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2VC7
Biol. Unit 1
Info
Asym.Unit (242 KB)
Biol.Unit 1 (120 KB)
Biol.Unit 2 (119 KB)
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(1)
Title
:
STRUCTURAL BASIS FOR NATURAL LACTONASE AND PROMISCUOUS PHOSPHOTRIESTERASE ACTIVITIES
Authors
:
M. Elias, J. Dupuy, L. Merone, L. Mandrich, S. Moniot, D. Rochu, C. Lecomte, M. Rossi, P. Masson, G. Manco, E. Chabriere
Date
:
19 Sep 07 (Deposition) - 15 Apr 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.05
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Phosphotriesterase, Promiscuous Activities, Enzyme Evolution, Hyperthermophilic, Lactonase, Hydrolase, Biotechnology, Quorum Sensing
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Elias, J. Dupuy, L. Merone, L. Mandrich, E. Porzio, S. Moniot, D. Rochu, C. Lecomte, M. Rossi, P. Masson, G. Manco, E. Chabriere
Structural Basis For Natural Lactonase And Promiscuous Phosphotriesterase Activities.
J. Mol. Biol. V. 379 1017 2008
[
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Hetero Components
(4, 33)
Info
All Hetero Components
1a: COBALT (II) ION (COa)
1b: COBALT (II) ION (COb)
1c: COBALT (II) ION (COc)
1d: COBALT (II) ION (COd)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
2k: 1,2-ETHANEDIOL (EDOk)
2l: 1,2-ETHANEDIOL (EDOl)
2m: 1,2-ETHANEDIOL (EDOm)
2n: 1,2-ETHANEDIOL (EDOn)
2o: 1,2-ETHANEDIOL (EDOo)
2p: 1,2-ETHANEDIOL (EDOp)
2q: 1,2-ETHANEDIOL (EDOq)
2r: 1,2-ETHANEDIOL (EDOr)
2s: 1,2-ETHANEDIOL (EDOs)
2t: 1,2-ETHANEDIOL (EDOt)
2u: 1,2-ETHANEDIOL (EDOu)
2v: 1,2-ETHANEDIOL (EDOv)
2w: 1,2-ETHANEDIOL (EDOw)
2x: 1,2-ETHANEDIOL (EDOx)
2y: 1,2-ETHANEDIOL (EDOy)
3a: FE (III) ION (FEa)
3b: FE (III) ION (FEb)
3c: FE (III) ION (FEc)
3d: FE (III) ION (FEd)
4a: GLYCEROL (GOLa)
4aa: GLYCEROL (GOLaa)
4ab: GLYCEROL (GOLab)
4b: GLYCEROL (GOLb)
4c: GLYCEROL (GOLc)
4d: GLYCEROL (GOLd)
4e: GLYCEROL (GOLe)
4f: GLYCEROL (GOLf)
4g: GLYCEROL (GOLg)
4h: GLYCEROL (GOLh)
4i: GLYCEROL (GOLi)
4j: GLYCEROL (GOLj)
4k: GLYCEROL (GOLk)
4l: GLYCEROL (GOLl)
4m: GLYCEROL (GOLm)
4n: GLYCEROL (GOLn)
4o: GLYCEROL (GOLo)
4p: GLYCEROL (GOLp)
4q: GLYCEROL (GOLq)
4r: GLYCEROL (GOLr)
4s: GLYCEROL (GOLs)
4t: GLYCEROL (GOLt)
4u: GLYCEROL (GOLu)
4v: GLYCEROL (GOLv)
4w: GLYCEROL (GOLw)
4x: GLYCEROL (GOLx)
4y: GLYCEROL (GOLy)
4z: GLYCEROL (GOLz)
5a: (4S)-4-(DECANOYLAMINO)-5-HYDROXY-3... (HT5a)
5b: (4S)-4-(DECANOYLAMINO)-5-HYDROXY-3... (HT5b)
5c: (4S)-4-(DECANOYLAMINO)-5-HYDROXY-3... (HT5c)
5d: (4S)-4-(DECANOYLAMINO)-5-HYDROXY-3... (HT5d)
6a: LYSINE NZ-CARBOXYLIC ACID (KCXa)
6b: LYSINE NZ-CARBOXYLIC ACID (KCXb)
6c: LYSINE NZ-CARBOXYLIC ACID (KCXc)
6d: LYSINE NZ-CARBOXYLIC ACID (KCXd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CO
-1
Ligand/Ion
COBALT (II) ION
2
EDO
11
Ligand/Ion
1,2-ETHANEDIOL
3
FE
-1
Ligand/Ion
FE (III) ION
4
GOL
18
Ligand/Ion
GLYCEROL
5
HT5
2
Ligand/Ion
(4S)-4-(DECANOYLAMINO)-5-HYDROXY-3,4-DIHYDRO-2H-THIOPHENIUM
6
KCX
2
Mod. Amino Acid
LYSINE NZ-CARBOXYLIC ACID
[
close Hetero Component info
]
Sites
(36, 36)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC9 (SOFTWARE)
06: BC1 (SOFTWARE)
07: BC2 (SOFTWARE)
08: BC3 (SOFTWARE)
09: BC4 (SOFTWARE)
10: BC5 (SOFTWARE)
11: BC6 (SOFTWARE)
12: BC7 (SOFTWARE)
13: CC2 (SOFTWARE)
14: CC3 (SOFTWARE)
15: CC4 (SOFTWARE)
16: CC6 (SOFTWARE)
17: CC7 (SOFTWARE)
18: CC8 (SOFTWARE)
19: CC9 (SOFTWARE)
20: DC2 (SOFTWARE)
21: DC3 (SOFTWARE)
22: DC4 (SOFTWARE)
23: DC5 (SOFTWARE)
24: DC6 (SOFTWARE)
25: DC8 (SOFTWARE)
26: DC9 (SOFTWARE)
27: EC1 (SOFTWARE)
28: EC2 (SOFTWARE)
29: EC7 (SOFTWARE)
30: EC8 (SOFTWARE)
31: EC9 (SOFTWARE)
32: FC1 (SOFTWARE)
33: FC2 (SOFTWARE)
34: FC8 (SOFTWARE)
35: GC9 (SOFTWARE)
36: HC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:22 , HIS A:24 , KCX A:137 , ASP A:256 , CO A:1316 , HT5 A:1335 , HOH A:2200
BINDING SITE FOR RESIDUE FE A1315
02
AC2
SOFTWARE
KCX A:137 , HIS A:170 , HIS A:199 , FE A:1315 , HT5 A:1335 , HOH A:2200
BINDING SITE FOR RESIDUE CO A1316
03
AC3
SOFTWARE
HIS B:22 , HIS B:24 , KCX B:137 , ASP B:256 , CO B:1316 , HT5 B:1328 , HOH B:2161
BINDING SITE FOR RESIDUE FE B1315
04
AC4
SOFTWARE
KCX B:137 , HIS B:170 , HIS B:199 , ARG B:223 , FE B:1315 , HT5 B:1328 , HOH B:2161
BINDING SITE FOR RESIDUE CO B1316
05
AC9
SOFTWARE
PRO A:4 , LEU A:5 , LYS A:8 , ASP A:9 , SER A:10 , ASN A:131 , LYS A:132 , HOH A:2201
BINDING SITE FOR RESIDUE GOL A1317
06
BC1
SOFTWARE
ASN B:160 , LYS B:164 , GLY B:189 , ASP B:191 , LYS B:194
BINDING SITE FOR RESIDUE GOL B1317
07
BC2
SOFTWARE
GLY A:201 , THR A:203 , LEU A:221 , LEU A:230 , ARG A:235 , THR A:238 , THR A:239 , HOH A:2202
BINDING SITE FOR RESIDUE EDO A1318
08
BC3
SOFTWARE
ASP A:141 , SER A:171 , ASN A:172 , ALA A:173 , HIS A:199 , ASP A:202 , ARG A:223 , PHE A:229
BINDING SITE FOR RESIDUE GOL A1319
09
BC4
SOFTWARE
LYS A:215 , HOH A:2203 , LYS B:292 , GLY B:295
BINDING SITE FOR RESIDUE EDO A1320
10
BC5
SOFTWARE
LYS A:8 , LYS A:84 , GLY A:87 , HOH A:2204 , GLU B:187 , GLY B:189
BINDING SITE FOR RESIDUE GOL A1321
11
BC6
SOFTWARE
GLU A:298 , GOL A:1324
BINDING SITE FOR RESIDUE EDO A1322
12
BC7
SOFTWARE
HOH A:2171 , ASP B:233 , ASN B:236 , PHE B:290
BINDING SITE FOR RESIDUE EDO B1318
13
CC2
SOFTWARE
ASN A:160 , LYS A:164 , GLY A:189 , ASP A:191 , LYS A:194 , EDO A:1331
BINDING SITE FOR RESIDUE GOL A1323
14
CC3
SOFTWARE
PHE A:59 , PHE A:284 , EDO A:1322 , HOH A:2206 , GLN C:58 , PHE C:59
BINDING SITE FOR RESIDUE GOL A1324
15
CC4
SOFTWARE
ILE A:98 , TYR A:99 , ILE A:100 , ASP A:101 , HOH A:2207 , HOH A:2208 , HOH A:2210 , ASP B:101 , LEU B:102 , PHE B:104
BINDING SITE FOR RESIDUE GOL A1325
16
CC6
SOFTWARE
ALA A:173 , HIS A:174 , ASN A:175 , ASN A:176 , ASN A:205 , TYR A:208 , HOH A:2147
BINDING SITE FOR RESIDUE GOL A1326
17
CC7
SOFTWARE
ASP A:101 , PHE A:104 , GOL A:1328 , HOH A:2093 , ILE B:98 , TYR B:99 , ILE B:100 , ASP B:101
BINDING SITE FOR RESIDUE EDO B1319
18
CC8
SOFTWARE
LYS A:8 , ASP A:9 , ILE A:11 , ASN A:89
BINDING SITE FOR RESIDUE EDO A1327
19
CC9
SOFTWARE
ASP A:101 , LEU A:102 , PRO A:103 , PHE A:104 , HOH A:2091 , HOH A:2211 , EDO B:1319 , HOH B:2065
BINDING SITE FOR RESIDUE GOL A1328
20
DC2
SOFTWARE
ASP A:101 , LEU A:102 , ASP A:148 , HOH A:2213
BINDING SITE FOR RESIDUE GOL A1329
21
DC3
SOFTWARE
LYS A:62 , GLY A:87 , ASN A:89
BINDING SITE FOR RESIDUE EDO A1330
22
DC4
SOFTWARE
PHE B:18 , GLU B:298
BINDING SITE FOR RESIDUE EDO B1320
23
DC5
SOFTWARE
LYS A:271 , ARG A:277 , HOH A:2183 , PRO C:289 , ARG C:293 , HOH C:2195
BINDING SITE FOR RESIDUE GOL C1320
24
DC6
SOFTWARE
PRO B:4 , LEU B:5 , LYS B:8 , SER B:10 , LEU B:130 , ASN B:131 , LYS B:132
BINDING SITE FOR RESIDUE GOL B1321
25
DC8
SOFTWARE
ASP B:214 , GLY B:246 , TYR B:247 , ASP B:249 , LYS B:250
BINDING SITE FOR RESIDUE GOL B1322
26
DC9
SOFTWARE
GLY B:295 , ASN B:297 , LYS D:14 , ASP D:15
BINDING SITE FOR RESIDUE GOL B1323
27
EC1
SOFTWARE
ASP B:112 , ASP B:116 , ILE B:119
BINDING SITE FOR RESIDUE EDO B1324
28
EC2
SOFTWARE
VAL A:190 , GOL A:1323 , MET D:1 , ASP D:9
BINDING SITE FOR RESIDUE EDO A1331
29
EC7
SOFTWARE
ARG A:55 , GLN A:58 , HOH A:2215 , PHE C:18 , ILE C:288 , GLU C:298
BINDING SITE FOR RESIDUE GOL A1332
30
EC8
SOFTWARE
GLY B:295 , ASN B:297 , MET D:1 , ILE D:11 , GLU D:12 , ASP D:15
BINDING SITE FOR RESIDUE GOL B1325
31
EC9
SOFTWARE
TYR A:99 , HIS A:170 , ARG A:223 , TRP A:263 , HT5 A:1335 , HOH A:2216 , HOH A:2217
BINDING SITE FOR RESIDUE GOL A1333
32
FC1
SOFTWARE
MET A:1 , ARG A:2 , GLU C:162 , LYS C:164
BINDING SITE FOR RESIDUE GOL A1334
33
FC2
SOFTWARE
LYS B:244 , MET C:1 , LYS D:14
BINDING SITE FOR RESIDUE EDO B1326
34
FC8
SOFTWARE
ASN B:172 , ALA B:173 , HIS B:174 , ASP B:202 , ARG B:223 , PHE B:229 , HOH B:2089 , HOH B:2162
BINDING SITE FOR RESIDUE GOL B1327
35
GC9
SOFTWARE
HIS A:24 , TYR A:97 , KCX A:137 , HIS A:170 , ARG A:223 , LEU A:226 , PHE A:229 , ASP A:256 , TRP A:263 , ALA A:266 , TRP A:278 , FE A:1315 , CO A:1316 , GOL A:1333 , HOH A:2200
BINDING SITE FOR RESIDUE HT5 A1335
36
HC1
SOFTWARE
HIS B:24 , TYR B:97 , KCX B:137 , HIS B:170 , ARG B:223 , LEU B:226 , LEU B:228 , PHE B:229 , CYS B:258 , ILE B:261 , TRP B:263 , THR B:265 , LYS B:271 , FE B:1315 , CO B:1316 , HOH B:2161
BINDING SITE FOR RESIDUE HT5 B1328
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: PHOSPHOTRIESTERASE_2 (A:2-314,B:2-314)
2: PHOSPHOTRIESTERASE_1 (A:17-25,B:17-25)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PHOSPHOTRIESTERASE_2
PS51347
Phosphotriesterase family profile.
PHP_SULSO
2-314
2
A:2-314
B:2-314
-
-
2
PHOSPHOTRIESTERASE_1
PS01322
Phosphotriesterase family signature 1.
PHP_SULSO
17-25
2
A:17-25
B:17-25
-
-
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2vc7a_ (A:)
1b: SCOP_d2vc7b_ (B:)
1c: SCOP_d2vc7c_ (C:)
1d: SCOP_d2vc7d_ (D:)
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Protein Domains
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(
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Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Metallo-dependent hydrolases
(273)
Family
:
automated matches
(44)
Protein domain
:
automated matches
(44)
Sulfolobus solfataricus [TaxId: 2287]
(10)
1a
d2vc7a_
A:
1b
d2vc7b_
B:
1c
d2vc7c_
C:
1d
d2vc7d_
D:
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_PTE_2vc7D01 (D:11-314)
1b: PFAM_PTE_2vc7D02 (D:11-314)
1c: PFAM_PTE_2vc7D03 (D:11-314)
1d: PFAM_PTE_2vc7D04 (D:11-314)
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Clans
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(
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Organisms
(
)
(
)
Clan
:
Amidohydrolase
(126)
Family
:
PTE
(19)
Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
(2)
1a
PTE-2vc7D01
D:11-314
1b
PTE-2vc7D02
D:11-314
1c
PTE-2vc7D03
D:11-314
1d
PTE-2vc7D04
D:11-314
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