
tobi
osyn
thet
ic pa
thwa
yR
egul
ator
s
Stre
ptid
ine
6-P
synt
hesis
Res
ista
nce
Tran
spor
ters
Phos
phat
ases
SPC
cond
ensa
tion,
last
step
s
dTDP
-dih
ydro
-st
rept
oses
ynth
esis
ND
P-ka
suga
min
ebi
osyn
thes
isNDP-
NM
LG-
bios
ynth
esis
strW
[stsA
B C
D E
F G
]
str X
V VX
UQ
PH
GF
B1A
KS
TR
DE
LM
N
NT
AB
CD
XE
YF
GH
IJ
N
OB2
Wst
sGst
sFst
sEst
sDst
sCst
sBst
sAst
rON
B2M
LE
DR
AB1
insA ka
sT
aph
Dst
rKs
trB
spcR
orf4
STR
S.gr
iseus
STR
S.gl
auce
scen
s
SPC
KA
S
FG
HI
KS
TZ
UJ
KL
MN
OP
QR
AB
CD
GF
EI
kac 3
38
Figu
re2.
2.B
iosy
nthe
ticge
necl
uste
rsfo
rSTR
-rel
ated
AG
As.
Fun
ctio
nally
rela
ted
gro
ups
ofg
enes
are
diffe
ren
tiate
dby
the
colo
rco
degi
ven
belo
w.N
MLG
,N-m
ethy
l-L-g
luco
sam
ine.
Rel
ated
grou
pso
fgen
esar
edi
ffere
ntia
ted
byth
eco
lorc
ode
give
nab
ove.
-
COLOR PLATES
aph
aph
parE
SC
MT
UQ
NP
XF
DL
BA
ZI
pph
YG
H
SC
MT
UQ
NP
FD
LB
ZI
HG
ribG
neo
G
RIB
NEO
PAR
LIV
BTR
H H
IE
SC
UM
IE
SC
MT
UQ
NP
XF
DL
BA
aa
cC8
QT
NP
XF
DL
BA
Ra
acC
8(Y
)
livE
R2T
SN
ML
AB
CD
EF
GH
IJ
KO
PQ
btrU
Unkn
own
rela
tion
tobi
osyn
thet
ic pa
thwa
y
Reg
ulat
ors
Cycli
tol m
onom
erbi
osyn
thes
is
4-G
luco
sam
inylt
rans
fer
an
d 3'
,4'-m
odific
atio
n(4
galac
tosylt
ransfe
r inH
yg)
Res
ista
nce
Tran
spor
ters
Rib
osta
myc
in3
-gl
ucos
amin
yl tra
nsfe
ra
nd
mod
ificat
ion
(NM-
family
)
Phos
phat
ases
6'-m
odific
atio
n(bi
functi
onali
n NM-
fam
ily, a
lso fo
r 6
mo
dific
atio
n)
2DO
S 5-
ribos
yltra
nsfe
ra
nd
mod
ificat
ion
(NM-
fam
ily)
gene
s out
side
of t
he cl
uste
rs
Sens
or/k
inas
ere
gula
tor s
yste
m
A B
AX
OV
WY
Figu
re2.
9.B
iosy
nthe
ticge
necl
uste
rsfo
rNEO
-fam
ilyA
GA
s.Fu
nct
iona
llyre
late
dgr
ou
pso
fgen
esar
edi
ffere
ntia
ted
byth
eco
lorc
ode
give
nbe
low
:(A)
colo
rco
deu
sed
inal
lgen
etic
map
sfo
r2D
OS
and
2DO
S-re
late
dA
GA
s;(B
)co
lorc
ode
forp
athw
ay-s
peci
ficfu
nctio
nsin
the
NEO
fam
ily.
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COLOR PLATES
kanZ
tobE
genN D T I H G F A Y E V U X B2 K B3 B4P W S2 D1 M2 D2 C S1 M1 D3 Q OB1
T B Q Z S1 C D2 M2 M1 L U A D3 O RD1 S2 (Tn)
Y X W A G H I R E T B Q S1 S2C D J K L O P UD3kmrD2 M2 M1
GEN
KAN
TOB
gmrA gmrB
Figure 2.15. Biosynthetic gene clusters for KAN/GEN-related AGAs. 2DOS 6-glycosyltransfer and modification-specific genes, all other colors see Figure 2.9.
"erosion zone"
1 2
FOR M. olivasterosp ora
IST
FOR? Frankia CcI3
forY H I J Q W V M S E O L2 D P B K Z X G N A L R O F E D C fmrP B Afmr fosG
3357 3358 3359 3360 3361 3362 3363 33643365
33663367
3368 3369 3370 3371 3372 3373 3374 3375
imrA istA D P B J F G1 Z H W Q C L3 L I S N X M L2 O E
Figure 2.22. Biosynthetic gene clusters for fortimicin (FOR), the putative FOR clusterfrom Frankia sp. CcI3 (fra cluster, cf. Table 18) and istamycin (IST) AGAs. Latecyclitol modification, for all other colors see Figure 2.9. See color plates.
APR Streptoall.hindustanus
APR S.tenebrarius
HYG
aprR2
aprN
hygV W A K U D O E P X L J Y N C M S T I H G
W V U A kamB O D1 F G H I J K C S E P D2 D3 Q D4 Z L D5
R1 N W V B aprA kamB aprO D1 F G H I J K M
M
F
C S E P D2 D3 Q D4 Z L D5CU tatA
Figure 2.25. Biosynthetic gene clusters for APR and HYG-B. octose synthase, transfer,
modification (APR), 8Glycosyltransfer/modification (APR), HYG-specific genes; allother colors see Figure 2.9.
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COLOR PLATES
Helix 44
(a)
(b)530 Loop
Figure 5.2. Design of a model oligonucleotide for the decoding site. See text for fullcaption.
(a)
(b)
Figure 5.3. NMR structure of the A-site oligonucleotide. See text for full caption.
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COLOR PLATES
(a) (b)
Figure 5.5. NMR structures of paromomycin and gentamicin C1a in complex with theA-site oligonucleotide. See text for full caption.
(a) (b)
Figure 5.7. Structural origins of aminoglycoside specificity. See text for full caption.
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COLOR PLATES
Figure 6.3. Conserved interactions between the prokaryotic A-site and the neaminecore of 4,5- and 4,6-disubstituted aminoglycosides as deduced from crystalstructures.1,3,6,10,12 20
(a)
(c)
(b)
(d)
Figure 6.5. The observed structures of the resting off state of the prokaryotic (a(references24), b (reference25), c (reference6), d (reference25), e (reference9), f (reference3),and the eukaryotic (g (reference5), h (reference26)) cytoplasmic A-site.
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COLOR PLATES
(e)
(g)
(f)
(h)
Figure 6.5. (continued )
Figure 10.1. Schematic illustration of the life cycle of HIV-1. See text for full caption.
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COLOR PLATES
Figure 10.3. Schematic view of the HIV-1 genome, showing gene structure and splicingpatterns, as well as important RNA sites localized in the 5-long terminal repeat (LTR)and the -site.
Figure 10.8. Left : The sequence of RRE IIB, a fragment used to study RREligandbinding. Right : The components of our solid-phase assay that utilize the native RREsequence.
Major Groove
Minor Groove
Figure 11.2. Globular conformations of an A-type duplex (left) and a B-type duplex(right), generally seen for RNARNA and DNADNA duplexes, respectively. See text forfull caption.
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