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2NXH
Asym. Unit
Info
Asym.Unit (536 KB)
Biol.Unit 1 (184 KB)
Biol.Unit 2 (181 KB)
Biol.Unit 3 (182 KB)
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(1)
Title
:
STRUCTURAL AND MECHANISTIC CHANGES ALONG AN ENGINEERED PATH FROM METALLO TO NON-METALLO KDO8P SYNTHASE.
Authors
:
F. Kona, X. Xu, P. Martin, P. Kuzmic, D. L. Gatti
Date
:
17 Nov 06 (Deposition) - 24 Apr 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.11
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Biol. Unit 3: I,J,K,L (1x)
Keywords
:
Kdo, Kdo8P, Kdo8Ps, Pep, A5P, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. Kona, X. Xu, P. Martin, P. Kuzmic, D. L. Gatti
Structural And Mechanistic Changes Along An Engineered Path From Metallo To Nonmetallo 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthases.
Biochemistry V. 46 4532 2007
(for further references see the
PDB file header
)
[
close entry info
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Hetero Components
(2, 24)
Info
All Hetero Components
1a: PHOSPHOENOLPYRUVATE (PEPa)
1b: PHOSPHOENOLPYRUVATE (PEPb)
1c: PHOSPHOENOLPYRUVATE (PEPc)
1d: PHOSPHOENOLPYRUVATE (PEPd)
1e: PHOSPHOENOLPYRUVATE (PEPe)
1f: PHOSPHOENOLPYRUVATE (PEPf)
1g: PHOSPHOENOLPYRUVATE (PEPg)
1h: PHOSPHOENOLPYRUVATE (PEPh)
1i: PHOSPHOENOLPYRUVATE (PEPi)
1j: PHOSPHOENOLPYRUVATE (PEPj)
1k: PHOSPHOENOLPYRUVATE (PEPk)
1l: PHOSPHOENOLPYRUVATE (PEPl)
2a: PHOSPHATE ION (PO4a)
2b: PHOSPHATE ION (PO4b)
2c: PHOSPHATE ION (PO4c)
2d: PHOSPHATE ION (PO4d)
2e: PHOSPHATE ION (PO4e)
2f: PHOSPHATE ION (PO4f)
2g: PHOSPHATE ION (PO4g)
2h: PHOSPHATE ION (PO4h)
2i: PHOSPHATE ION (PO4i)
2j: PHOSPHATE ION (PO4j)
2k: PHOSPHATE ION (PO4k)
2l: PHOSPHATE ION (PO4l)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
PEP
12
Ligand/Ion
PHOSPHOENOLPYRUVATE
2
PO4
12
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
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Sites
(24, 24)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:1049 , SER A:1050 , LYS A:1196 , SER A:1197 , HOH A:5079 , HOH A:6212
BINDING SITE FOR RESIDUE PO4 A 1280
02
AC2
SOFTWARE
ARG B:2049 , SER B:2050 , LYS B:2196 , SER B:2197 , HOH B:5152 , HOH B:5484 , HOH B:6483
BINDING SITE FOR RESIDUE PO4 B 1281
03
AC3
SOFTWARE
ARG C:3049 , SER C:3050 , SER C:3197 , HOH C:5889 , HOH C:6214 , ARG D:4106
BINDING SITE FOR RESIDUE PO4 C 1282
04
AC4
SOFTWARE
ARG D:4049 , SER D:4050 , LYS D:4196 , SER D:4197 , HOH D:5701 , HOH D:6095
BINDING SITE FOR RESIDUE PO4 D 1283
05
AC5
SOFTWARE
ARG E:1049 , SER E:1050 , SER E:1197
BINDING SITE FOR RESIDUE PO4 E 1284
06
AC6
SOFTWARE
ARG F:2049 , SER F:2050 , LYS F:2196 , SER F:2197 , HOH F:6145
BINDING SITE FOR RESIDUE PO4 F 1285
07
AC7
SOFTWARE
ARG G:3049 , SER G:3050 , LYS G:3196 , SER G:3197 , HOH G:5692 , HOH G:5916 , HOH G:6516 , HOH G:6529
BINDING SITE FOR RESIDUE PO4 G 1286
08
AC8
SOFTWARE
ARG H:4049 , SER H:4050 , HOH H:5429 , HOH H:5879 , HOH H:6044 , HOH H:6463
BINDING SITE FOR RESIDUE PO4 H 1287
09
AC9
SOFTWARE
ARG I:1049 , SER I:1050 , LYS I:1196 , SER I:1197 , HOH I:5098 , HOH I:5612
BINDING SITE FOR RESIDUE PO4 I 1288
10
BC1
SOFTWARE
ARG J:2049 , SER J:2050 , HOH J:5475 , HOH J:5988
BINDING SITE FOR RESIDUE PO4 J 1289
11
BC2
SOFTWARE
ARG K:3049 , SER K:3050 , LYS K:3196 , SER K:3197 , HOH K:6104 , HOH K:6207
BINDING SITE FOR RESIDUE PO4 K 1290
12
BC3
SOFTWARE
ARG K:3106 , ARG L:4049 , SER L:4050 , SER L:4197 , HOH L:6025 , HOH L:6249
BINDING SITE FOR RESIDUE PO4 L 1291
13
BC4
SOFTWARE
LYS A:1041 , SER A:1043 , LYS A:1046 , GLN A:1099 , PRO A:1101 , ALA A:1102 , LYS A:1124 , ARG A:1154 , HIS A:1185 , PHE A:1220 , HOH A:5071 , HOH A:5095 , HOH A:5140 , HOH A:5357
BINDING SITE FOR RESIDUE PEP A 1268
14
BC5
SOFTWARE
LYS B:2041 , SER B:2043 , LYS B:2046 , GLN B:2099 , PRO B:2101 , ALA B:2102 , LYS B:2124 , ARG B:2154 , HIS B:2185 , PHE B:2220 , HOH B:5030 , HOH B:5060 , HOH B:5108 , HOH B:5155
BINDING SITE FOR RESIDUE PEP B 1269
15
BC6
SOFTWARE
LYS C:3041 , SER C:3043 , LYS C:3046 , GLN C:3099 , PRO C:3101 , ALA C:3102 , LYS C:3124 , ARG C:3154 , HIS C:3185 , PHE C:3220 , HOH C:5543 , HOH C:5587 , HOH C:5607
BINDING SITE FOR RESIDUE PEP C 1270
16
BC7
SOFTWARE
ASN D:4011 , LYS D:4041 , SER D:4043 , LYS D:4046 , GLN D:4099 , PRO D:4101 , ALA D:4102 , LYS D:4124 , ARG D:4154 , HIS D:4185 , PHE D:4220 , GLU D:4222 , HOH D:5345 , HOH D:5768 , HOH D:5977
BINDING SITE FOR RESIDUE PEP D 1271
17
BC8
SOFTWARE
ASN E:1011 , LYS E:1041 , SER E:1043 , LYS E:1046 , GLN E:1099 , PRO E:1101 , ALA E:1102 , LYS E:1124 , ARG E:1154 , HIS E:1185 , PHE E:1220 , GLU E:1222 , HOH E:5830
BINDING SITE FOR RESIDUE PEP E 1272
18
BC9
SOFTWARE
LYS F:2041 , SER F:2043 , LYS F:2046 , GLN F:2099 , PRO F:2101 , ALA F:2102 , LYS F:2124 , ARG F:2154 , HIS F:2185 , PHE F:2220 , GLU F:2222 , HOH F:5595 , HOH F:5903 , HOH F:6076
BINDING SITE FOR RESIDUE PEP F 1273
19
CC1
SOFTWARE
LYS G:3041 , SER G:3043 , LYS G:3046 , GLN G:3099 , PRO G:3101 , ALA G:3102 , LYS G:3124 , ARG G:3154 , HIS G:3185 , PHE G:3220 , HOH G:5092 , HOH G:5162 , HOH G:5221 , HOH G:5386
BINDING SITE FOR RESIDUE PEP G 1274
20
CC2
SOFTWARE
LYS H:4041 , SER H:4043 , LYS H:4046 , GLN H:4099 , PRO H:4101 , ALA H:4102 , LYS H:4124 , ARG H:4154 , HIS H:4185 , PHE H:4220 , HOH H:5085 , HOH H:5169 , HOH H:5299 , HOH H:5403
BINDING SITE FOR RESIDUE PEP H 1275
21
CC3
SOFTWARE
LYS I:1041 , SER I:1043 , LYS I:1046 , GLN I:1099 , PRO I:1101 , ALA I:1102 , LYS I:1124 , ARG I:1154 , HIS I:1185 , PHE I:1220 , HOH I:5049 , HOH I:5135 , HOH I:5151 , HOH I:5170
BINDING SITE FOR RESIDUE PEP I 1276
22
CC4
SOFTWARE
LYS J:2041 , SER J:2043 , LYS J:2046 , GLN J:2099 , PRO J:2101 , ALA J:2102 , LYS J:2124 , ARG J:2154 , HIS J:2185 , PHE J:2220 , HOH J:5041 , HOH J:5156 , HOH J:5306 , HOH J:5650
BINDING SITE FOR RESIDUE PEP J 1277
23
CC5
SOFTWARE
ASN K:3011 , LYS K:3041 , SER K:3043 , LYS K:3046 , GLN K:3099 , PRO K:3101 , ALA K:3102 , LYS K:3124 , ARG K:3154 , HIS K:3185 , GLU K:3222 , HOH K:5313 , HOH K:5921
BINDING SITE FOR RESIDUE PEP K 1278
24
CC6
SOFTWARE
LYS L:4041 , SER L:4043 , LYS L:4046 , GLN L:4099 , PRO L:4101 , ALA L:4102 , LYS L:4124 , ARG L:4154 , PHE L:4220 , HOH L:5550 , HOH L:5951 , HOH L:6343 , HOH L:6632
BINDING SITE FOR RESIDUE PEP L 1279
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 12)
Info
All SCOP Domains
1a: SCOP_d2nxha_ (A:)
1b: SCOP_d2nxhb_ (B:)
1c: SCOP_d2nxhc_ (C:)
1d: SCOP_d2nxhd_ (D:)
1e: SCOP_d2nxhe_ (E:)
1f: SCOP_d2nxhf_ (F:)
1g: SCOP_d2nxhg_ (G:)
1h: SCOP_d2nxhh_ (H:)
1i: SCOP_d2nxhi_ (I:)
1j: SCOP_d2nxhj_ (J:)
1k: SCOP_d2nxhk_ (K:)
1l: SCOP_d2nxhl_ (L:)
View:
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Classes
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)
(
)
Folds
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)
(
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)
(
)
Families
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Aldolase
(457)
Family
:
Class I DAHP synthetase
(87)
Protein domain
:
3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8P synthase)
(44)
Aquifex aeolicus [TaxId: 63363]
(32)
1a
d2nxha_
A:
1b
d2nxhb_
B:
1c
d2nxhc_
C:
1d
d2nxhd_
D:
1e
d2nxhe_
E:
1f
d2nxhf_
F:
1g
d2nxhg_
G:
1h
d2nxhh_
H:
1i
d2nxhi_
I:
1j
d2nxhj_
J:
1k
d2nxhk_
K:
1l
d2nxhl_
L:
[
close SCOP info
]
CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_2nxhA00 (A:1003-1264)
1b: CATH_2nxhB00 (B:2003-2264)
1c: CATH_2nxhC00 (C:3003-3264)
1d: CATH_2nxhD00 (D:4003-4264)
1e: CATH_2nxhF00 (F:2003-2264)
1f: CATH_2nxhG00 (G:3003-3264)
1g: CATH_2nxhI00 (I:1003-1264)
1h: CATH_2nxhK00 (K:3003-3264)
1i: CATH_2nxhL00 (L:4003-4264)
1j: CATH_2nxhE00 (E:1003-1264)
1k: CATH_2nxhH00 (H:4003-4264)
1l: CATH_2nxhJ00 (J:2003-2264)
View:
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)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Aldolase class I
(887)
Aquifex aeolicus. Organism_taxid: 63363.
(20)
1a
2nxhA00
A:1003-1264
1b
2nxhB00
B:2003-2264
1c
2nxhC00
C:3003-3264
1d
2nxhD00
D:4003-4264
1e
2nxhF00
F:2003-2264
1f
2nxhG00
G:3003-3264
1g
2nxhI00
I:1003-1264
1h
2nxhK00
K:3003-3264
1i
2nxhL00
L:4003-4264
1j
2nxhE00
E:1003-1264
1k
2nxhH00
H:4003-4264
1l
2nxhJ00
J:2003-2264
[
close CATH info
]
Pfam Domains
(1, 12)
Info
all PFAM domains
1a: PFAM_DAHP_synth_1_2nxhL01 (L:4003-4259)
1b: PFAM_DAHP_synth_1_2nxhL02 (L:4003-4259)
1c: PFAM_DAHP_synth_1_2nxhL03 (L:4003-4259)
1d: PFAM_DAHP_synth_1_2nxhL04 (L:4003-4259)
1e: PFAM_DAHP_synth_1_2nxhL05 (L:4003-4259)
1f: PFAM_DAHP_synth_1_2nxhL06 (L:4003-4259)
1g: PFAM_DAHP_synth_1_2nxhL07 (L:4003-4259)
1h: PFAM_DAHP_synth_1_2nxhL08 (L:4003-4259)
1i: PFAM_DAHP_synth_1_2nxhL09 (L:4003-4259)
1j: PFAM_DAHP_synth_1_2nxhL10 (L:4003-4259)
1k: PFAM_DAHP_synth_1_2nxhL11 (L:4003-4259)
1l: PFAM_DAHP_synth_1_2nxhL12 (L:4003-4259)
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Clans
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)
Organisms
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(
)
Clan
:
TIM_barrel
(694)
Family
:
DAHP_synth_1
(46)
Aquifex aeolicus
(17)
1a
DAHP_synth_1-2nxhL01
L:4003-4259
1b
DAHP_synth_1-2nxhL02
L:4003-4259
1c
DAHP_synth_1-2nxhL03
L:4003-4259
1d
DAHP_synth_1-2nxhL04
L:4003-4259
1e
DAHP_synth_1-2nxhL05
L:4003-4259
1f
DAHP_synth_1-2nxhL06
L:4003-4259
1g
DAHP_synth_1-2nxhL07
L:4003-4259
1h
DAHP_synth_1-2nxhL08
L:4003-4259
1i
DAHP_synth_1-2nxhL09
L:4003-4259
1j
DAHP_synth_1-2nxhL10
L:4003-4259
1k
DAHP_synth_1-2nxhL11
L:4003-4259
1l
DAHP_synth_1-2nxhL12
L:4003-4259
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