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1YKK
Asym. Unit
Info
Asym.Unit (438 KB)
Biol.Unit 1 (856 KB)
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(1)
Title
:
PROTOCATECHUATE 3,4-DIOXYGENASE Y408C MUTANT
Authors
:
C. K. Brown, D. H. Ohlendorf
Date
:
18 Jan 05 (Deposition) - 16 Aug 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.06
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L (2x)
Keywords
:
3, 4-Pcd, Catechol, Protocatechuate, Dioxygenase, Oxidoreductase
(Keyword Search:
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]
)
Reference
:
M. P. Valley, C. K. Brown, D. L. Burk, M. W. Vetting, D. H. Ohlendorf, J. D. Lipscomb
Roles Of The Equatorial Tyrosyl Iron Ligand Of Protocatechuate 3, 4-Dioxygenase In Catalysis
Biochemistry V. 44 11024 2005
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Hetero Components
(2, 12)
Info
All Hetero Components
1a: S,S-(2-HYDROXYETHYL)THIOCYSTEINE (CMEa)
1b: S,S-(2-HYDROXYETHYL)THIOCYSTEINE (CMEb)
1c: S,S-(2-HYDROXYETHYL)THIOCYSTEINE (CMEc)
1d: S,S-(2-HYDROXYETHYL)THIOCYSTEINE (CMEd)
1e: S,S-(2-HYDROXYETHYL)THIOCYSTEINE (CMEe)
1f: S,S-(2-HYDROXYETHYL)THIOCYSTEINE (CMEf)
2a: FE (III) ION (FEa)
2b: FE (III) ION (FEb)
2c: FE (III) ION (FEc)
2d: FE (III) ION (FEd)
2e: FE (III) ION (FEe)
2f: FE (III) ION (FEf)
View:
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Label:
No.
Name
Count
Type
Full Name
1
CME
6
Mod. Amino Acid
S,S-(2-HYDROXYETHYL)THIOCYSTEINE
2
FE
6
Ligand/Ion
FE (III) ION
[
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
TYR B:447 , HIS B:460 , HIS B:462 , HOH B:680
BINDING SITE FOR RESIDUE FE B 600
2
AC2
SOFTWARE
TYR D:447 , HIS D:460 , HIS D:462 , HOH D:682
BINDING SITE FOR RESIDUE FE D 600
3
AC3
SOFTWARE
TYR F:447 , HIS F:460 , HIS F:462 , HOH F:682
BINDING SITE FOR RESIDUE FE F 600
4
AC4
SOFTWARE
TYR H:447 , HIS H:460 , HIS H:462 , HOH H:680
BINDING SITE FOR RESIDUE FE H 600
5
AC5
SOFTWARE
TYR J:447 , HIS J:460 , HIS J:462 , HOH J:680
BINDING SITE FOR RESIDUE FE J 600
6
AC6
SOFTWARE
TYR L:447 , HIS L:460 , HIS L:462 , HOH L:784
BINDING SITE FOR RESIDUE FE L 600
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 12)
Info
All PROSITE Patterns/Profiles
1: INTRADIOL_DIOXYGENAS (A:51-79,C:51-79,E:51-79,G:51-79,I:...)
;
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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
6
A:51-79
C:51-79
E:51-79
G:51-79
I:51-79
K:51-79
PCXB_PSEPU
81-109
6
B:380-407
D:380-407
F:380-407
H:380-407
J:380-407
L:380-407
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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.
SCOP Domains
(2, 12)
Info
All SCOP Domains
1a: SCOP_d1ykka_ (A:)
1b: SCOP_d1ykkc_ (C:)
1c: SCOP_d1ykke_ (E:)
1d: SCOP_d1ykkg_ (G:)
1e: SCOP_d1ykki_ (I:)
1f: SCOP_d1ykkk_ (K:)
2a: SCOP_d1ykkb1 (B:301-538)
2b: SCOP_d1ykkd_ (D:)
2c: SCOP_d1ykkf_ (F:)
2d: SCOP_d1ykkh_ (H:)
2e: SCOP_d1ykkj_ (J:)
2f: SCOP_d1ykkl_ (L:)
View:
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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
d1ykka_
A:
1b
d1ykkc_
C:
1c
d1ykke_
E:
1d
d1ykkg_
G:
1e
d1ykki_
I:
1f
d1ykkk_
K:
Protein domain
:
Protocatechuate-3,4-dioxygenase, beta chain
(44)
Pseudomonas putida [TaxId: 303]
(31)
2a
d1ykkb1
B:301-538
2b
d1ykkd_
D:
2c
d1ykkf_
F:
2d
d1ykkh_
H:
2e
d1ykkj_
J:
2f
d1ykkl_
L:
[
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CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_1ykkB00 (B:301-538)
1b: CATH_1ykkA00 (A:1-200)
1c: CATH_1ykkC00 (C:1-200)
1d: CATH_1ykkE00 (E:1-200)
1e: CATH_1ykkG00 (G:1-200)
1f: CATH_1ykkI00 (I:1-200)
1g: CATH_1ykkK00 (K:1-200)
1h: CATH_1ykkD00 (D:301-538)
1i: CATH_1ykkF00 (F:301-538)
1j: CATH_1ykkH00 (H:301-538)
1k: CATH_1ykkJ00 (J:301-538)
1l: CATH_1ykkL00 (L:301-538)
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)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Protocatechuate 3,4-Dioxygenase, subunit A
(43)
Homologous Superfamily
:
Protocatechuate 3,4-Dioxygenase, subunit A
(43)
Pseudomonas putida. Organism_taxid: 303.
(20)
1a
1ykkB00
B:301-538
1b
1ykkA00
A:1-200
1c
1ykkC00
C:1-200
1d
1ykkE00
E:1-200
1e
1ykkG00
G:1-200
1f
1ykkI00
I:1-200
1g
1ykkK00
K:1-200
1h
1ykkD00
D:301-538
1i
1ykkF00
F:301-538
1j
1ykkH00
H:301-538
1k
1ykkJ00
J:301-538
1l
1ykkL00
L:301-538
[
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Pfam Domains
(2, 18)
Info
all PFAM domains
1a: PFAM_Dioxygenase_C_1ykkK01 (K:23-192)
1b: PFAM_Dioxygenase_C_1ykkK02 (K:23-192)
1c: PFAM_Dioxygenase_C_1ykkK03 (K:23-192)
1d: PFAM_Dioxygenase_C_1ykkK04 (K:23-192)
1e: PFAM_Dioxygenase_C_1ykkK05 (K:23-192)
1f: PFAM_Dioxygenase_C_1ykkK06 (K:23-192)
1g: PFAM_Dioxygenase_C_1ykkL01 (L:346-530)
1h: PFAM_Dioxygenase_C_1ykkL02 (L:346-530)
1i: PFAM_Dioxygenase_C_1ykkL03 (L:346-530)
1j: PFAM_Dioxygenase_C_1ykkL04 (L:346-530)
1k: PFAM_Dioxygenase_C_1ykkL05 (L:346-530)
1l: PFAM_Dioxygenase_C_1ykkL06 (L:346-530)
2a: PFAM_PCDO_beta_N_1ykkL07 (L:308-343)
2b: PFAM_PCDO_beta_N_1ykkL08 (L:308-343)
2c: PFAM_PCDO_beta_N_1ykkL09 (L:308-343)
2d: PFAM_PCDO_beta_N_1ykkL10 (L:308-343)
2e: PFAM_PCDO_beta_N_1ykkL11 (L:308-343)
2f: PFAM_PCDO_beta_N_1ykkL12 (L:308-343)
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(
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Organisms
(
)
(
)
Clan
:
Transthyretin
(88)
Family
:
Dioxygenase_C
(32)
Pseudomonas putida (Arthrobacter siderocapsulatus)
(27)
1a
Dioxygenase_C-1ykkK01
K:23-192
1b
Dioxygenase_C-1ykkK02
K:23-192
1c
Dioxygenase_C-1ykkK03
K:23-192
1d
Dioxygenase_C-1ykkK04
K:23-192
1e
Dioxygenase_C-1ykkK05
K:23-192
1f
Dioxygenase_C-1ykkK06
K:23-192
1g
Dioxygenase_C-1ykkL01
L:346-530
1h
Dioxygenase_C-1ykkL02
L:346-530
1i
Dioxygenase_C-1ykkL03
L:346-530
1j
Dioxygenase_C-1ykkL04
L:346-530
1k
Dioxygenase_C-1ykkL05
L:346-530
1l
Dioxygenase_C-1ykkL06
L: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-1ykkL07
L:308-343
2b
PCDO_beta_N-1ykkL08
L:308-343
2c
PCDO_beta_N-1ykkL09
L:308-343
2d
PCDO_beta_N-1ykkL10
L:308-343
2e
PCDO_beta_N-1ykkL11
L:308-343
2f
PCDO_beta_N-1ykkL12
L:308-343
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