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3LMX
Biol. Unit 1
Info
Asym.Unit (237 KB)
Biol.Unit 1 (897 KB)
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(1)
Title
:
TYROSINE 447 OF PROTOCATECHUATE 34,-DIOXYGENASE CONTROLS EFFICIENT PROGRESS THROUGH CATALYSIS
Authors
:
V. M. Purpero, J. D. Lipscomb, K. Shi
Date
:
01 Feb 10 (Deposition) - 16 Feb 11 (Release) - 16 Feb 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,M,N,O
Biol. Unit 1: A,B,C,M,N,O (4x)
Keywords
:
Protocatechuate, Dihydroxybenzoic Acid, Es Complex, Dioxygenase, Non- Heme, Iron Dependent, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
V. M. Purpero, J. D. Lipscomb, D. H. Ohlendorf, K. Shi, K. B. Dolbeare, C. K. Brown, D. Burk
Tyrosine 447 Of Protocatechuate 34, -Dioxygenase Controls Efficient Progress Through Catalysis
To Be Published
[
close entry info
]
Hetero Components
(4, 200)
Info
All Hetero Components
1a: BETA-MERCAPTOETHANOL (BMEa)
1b: BETA-MERCAPTOETHANOL (BMEb)
1c: BETA-MERCAPTOETHANOL (BMEc)
1d: BETA-MERCAPTOETHANOL (BMEd)
1e: BETA-MERCAPTOETHANOL (BMEe)
1f: BETA-MERCAPTOETHANOL (BMEf)
1g: BETA-MERCAPTOETHANOL (BMEg)
1h: BETA-MERCAPTOETHANOL (BMEh)
1i: BETA-MERCAPTOETHANOL (BMEi)
1j: BETA-MERCAPTOETHANOL (BMEj)
1k: BETA-MERCAPTOETHANOL (BMEk)
1l: BETA-MERCAPTOETHANOL (BMEl)
1m: BETA-MERCAPTOETHANOL (BMEm)
1n: BETA-MERCAPTOETHANOL (BMEn)
1o: BETA-MERCAPTOETHANOL (BMEo)
1p: BETA-MERCAPTOETHANOL (BMEp)
1q: BETA-MERCAPTOETHANOL (BMEq)
1r: BETA-MERCAPTOETHANOL (BMEr)
1s: BETA-MERCAPTOETHANOL (BMEs)
1t: BETA-MERCAPTOETHANOL (BMEt)
1u: BETA-MERCAPTOETHANOL (BMEu)
1v: BETA-MERCAPTOETHANOL (BMEv)
1w: BETA-MERCAPTOETHANOL (BMEw)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
2f: CHLORIDE ION (CLf)
3a: 3,4-DIHYDROXYBENZOIC ACID (DHBa)
3b: 3,4-DIHYDROXYBENZOIC ACID (DHBb)
3c: 3,4-DIHYDROXYBENZOIC ACID (DHBc)
3d: 3,4-DIHYDROXYBENZOIC ACID (DHBd)
3e: 3,4-DIHYDROXYBENZOIC ACID (DHBe)
3f: 3,4-DIHYDROXYBENZOIC ACID (DHBf)
4a: FE (III) ION (FEa)
4b: FE (III) ION (FEb)
4c: FE (III) ION (FEc)
5a: GLYCEROL (GOLa)
5b: GLYCEROL (GOLb)
5c: GLYCEROL (GOLc)
5d: GLYCEROL (GOLd)
5e: GLYCEROL (GOLe)
5f: GLYCEROL (GOLf)
5g: GLYCEROL (GOLg)
5h: GLYCEROL (GOLh)
5i: GLYCEROL (GOLi)
5j: GLYCEROL (GOLj)
6a: SULFATE ION (SO4a)
6b: SULFATE ION (SO4b)
6c: SULFATE ION (SO4c)
6d: SULFATE ION (SO4d)
6e: SULFATE ION (SO4e)
6f: SULFATE ION (SO4f)
6g: SULFATE ION (SO4g)
6h: SULFATE ION (SO4h)
6i: SULFATE ION (SO4i)
6j: SULFATE ION (SO4j)
6k: SULFATE ION (SO4k)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BME
92
Ligand/Ion
BETA-MERCAPTOETHANOL
2
CL
-1
Ligand/Ion
CHLORIDE ION
3
DHB
24
Ligand/Ion
3,4-DIHYDROXYBENZOIC ACID
4
FE
-1
Ligand/Ion
FE (III) ION
5
GOL
40
Ligand/Ion
GLYCEROL
6
SO4
44
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(57, 57)
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)
44: EC8 (SOFTWARE)
45: EC9 (SOFTWARE)
46: FC1 (SOFTWARE)
47: FC2 (SOFTWARE)
48: FC3 (SOFTWARE)
49: FC4 (SOFTWARE)
50: FC5 (SOFTWARE)
51: FC6 (SOFTWARE)
52: FC7 (SOFTWARE)
53: FC8 (SOFTWARE)
54: FC9 (SOFTWARE)
55: GC1 (SOFTWARE)
56: GC2 (SOFTWARE)
57: GC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ILE A:171 , ARG A:184 , ASP A:186
BINDING SITE FOR RESIDUE GOL A 201
02
AC2
SOFTWARE
ASN A:37 , THR A:105 , HIS A:107 , HOH A:271
BINDING SITE FOR RESIDUE SO4 A 202
03
AC3
SOFTWARE
PRO A:42 , HIS A:48 , LYS A:180 , HOH A:262
BINDING SITE FOR RESIDUE SO4 A 203
04
AC4
SOFTWARE
PRO A:1 , GLU A:3 , HOH A:319 , LYS N:507
BINDING SITE FOR RESIDUE BME A 204
05
AC5
SOFTWARE
PRO A:164
BINDING SITE FOR RESIDUE BME A 205
06
AC6
SOFTWARE
ARG A:167
BINDING SITE FOR RESIDUE CL A 206
07
AC7
SOFTWARE
ARG A:38 , LEU A:39 , LYS A:41 , ASN A:87 , ASN A:90
BINDING SITE FOR RESIDUE BME A 207
08
AC8
SOFTWARE
CYS A:175 , ARG A:184
BINDING SITE FOR RESIDUE BME A 208
09
AC9
SOFTWARE
DHB M:1 , TYR M:408 , HIS M:460 , HIS M:462
BINDING SITE FOR RESIDUE FE M 600
10
BC1
SOFTWARE
PRO A:15 , TYR M:324 , TYR M:408 , HIS M:447 , TRP M:449 , ARG M:457 , HIS M:460 , HIS M:462 , FE M:600
BINDING SITE FOR RESIDUE DHB M 1
11
BC2
SOFTWARE
HOH M:116 , ILE M:328 , SO4 N:32 , ARG O:333
BINDING SITE FOR RESIDUE DHB M 4
12
BC3
SOFTWARE
LYS M:318 , ARG M:333 , HOH M:574 , SO4 N:32 , ILE N:328
BINDING SITE FOR RESIDUE DHB M 6
13
BC4
SOFTWARE
GLN M:503 , ILE M:505 , ARG M:522 , PHE M:523 , ASP M:524
BINDING SITE FOR RESIDUE GOL M 539
14
BC5
SOFTWARE
GLN M:530 , ARG M:531 , HOH M:559
BINDING SITE FOR RESIDUE GOL M 10
15
BC6
SOFTWARE
ARG M:383
BINDING SITE FOR RESIDUE GOL M 13
16
BC7
SOFTWARE
ARG M:409 , PRO M:421
BINDING SITE FOR RESIDUE SO4 M 15
17
BC8
SOFTWARE
ARG M:407 , LEU M:419
BINDING SITE FOR RESIDUE BME M 20
18
BC9
SOFTWARE
PHE M:535 , GLU M:536 , HOH M:578
BINDING SITE FOR RESIDUE BME M 21
19
CC1
SOFTWARE
SER M:433
BINDING SITE FOR RESIDUE CL M 27
20
CC2
SOFTWARE
ARG M:450 , PRO M:453 , PRO M:515 , HOH M:596 , SER O:338
BINDING SITE FOR RESIDUE BME M 28
21
CC3
SOFTWARE
ALA M:358
BINDING SITE FOR RESIDUE CL M 30
22
CC4
SOFTWARE
HIS M:361 , CYS M:429 , SER M:438
BINDING SITE FOR RESIDUE BME M 41
23
CC5
SOFTWARE
HOH M:263 , ARG M:307 , PHE M:308 , ILE M:310 , HOH M:562 , ASN N:511 , PRO N:515
BINDING SITE FOR RESIDUE BME M 45
24
CC6
SOFTWARE
SER M:338 , PRO M:340 , ARG N:450 , PRO N:453
BINDING SITE FOR RESIDUE BME M 46
25
CC7
SOFTWARE
ARG M:383 , TYR M:436 , ASP M:524
BINDING SITE FOR RESIDUE BME M 49
26
CC8
SOFTWARE
THR B:169 , ILE B:171 , ARG B:184 , PHE B:185 , ASP B:186 , HOH B:337
BINDING SITE FOR RESIDUE GOL B 201
27
CC9
SOFTWARE
ASN B:37 , THR B:105 , HIS B:107
BINDING SITE FOR RESIDUE SO4 B 202
28
DC1
SOFTWARE
CYS B:175 , ARG B:184
BINDING SITE FOR RESIDUE BME B 203
29
DC2
SOFTWARE
DHB N:2 , TYR N:408 , HIS N:460 , HIS N:462
BINDING SITE FOR RESIDUE FE N 600
30
DC3
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 , HOH N:586 , FE N:600
BINDING SITE FOR RESIDUE DHB N 2
31
DC4
SOFTWARE
SO4 N:32 , HOH N:64 , ARG N:333 , HOH N:583 , ILE O:328 , ARG O:333
BINDING SITE FOR RESIDUE DHB N 5
32
DC5
SOFTWARE
SO4 N:16 , ARG N:407 , PRO N:418 , LEU N:419
BINDING SITE FOR RESIDUE GOL N 11
33
DC6
SOFTWARE
GLN N:503 , LYS N:507 , ARG N:522 , ASP N:524
BINDING SITE FOR RESIDUE GOL N 12
34
DC7
SOFTWARE
GOL N:11 , ARG N:409 , PRO N:421
BINDING SITE FOR RESIDUE SO4 N 16
35
DC8
SOFTWARE
ASP B:32 , ALA N:358
BINDING SITE FOR RESIDUE GOL N 24
36
DC9
SOFTWARE
DHB M:4 , DHB M:6 , LEU M:320 , ARG M:333 , DHB N:5 , LEU N:320 , LEU O:320
BINDING SITE FOR RESIDUE SO4 N 32
37
EC1
SOFTWARE
HOH N:108 , PHE N:535 , GLU N:536
BINDING SITE FOR RESIDUE BME N 33
38
EC2
SOFTWARE
HOH N:160 , ASN N:314 , LYS N:318 , ALA N:496
BINDING SITE FOR RESIDUE BME N 40
39
EC3
SOFTWARE
ASP N:524
BINDING SITE FOR RESIDUE CL N 42
40
EC4
SOFTWARE
CYS N:429
BINDING SITE FOR RESIDUE BME N 47
41
EC5
SOFTWARE
ARG N:383 , HOH N:591
BINDING SITE FOR RESIDUE GOL N 48
42
EC6
SOFTWARE
HOH N:21 , ILE N:339 , PRO N:340 , PRO O:453
BINDING SITE FOR RESIDUE BME N 50
43
EC7
SOFTWARE
ASN C:37 , ARG C:38 , THR C:105 , HIS C:107
BINDING SITE FOR RESIDUE SO4 C 201
44
EC8
SOFTWARE
HIS C:61 , LEU C:62 , ARG C:64 , HOH C:571
BINDING SITE FOR RESIDUE SO4 C 202
45
EC9
SOFTWARE
THR C:98 , PHE C:99 , ASP C:100
BINDING SITE FOR RESIDUE SO4 C 203
46
FC1
SOFTWARE
ARG C:38
BINDING SITE FOR RESIDUE SO4 C 204
47
FC2
SOFTWARE
GLU C:168 , ILE C:171 , ARG C:184 , PHE C:185 , ASP C:186
BINDING SITE FOR RESIDUE BME C 206
48
FC3
SOFTWARE
DHB O:3 , TYR O:408 , HIS O:460 , HIS O:462
BINDING SITE FOR RESIDUE FE O 600
49
FC4
SOFTWARE
PRO C:15 , ARG C:133 , 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
BINDING SITE FOR RESIDUE DHB O 3
50
FC5
SOFTWARE
HIS O:361 , CYS O:429 , SER O:438
BINDING SITE FOR RESIDUE BME O 5
51
FC6
SOFTWARE
ARG O:409 , PRO O:421
BINDING SITE FOR RESIDUE SO4 O 14
52
FC7
SOFTWARE
ASP O:432 , SER O:433
BINDING SITE FOR RESIDUE BME O 22
53
FC8
SOFTWARE
THR O:533 , HIS O:534 , PHE O:535 , GLU O:536 , HOH O:548
BINDING SITE FOR RESIDUE BME O 26
54
FC9
SOFTWARE
MET M:510 , ASN M:511 , ALA M:513 , HOH O:142 , PHE O:308 , VAL O:309 , ILE O:310 , ARG O:531
BINDING SITE FOR RESIDUE GOL O 34
55
GC1
SOFTWARE
ILE B:2 , ARG O:522 , PHE O:523 , ASP O:524
BINDING SITE FOR RESIDUE BME O 37
56
GC2
SOFTWARE
HOH N:267 , PHE N:308 , ILE N:310 , ASN O:511 , ALA O:513
BINDING SITE FOR RESIDUE BME O 38
57
GC3
SOFTWARE
HOH O:143 , LYS O:493 , ALA O:496 , HOH O:597
BINDING SITE FOR RESIDUE BME O 39
[
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_d3lmxa_ (A:)
1b: SCOP_d3lmxb_ (B:)
1c: SCOP_d3lmxc_ (C:)
2a: SCOP_d3lmxm_ (M:)
2b: SCOP_d3lmxn_ (N:)
2c: SCOP_d3lmxo_ (O:)
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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
d3lmxa_
A:
1b
d3lmxb_
B:
1c
d3lmxc_
C:
Protein domain
:
Protocatechuate-3,4-dioxygenase, beta chain
(44)
Pseudomonas putida [TaxId: 303]
(31)
2a
d3lmxm_
M:
2b
d3lmxn_
N:
2c
d3lmxo_
O:
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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Pfam Domains
(2, 9)
Info
all PFAM domains
1a: PFAM_Dioxygenase_C_3lmxC01 (C:23-192)
1b: PFAM_Dioxygenase_C_3lmxC02 (C:23-192)
1c: PFAM_Dioxygenase_C_3lmxC03 (C:23-192)
1d: PFAM_Dioxygenase_C_3lmxO01 (O:346-530)
1e: PFAM_Dioxygenase_C_3lmxO02 (O:346-530)
1f: PFAM_Dioxygenase_C_3lmxO03 (O:346-530)
2a: PFAM_PCDO_beta_N_3lmxO04 (O:308-343)
2b: PFAM_PCDO_beta_N_3lmxO05 (O:308-343)
2c: PFAM_PCDO_beta_N_3lmxO06 (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-3lmxC01
C:23-192
1b
Dioxygenase_C-3lmxC02
C:23-192
1c
Dioxygenase_C-3lmxC03
C:23-192
1d
Dioxygenase_C-3lmxO01
O:346-530
1e
Dioxygenase_C-3lmxO02
O:346-530
1f
Dioxygenase_C-3lmxO03
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-3lmxO04
O:308-343
2b
PCDO_beta_N-3lmxO05
O:308-343
2c
PCDO_beta_N-3lmxO06
O:308-343
[
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