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2VC5
Asym. Unit
Info
Asym.Unit (217 KB)
Biol.Unit 1 (108 KB)
Biol.Unit 2 (107 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, C. Lecomte, M. Rossi, P. Masson, G. Manco, E. Chabriere
Date
:
18 Sep 07 (Deposition) - 15 Apr 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
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
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(5, 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)
3a: FE (III) ION (FEa)
3b: FE (III) ION (FEb)
3c: FE (III) ION (FEc)
3d: FE (III) ION (FEd)
4a: GLYCEROL (GOLa)
4b: GLYCEROL (GOLb)
4c: GLYCEROL (GOLc)
4d: GLYCEROL (GOLd)
4e: GLYCEROL (GOLe)
4f: GLYCEROL (GOLf)
5a: LYSINE NZ-CARBOXYLIC ACID (KCXa)
5b: LYSINE NZ-CARBOXYLIC ACID (KCXb)
5c: LYSINE NZ-CARBOXYLIC ACID (KCXc)
5d: LYSINE NZ-CARBOXYLIC ACID (KCXd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CO
4
Ligand/Ion
COBALT (II) ION
2
EDO
15
Ligand/Ion
1,2-ETHANEDIOL
3
FE
4
Ligand/Ion
FE (III) ION
4
GOL
6
Ligand/Ion
GLYCEROL
5
KCX
4
Mod. Amino Acid
LYSINE NZ-CARBOXYLIC ACID
[
close Hetero Component info
]
Sites
(29, 29)
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)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (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 , HOH A:2064
BINDING SITE FOR RESIDUE FE A1315
02
AC2
SOFTWARE
KCX A:137 , HIS A:170 , HIS A:199 , ARG A:223 , FE A:1315 , HOH A:2064
BINDING SITE FOR RESIDUE CO A1316
03
AC3
SOFTWARE
HIS B:22 , HIS B:24 , KCX B:137 , ASP B:256 , CO B:1316 , HOH B:2062
BINDING SITE FOR RESIDUE FE B1315
04
AC4
SOFTWARE
KCX B:137 , HIS B:170 , HIS B:199 , ARG B:223 , FE B:1315 , HOH B:2062
BINDING SITE FOR RESIDUE CO B1316
05
AC5
SOFTWARE
HIS C:22 , HIS C:24 , KCX C:137 , ASP C:256 , CO C:1316 , HOH C:2056
BINDING SITE FOR RESIDUE FE C1315
06
AC6
SOFTWARE
KCX C:137 , HIS C:170 , HIS C:199 , ARG C:223 , FE C:1315 , HOH C:2013 , HOH C:2056
BINDING SITE FOR RESIDUE CO C1316
07
AC7
SOFTWARE
HIS D:22 , HIS D:24 , KCX D:137 , ASP D:256 , CO D:1316 , HOH D:2061
BINDING SITE FOR RESIDUE FE D1315
08
AC8
SOFTWARE
KCX D:137 , HIS D:170 , HIS D:199 , ARG D:223 , FE D:1315 , HOH D:2061
BINDING SITE FOR RESIDUE CO D1316
09
AC9
SOFTWARE
TYR A:99 , ILE A:100 , ASP A:101 , PHE B:104 , EDO B:1321
BINDING SITE FOR RESIDUE EDO A1317
10
BC1
SOFTWARE
ASN D:172 , ALA D:173 , HIS D:174 , ASP D:202 , PHE D:229 , HOH D:2045
BINDING SITE FOR RESIDUE EDO D1317
11
BC2
SOFTWARE
ASN C:160 , LYS C:164 , GLY C:189 , ASP C:191
BINDING SITE FOR RESIDUE EDO C1317
12
BC3
SOFTWARE
PHE C:104 , TYR D:99 , ILE D:100 , ASP D:101
BINDING SITE FOR RESIDUE EDO D1318
13
BC4
SOFTWARE
TYR B:257 , CYS B:258 , ILE B:261 , ALA B:266 , LYS B:271
BINDING SITE FOR RESIDUE EDO B1317
14
BC5
SOFTWARE
ASN A:160 , LYS A:164 , GLY A:189 , ASP A:191 , LYS A:194
BINDING SITE FOR RESIDUE GOL A1318
15
BC6
SOFTWARE
ASN B:160 , LYS B:164 , GLY B:189 , VAL B:190 , ASP B:191
BINDING SITE FOR RESIDUE GOL B1318
16
BC7
SOFTWARE
ASN D:160 , LYS D:164 , GLY D:189 , VAL D:190 , ASP D:191
BINDING SITE FOR RESIDUE GOL D1319
17
BC8
SOFTWARE
SER B:171 , ASN B:172 , ALA B:173 , ASP B:202 , ARG B:223 , PHE B:229
BINDING SITE FOR RESIDUE GOL B1319
18
BC9
SOFTWARE
PHE A:104 , ILE B:98 , TYR B:99 , ILE B:100 , ASP B:101 , EDO B:1321
BINDING SITE FOR RESIDUE GOL B1320
19
CC1
SOFTWARE
LYS A:14 , GLY A:17
BINDING SITE FOR RESIDUE EDO A1319
20
CC2
SOFTWARE
GLY D:128 , THR D:129
BINDING SITE FOR RESIDUE EDO D1320
21
CC3
SOFTWARE
LEU A:5 , ASP A:9 , SER A:10 , ASN A:131 , LYS A:132
BINDING SITE FOR RESIDUE EDO A1320
22
CC4
SOFTWARE
EDO A:1317 , ASP B:101 , LEU B:102 , PHE B:104 , GOL B:1320 , EDO B:1323
BINDING SITE FOR RESIDUE EDO B1321
23
CC5
SOFTWARE
LEU C:39 , ILE C:261
BINDING SITE FOR RESIDUE EDO C1318
24
CC6
SOFTWARE
ALA B:266 , TRP B:278
BINDING SITE FOR RESIDUE EDO B1322
25
CC7
SOFTWARE
LEU B:102 , PRO B:103 , LEU B:107 , ASP B:148 , EDO B:1321
BINDING SITE FOR RESIDUE EDO B1323
26
CC8
SOFTWARE
ASP A:141 , SER A:171 , ASN A:172 , ALA A:173 , ASP A:202 , ARG A:223 , PHE A:229
BINDING SITE FOR RESIDUE GOL A1321
27
CC9
SOFTWARE
TYR C:99 , ILE C:100 , ASP C:101 , PHE D:104
BINDING SITE FOR RESIDUE EDO C1319
28
DC1
SOFTWARE
SER A:29 , GLY A:71 , PRO B:103 , PHE B:104
BINDING SITE FOR RESIDUE EDO B1324
29
DC2
SOFTWARE
ALA D:266
BINDING SITE FOR RESIDUE EDO D1321
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: PHOSPHOTRIESTERASE_2 (A:2-314,B:2-314,C:2-314,D:2-314)
2: PHOSPHOTRIESTERASE_1 (A:17-25,B:17-25,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
4
A:2-314
B:2-314
C:2-314
D:2-314
2
PHOSPHOTRIESTERASE_1
PS01322
Phosphotriesterase family signature 1.
PHP_SULSO
17-25
4
A:17-25
B:17-25
C:17-25
D:17-25
[
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]
Exons
(0, 0)
Info
All Exons
View:
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2vc5a_ (A:)
1b: SCOP_d2vc5b_ (B:)
1c: SCOP_d2vc5c_ (C:)
1d: SCOP_d2vc5d_ (D:)
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Classes
(
)
(
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Folds
(
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(
)
Superfamilies
(
)
(
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(
)
(
)
Protein Domains
(
)
(
)
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
d2vc5a_
A:
1b
d2vc5b_
B:
1c
d2vc5c_
C:
1d
d2vc5d_
D:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_PTE_2vc5D01 (D:11-314)
1b: PFAM_PTE_2vc5D02 (D:11-314)
1c: PFAM_PTE_2vc5D03 (D:11-314)
1d: PFAM_PTE_2vc5D04 (D:11-314)
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Clans
(
)
(
)
Families
(
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(
)
Organisms
(
)
(
)
Clan
:
Amidohydrolase
(126)
Family
:
PTE
(19)
Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
(2)
1a
PTE-2vc5D01
D:11-314
1b
PTE-2vc5D02
D:11-314
1c
PTE-2vc5D03
D:11-314
1d
PTE-2vc5D04
D:11-314
[
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]
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Asym.Unit (217 KB)
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