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2VC7
Biol. Unit 2
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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, 28)
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
14
Ligand/Ion
1,2-ETHANEDIOL
3
FE
-1
Ligand/Ion
FE (III) ION
4
GOL
10
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
(37, 37)
Info
All Sites
01: AC5 (SOFTWARE)
02: AC6 (SOFTWARE)
03: AC7 (SOFTWARE)
04: AC8 (SOFTWARE)
05: BC8 (SOFTWARE)
06: BC9 (SOFTWARE)
07: CC1 (SOFTWARE)
08: CC3 (SOFTWARE)
09: CC5 (SOFTWARE)
10: DC1 (SOFTWARE)
11: DC5 (SOFTWARE)
12: DC7 (SOFTWARE)
13: DC9 (SOFTWARE)
14: EC2 (SOFTWARE)
15: EC3 (SOFTWARE)
16: EC4 (SOFTWARE)
17: EC5 (SOFTWARE)
18: EC6 (SOFTWARE)
19: EC7 (SOFTWARE)
20: EC8 (SOFTWARE)
21: FC1 (SOFTWARE)
22: FC2 (SOFTWARE)
23: FC3 (SOFTWARE)
24: FC4 (SOFTWARE)
25: FC5 (SOFTWARE)
26: FC6 (SOFTWARE)
27: FC7 (SOFTWARE)
28: FC9 (SOFTWARE)
29: GC1 (SOFTWARE)
30: GC2 (SOFTWARE)
31: GC3 (SOFTWARE)
32: GC4 (SOFTWARE)
33: GC5 (SOFTWARE)
34: GC6 (SOFTWARE)
35: GC7 (SOFTWARE)
36: GC8 (SOFTWARE)
37: HC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC5
SOFTWARE
HIS C:22 , HIS C:24 , KCX C:137 , ASP C:256 , CO C:1316 , HT5 C:1329 , HOH C:2189
BINDING SITE FOR RESIDUE FE C1315
02
AC6
SOFTWARE
KCX C:137 , HIS C:170 , HIS C:199 , FE C:1315 , HT5 C:1329 , HOH C:2189
BINDING SITE FOR RESIDUE CO C1316
03
AC7
SOFTWARE
HIS D:22 , HIS D:24 , KCX D:137 , ASP D:256 , CO D:1316 , HT5 D:1329 , HOH D:2166
BINDING SITE FOR RESIDUE FE D1315
04
AC8
SOFTWARE
KCX D:137 , HIS D:170 , HIS D:199 , ARG D:223 , FE D:1315 , HT5 D:1329 , HOH D:2166
BINDING SITE FOR RESIDUE CO D1316
05
BC8
SOFTWARE
ASN C:160 , LYS C:164 , GLY C:189 , VAL C:190 , ASP C:191 , LYS C:194 , HOH C:2117 , HOH C:2191 , HOH C:2192
BINDING SITE FOR RESIDUE GOL C1317
06
BC9
SOFTWARE
ASN D:160 , LYS D:164 , GLY D:189 , VAL D:190 , ASP D:191
BINDING SITE FOR RESIDUE GOL D1317
07
CC1
SOFTWARE
PRO C:4 , LEU C:5 , LYS C:8 , ASP C:9 , SER C:10 , LEU C:130 , ASN C:131 , LYS C:132 , EDO C:1326
BINDING SITE FOR RESIDUE EDO C1318
08
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
09
CC5
SOFTWARE
PRO D:4 , LEU D:5 , LYS D:8 , ASP D:9 , SER D:10 , ASN D:131 , LYS D:132 , EDO D:1328
BINDING SITE FOR RESIDUE EDO D1318
10
DC1
SOFTWARE
LEU C:5 , LYS C:8 , ASP C:9 , ILE C:11 , ASP C:15 , LYS C:62 , ASN C:89 , HOH C:2193 , HOH C:2194
BINDING SITE FOR RESIDUE GOL C1319
11
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
12
DC7
SOFTWARE
HIS C:120 , GLY C:128 , THR C:129 , HOH C:2197 , LYS D:164
BINDING SITE FOR RESIDUE EDO C1321
13
DC9
SOFTWARE
GLY B:295 , ASN B:297 , LYS D:14 , ASP D:15
BINDING SITE FOR RESIDUE GOL B1323
14
EC2
SOFTWARE
VAL A:190 , GOL A:1323 , MET D:1 , ASP D:9
BINDING SITE FOR RESIDUE EDO A1331
15
EC3
SOFTWARE
HIS C:38 , HOH C:2199 , HOH C:2200 , HIS D:120
BINDING SITE FOR RESIDUE EDO C1322
16
EC4
SOFTWARE
LYS C:62 , GLY C:87 , ASN C:89
BINDING SITE FOR RESIDUE EDO C1323
17
EC5
SOFTWARE
ASP D:214 , GLY D:246 , ASP D:249 , LYS D:250
BINDING SITE FOR RESIDUE EDO D1319
18
EC6
SOFTWARE
PHE D:59 , LYS D:292 , GLU D:298 , HOH D:2167
BINDING SITE FOR RESIDUE GOL D1320
19
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
20
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
21
FC1
SOFTWARE
MET A:1 , ARG A:2 , GLU C:162 , LYS C:164
BINDING SITE FOR RESIDUE GOL A1334
22
FC2
SOFTWARE
LYS B:244 , MET C:1 , LYS D:14
BINDING SITE FOR RESIDUE EDO B1326
23
FC3
SOFTWARE
ASP C:101 , LEU C:102 , PHE C:104 , ILE D:98 , TYR D:99 , ILE D:100 , ASP D:101 , HOH D:2169 , HOH D:2171
BINDING SITE FOR RESIDUE GOL D1321
24
FC4
SOFTWARE
GLU C:80 , LYS C:81 , LYS C:84 , HOH C:2201
BINDING SITE FOR RESIDUE GOL C1324
25
FC5
SOFTWARE
ASN D:172 , ALA D:173 , HIS D:174 , ASP D:202 , PHE D:229 , HOH D:2172
BINDING SITE FOR RESIDUE EDO D1322
26
FC6
SOFTWARE
TYR C:99 , ASP C:141 , GLU C:142 , HIS C:170 , ARG C:223 , PHE C:229 , HT5 C:1329
BINDING SITE FOR RESIDUE GOL C1325
27
FC7
SOFTWARE
MET C:1 , ARG C:2 , EDO C:1318
BINDING SITE FOR RESIDUE EDO C1326
28
FC9
SOFTWARE
TYR D:99 , TRP D:263 , HOH D:2173
BINDING SITE FOR RESIDUE EDO D1323
29
GC1
SOFTWARE
GLN C:34 , ARG D:26 , PHE D:28 , ARG D:33 , GLU D:42 , ASP D:75 , EDO D:1325
BINDING SITE FOR RESIDUE GOL D1324
30
GC2
SOFTWARE
ARG D:33 , PRO D:37 , GOL D:1324
BINDING SITE FOR RESIDUE EDO D1325
31
GC3
SOFTWARE
LYS C:311 , HOH C:2204 , GLU D:237 , ASN D:294
BINDING SITE FOR RESIDUE GOL C1327
32
GC4
SOFTWARE
ASN D:48 , ASN D:51 , GLU D:52 , HOH D:2175
BINDING SITE FOR RESIDUE EDO D1326
33
GC5
SOFTWARE
SER C:171 , ASN C:172 , ALA C:173 , ASP C:202 , HOH C:2121
BINDING SITE FOR RESIDUE EDO C1328
34
GC6
SOFTWARE
GLU D:42 , ASP D:43 , LYS D:81 , HOH D:2176
BINDING SITE FOR RESIDUE EDO D1327
35
GC7
SOFTWARE
LYS D:8 , ASN D:131 , EDO D:1318
BINDING SITE FOR RESIDUE EDO D1328
36
GC8
SOFTWARE
LEU C:72 , TYR C:97 , KCX C:137 , HIS C:170 , ARG C:223 , ILE C:261 , TRP C:263 , THR C:265 , ALA C:266 , LYS C:271 , FE C:1315 , CO C:1316 , GOL C:1325 , HOH C:2189
BINDING SITE FOR RESIDUE HT5 C1329
37
HC2
SOFTWARE
VAL D:27 , LEU D:72 , TYR D:97 , KCX D:137 , HIS D:170 , ARG D:223 , LEU D:226 , PHE D:229 , ASP D:256 , CYS D:258 , ILE D:261 , THR D:265 , ALA D:266 , FE D:1315 , CO D:1316 , HOH D:2166
BINDING SITE FOR RESIDUE HT5 D1329
[
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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 (C:2-314,D:2-314)
2: PHOSPHOTRIESTERASE_1 (C:17-25,D: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
-
-
C:2-314
D:2-314
2
PHOSPHOTRIESTERASE_1
PS01322
Phosphotriesterase family signature 1.
PHP_SULSO
17-25
2
-
-
C:17-25
D: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
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)
(
)
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
(
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(
)
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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Asymmetric Unit 1
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