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3LXV
Biol. Unit 1
Info
Asym.Unit (243 KB)
Biol.Unit 1 (926 KB)
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(1)
Title
:
TYROSINE 447 OF PROTOCATECHUATE 3,4-DIOXYGENASE CONTROLS EFFICIENT PROGRESS THROUGH CATALYSIS
Authors
:
V. M. Purpero, J. D. Lipscomb
Date
:
25 Feb 10 (Deposition) - 09 Mar 11 (Release) - 09 Mar 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C,M,N,O
Biol. Unit 1: A,B,C,M,N,O (4x)
Keywords
:
Dioxygenase, Non-Heme, Iron-Dependent, Aromatic Metabolism, 4- Nitrocatechol, Inhibitor, Oxidoreductase-Oxidoreductase Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
V. M. Purpero, M. P. Valley, D. H. Ohlendorf, J. D. Lipscomb
Tyrosine 447 Of Protocatechuate 3, 4-Dioxygenase Controls Efficient Progress Through Catalysis
To Be Published 2010
[
close entry info
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Hetero Components
(6, 148)
Info
All Hetero Components
1a: 4-NITROCATECHOL (4NCa)
1b: 4-NITROCATECHOL (4NCb)
1c: 4-NITROCATECHOL (4NCc)
1d: 4-NITROCATECHOL (4NCd)
2a: BETA-MERCAPTOETHANOL (BMEa)
2b: BETA-MERCAPTOETHANOL (BMEb)
2c: BETA-MERCAPTOETHANOL (BMEc)
2d: BETA-MERCAPTOETHANOL (BMEd)
2e: BETA-MERCAPTOETHANOL (BMEe)
2f: BETA-MERCAPTOETHANOL (BMEf)
2g: BETA-MERCAPTOETHANOL (BMEg)
2h: BETA-MERCAPTOETHANOL (BMEh)
2i: BETA-MERCAPTOETHANOL (BMEi)
2j: BETA-MERCAPTOETHANOL (BMEj)
2k: BETA-MERCAPTOETHANOL (BMEk)
2l: BETA-MERCAPTOETHANOL (BMEl)
2m: BETA-MERCAPTOETHANOL (BMEm)
2n: BETA-MERCAPTOETHANOL (BMEn)
2o: BETA-MERCAPTOETHANOL (BMEo)
3a: CHLORIDE ION (CLa)
3b: CHLORIDE ION (CLb)
3c: CHLORIDE ION (CLc)
4a: CARBONATE ION (CO3a)
4b: CARBONATE ION (CO3b)
4c: CARBONATE ION (CO3c)
4d: CARBONATE ION (CO3d)
4e: CARBONATE ION (CO3e)
5a: FE (III) ION (FEa)
5b: FE (III) ION (FEb)
5c: FE (III) ION (FEc)
6a: GLYCEROL (GOLa)
6b: GLYCEROL (GOLb)
6c: GLYCEROL (GOLc)
6d: GLYCEROL (GOLd)
6e: GLYCEROL (GOLe)
6f: GLYCEROL (GOLf)
6g: GLYCEROL (GOLg)
7a: SULFATE ION (SO4a)
7b: SULFATE ION (SO4b)
7c: SULFATE ION (SO4c)
8a: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSa)
8b: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSb)
8c: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
4NC
16
Ligand/Ion
4-NITROCATECHOL
2
BME
60
Ligand/Ion
BETA-MERCAPTOETHANOL
3
CL
-1
Ligand/Ion
CHLORIDE ION
4
CO3
20
Ligand/Ion
CARBONATE ION
5
FE
-1
Ligand/Ion
FE (III) ION
6
GOL
28
Ligand/Ion
GLYCEROL
7
SO4
12
Ligand/Ion
SULFATE ION
8
TRS
12
Ligand/Ion
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
[
close Hetero Component info
]
Sites
(43, 43)
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)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:37 , ARG A:38 , THR A:105 , HIS A:107 , HOH A:886
BINDING SITE FOR RESIDUE SO4 A 201
02
AC2
SOFTWARE
ARG A:38 , LEU A:39 , ALA A:40 , LYS A:41 , LEU A:85 , ASN A:87 , ALA A:88 , ASN A:90
BINDING SITE FOR RESIDUE GOL A 202
03
AC3
SOFTWARE
PRO A:42 , HIS A:48 , LYS A:180
BINDING SITE FOR RESIDUE BME A 203
04
AC4
SOFTWARE
LEU A:23 , ASN A:28 , PRO A:29 , HOH A:705 , VAL M:426
BINDING SITE FOR RESIDUE BME A 204
05
AC5
SOFTWARE
THR A:169 , ILE A:171 , ARG A:184 , PHE A:185 , ASP A:186 , ARG A:188 , HOH A:850 , HOH A:851 , HOH A:1000
BINDING SITE FOR RESIDUE TRS A 205
06
AC6
SOFTWARE
TYR A:56 , GLY A:60 , ARG A:188
BINDING SITE FOR RESIDUE CO3 A 206
07
AC7
SOFTWARE
4NC M:1 , TYR M:408 , HIS M:460 , HIS M:462 , HOH M:948
BINDING SITE FOR RESIDUE FE M 600
08
AC8
SOFTWARE
GLN M:503 , ILE M:505 , ARG M:522 , PHE M:523 , ASP M:524
BINDING SITE FOR RESIDUE GOL M 5
09
AC9
SOFTWARE
GLN N:503 , ILE N:505 , ARG N:522 , PHE N:523 , ASP N:524
BINDING SITE FOR RESIDUE GOL N 6
10
BC1
SOFTWARE
HOH M:117 , ARG M:307 , PHE M:308 , HOH M:788 , HOH M:815 , MET O:510 , ASN O:511 , ALA O:513 , PRO O:515 , HOH O:895
BINDING SITE FOR RESIDUE GOL M 7
11
BC2
SOFTWARE
PHE M:356 , CYS M:429 , LEU M:430 , HOH M:818 , HOH M:884
BINDING SITE FOR RESIDUE BME M 15
12
BC3
SOFTWARE
ILE M:328 , ARG N:333 , HOH N:1033
BINDING SITE FOR RESIDUE GOL N 9
13
BC4
SOFTWARE
ASP M:432 , SER M:433 , HOH M:891
BINDING SITE FOR RESIDUE BME M 16
14
BC5
SOFTWARE
ILE N:486 , VAL N:501 , GLN N:502 , ILE N:505 , HOH N:1035 , HOH N:1057
BINDING SITE FOR RESIDUE GOL N 10
15
BC6
SOFTWARE
ARG M:450 , PRO M:453 , PRO M:515 , HOH M:772 , SER N:338
BINDING SITE FOR RESIDUE BME M 18
16
BC7
SOFTWARE
ARG M:383
BINDING SITE FOR RESIDUE CO3 M 29
17
BC8
SOFTWARE
HIS N:534 , PHE N:535 , HOH N:883
BINDING SITE FOR RESIDUE BME N 12
18
BC9
SOFTWARE
PHE M:535 , HOH M:1031 , HOH O:1048
BINDING SITE FOR RESIDUE CO3 M 33
19
CC1
SOFTWARE
PRO A:15 , ARG A:133 , TYR M:324 , TYR M:408 , HIS M:447 , TRP M:449 , ARG M:457 , HIS M:460 , HIS M:462 , ILE M:491 , FE M:600 , HOH M:948 , HOH M:964 , HOH M:1010
BINDING SITE FOR RESIDUE 4NC M 1
20
CC2
SOFTWARE
ASN B:37 , ARG B:38 , THR B:105 , HIS B:107 , HOH B:457
BINDING SITE FOR RESIDUE SO4 B 201
21
CC3
SOFTWARE
ASN B:152 , PRO B:164 , ARG B:167 , HOH B:539
BINDING SITE FOR RESIDUE BME B 202
22
CC4
SOFTWARE
GLU B:168 , ILE B:171 , ARG B:184 , PHE B:185 , ASP B:186 , ARG B:188 , HOH B:937 , HOH B:965
BINDING SITE FOR RESIDUE TRS B 203
23
CC5
SOFTWARE
HIS B:61 , LEU B:62
BINDING SITE FOR RESIDUE CL B 204
24
CC6
SOFTWARE
4NC N:2 , TYR N:408 , HIS N:460 , HIS N:462 , HOH N:949
BINDING SITE FOR RESIDUE FE N 600
25
CC7
SOFTWARE
PRO M:515 , HOH M:590 , HOH M:1054 , ARG N:307 , PHE N:308 , ARG N:531 , HOH N:978 , HOH N:1039
BINDING SITE FOR RESIDUE BME N 22
26
CC8
SOFTWARE
PRO B:15 , ARG B:133 , TYR N:324 , TYR N:408 , HIS N:447 , TRP N:449 , ARG N:457 , HIS N:460 , HIS N:462 , ILE N:491 , FE N:600 , HOH N:949 , HOH N:957
BINDING SITE FOR RESIDUE 4NC N 2
27
CC9
SOFTWARE
ASN C:37 , THR C:105 , HIS C:107
BINDING SITE FOR RESIDUE SO4 C 201
28
DC1
SOFTWARE
ILE C:171 , ARG C:184 , ASP C:186 , ARG C:188 , HOH C:813
BINDING SITE FOR RESIDUE GOL C 202
29
DC2
SOFTWARE
ASN C:152 , ASN C:159 , ARG C:167 , GLU C:168
BINDING SITE FOR RESIDUE BME C 203
30
DC3
SOFTWARE
ARG C:133 , HOH C:975 , 4NC O:3 , TRP O:449 , ARG O:450 , HOH O:811 , HOH O:974
BINDING SITE FOR RESIDUE BME C 204
31
DC4
SOFTWARE
ARG N:450 , GLY N:452 , HOH N:591 , SER O:338
BINDING SITE FOR RESIDUE CO3 N 31
32
DC5
SOFTWARE
ARG C:38 , LEU C:39 , LYS C:41 , ASN C:84 , LEU C:85 , ASN C:87 , ASN C:90 , HOH C:1055
BINDING SITE FOR RESIDUE CO3 C 205
33
DC6
SOFTWARE
THR O:321 , PRO O:322 , ASP O:323 , LYS O:493 , HOH O:552
BINDING SITE FOR RESIDUE BME O 14
34
DC7
SOFTWARE
SER N:438 , HIS O:534 , PHE O:535
BINDING SITE FOR RESIDUE BME O 17
35
DC8
SOFTWARE
ARG O:407 , PRO O:418 , LEU O:419 , HOH O:1062
BINDING SITE FOR RESIDUE BME O 19
36
DC9
SOFTWARE
HIS N:359 , ASP N:362
BINDING SITE FOR RESIDUE CL N 34
37
EC1
SOFTWARE
ARG O:383
BINDING SITE FOR RESIDUE BME O 20
38
EC2
SOFTWARE
ILE N:328 , HOH N:1037 , ARG O:333
BINDING SITE FOR RESIDUE BME O 21
39
EC3
SOFTWARE
GLN O:503 , ILE O:505 , ARG O:522 , PHE O:523 , ASP O:524 , HOH O:1005
BINDING SITE FOR RESIDUE TRS O 27
40
EC4
SOFTWARE
ASP O:432 , SER O:433
BINDING SITE FOR RESIDUE CL O 36
41
EC5
SOFTWARE
HOH O:250 , PRO O:487 , LYS O:493 , VAL O:501 , GLN O:502 , ILE O:505 , HOH O:572
BINDING SITE FOR RESIDUE 4NC O 37
42
EC6
SOFTWARE
4NC O:3 , TYR O:408 , HIS O:460 , HIS O:462 , HOH O:952
BINDING SITE FOR RESIDUE FE O 600
43
EC7
SOFTWARE
PRO C:15 , ARG C:133 , BME C:204 , TYR O:324 , TYR O:408 , HIS O:447 , TRP O:449 , ARG O:457 , HIS O:460 , HIS O:462 , ILE O:491 , FE O:600 , HOH O:952 , HOH O:955 , HOH O:974
BINDING SITE FOR RESIDUE 4NC O 3
[
close Site info
]
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
(1, 24)
Info
All PROSITE Patterns/Profiles
1: INTRADIOL_DIOXYGENAS (M:380-408,N:380-408,O:380-408)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
INTRADIOL_DIOXYGENAS
PS00083
Intradiol ring-cleavage dioxygenases signature.
PCXA_PSEPU
52-80
12
A:51-79
B:51-79
C:51-79
PCXB_PSEPU
81-109
12
M:380-408
N:380-408
O:380-408
[
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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
(2, 6)
Info
All SCOP Domains
1a: SCOP_d3lxva_ (A:)
1b: SCOP_d3lxvb_ (B:)
1c: SCOP_d3lxvc_ (C:)
2a: SCOP_d3lxvm_ (M:)
2b: SCOP_d3lxvn_ (N:)
2c: SCOP_d3lxvo_ (O:)
View:
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Classes
(
)
(
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(
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(
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(
)
(
)
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(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Prealbumin-like
(433)
Superfamily
:
Aromatic compound dioxygenase
(111)
Family
:
Aromatic compound dioxygenase
(100)
Protein domain
:
Protocatechuate-3,4-dioxygenase, alpha chain
(37)
Pseudomonas putida [TaxId: 303]
(31)
1a
d3lxva_
A:
1b
d3lxvb_
B:
1c
d3lxvc_
C:
Protein domain
:
Protocatechuate-3,4-dioxygenase, beta chain
(44)
Pseudomonas putida [TaxId: 303]
(31)
2a
d3lxvm_
M:
2b
d3lxvn_
N:
2c
d3lxvo_
O:
[
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CATH Domains
(0, 0)
Info
all CATH domains
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Pfam Domains
(2, 9)
Info
all PFAM domains
1a: PFAM_Dioxygenase_C_3lxvC01 (C:23-192)
1b: PFAM_Dioxygenase_C_3lxvC02 (C:23-192)
1c: PFAM_Dioxygenase_C_3lxvC03 (C:23-192)
1d: PFAM_Dioxygenase_C_3lxvO01 (O:346-530)
1e: PFAM_Dioxygenase_C_3lxvO02 (O:346-530)
1f: PFAM_Dioxygenase_C_3lxvO03 (O:346-530)
2a: PFAM_PCDO_beta_N_3lxvO04 (O:308-343)
2b: PFAM_PCDO_beta_N_3lxvO05 (O:308-343)
2c: PFAM_PCDO_beta_N_3lxvO06 (O:308-343)
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Clans
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(
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Families
(
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(
)
Organisms
(
)
(
)
Clan
:
Transthyretin
(88)
Family
:
Dioxygenase_C
(32)
Pseudomonas putida (Arthrobacter siderocapsulatus)
(27)
1a
Dioxygenase_C-3lxvC01
C:23-192
1b
Dioxygenase_C-3lxvC02
C:23-192
1c
Dioxygenase_C-3lxvC03
C:23-192
1d
Dioxygenase_C-3lxvO01
O:346-530
1e
Dioxygenase_C-3lxvO02
O:346-530
1f
Dioxygenase_C-3lxvO03
O:346-530
Clan
:
no clan defined [family: PCDO_beta_N]
(26)
Family
:
PCDO_beta_N
(26)
Pseudomonas putida (Arthrobacter siderocapsulatus)
(26)
2a
PCDO_beta_N-3lxvO04
O:308-343
2b
PCDO_beta_N-3lxvO05
O:308-343
2c
PCDO_beta_N-3lxvO06
O:308-343
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