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1B4U
Asym. Unit
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Asym.Unit (144 KB)
Biol.Unit 1 (139 KB)
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(1)
Title
:
PROTOCATECHUATE 4,5-DIOXYGENASE (LIGAB) IN COMPLEX WITH PROTOCATECHUATE (PCA)
Authors
:
K. Sugimoto, T. Senda, Y. Mitsui
Date
:
29 Dec 98 (Deposition) - 27 Aug 99 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Extradiol Type Dioxygenase, Protocatechuate, Non-Heme Iron Protein
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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)
Reference
:
K. Sugimoto, T. Senda, H. Aoshima, E. Masai, M. Fukuda, Y. Mitsui
Crystal Structure Of An Aromatic Ring Opening Dioxygenase Ligab, A Protocatechuate 4, 5-Dioxygenase, Under Aerobic Conditions.
Structure Fold. Des. V. 7 953 1999
(for further references see the
PDB file header
)
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Hetero Components
(2, 4)
Info
All Hetero Components
1a: 3,4-DIHYDROXYBENZOIC ACID (DHBa)
1b: 3,4-DIHYDROXYBENZOIC ACID (DHBb)
2a: FE (III) ION (FEa)
2b: FE (III) ION (FEb)
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Label:
No.
Name
Count
Type
Full Name
1
DHB
2
Ligand/Ion
3,4-DIHYDROXYBENZOIC ACID
2
FE
2
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: FE1 (UNKNOWN)
6: FE2 (UNKNOWN)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS B:12 , HIS B:61 , GLU B:242 , DHB B:503
BINDING SITE FOR RESIDUE FE B 501
2
AC2
SOFTWARE
HIS D:12 , HIS D:61 , GLU D:242 , DHB D:504
BINDING SITE FOR RESIDUE FE D 502
3
AC3
SOFTWARE
PHE A:103 , HIS B:12 , PRO B:14 , HIS B:61 , HIS B:127 , HIS B:195 , GLU B:242 , SER B:269 , ASN B:270 , THR B:271 , FE B:501 , HOH B:513
BINDING SITE FOR RESIDUE DHB B 503
4
AC4
SOFTWARE
PHE C:103 , HIS D:12 , PRO D:14 , HIS D:61 , HIS D:127 , HIS D:195 , GLU D:242 , SER D:269 , ASN D:270 , THR D:271 , FE D:502 , HOH D:519
BINDING SITE FOR RESIDUE DHB D 504
5
FE1
UNKNOWN
FE B:501
NON-HEME IRON SITE
6
FE2
UNKNOWN
FE D:502
NON-HEME IRON SITE
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
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Exons
(0, 0)
Info
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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, 4)
Info
All SCOP Domains
1a: SCOP_d1b4ua_ (A:)
1b: SCOP_d1b4uc_ (C:)
2a: SCOP_d1b4ub_ (B:)
2b: SCOP_d1b4ud_ (D:)
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Protein Domains
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Organisms
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(
)
Class
:
All alpha proteins
(14657)
Fold
:
LigA subunit of an aromatic-ring-opening dioxygenase LigAB
(2)
Superfamily
:
LigA subunit of an aromatic-ring-opening dioxygenase LigAB
(2)
Family
:
LigA subunit of an aromatic-ring-opening dioxygenase LigAB
(2)
Protein domain
:
LigA subunit of an aromatic-ring-opening dioxygenase LigAB
(2)
Sphingomonas paucimobilis, formerly Pseudomonas paucimobilis [TaxId: 13689]
(2)
1a
d1b4ua_
A:
1b
d1b4uc_
C:
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Phosphorylase/hydrolase-like
(558)
Superfamily
:
LigB-like
(3)
Family
:
LigB-like
(3)
Protein domain
:
LigB subunit of an aromatic-ring-opening dioxygenase LigAB
(2)
Pseudomonas paucimobilis [TaxId: 13689]
(2)
2a
d1b4ub_
B:
2b
d1b4ud_
D:
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1b4uB00 (B:2-299)
1b: CATH_1b4uD00 (D:2-299)
2a: CATH_1b4uA00 (A:8-139)
2b: CATH_1b4uC00 (C:8-139)
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Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Protocatechuate 4,5-dioxygenase; Chain B
(3)
Homologous Superfamily
:
Protocatechuate 4,5-dioxygenase; Chain B
(3)
Sphingomonas paucimobilis. Organism_taxid: 13689. Strain: syk-6.
(1)
1a
1b4uB00
B:2-299
1b
1b4uD00
D:2-299
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Protocatechuate 4,5-dioxygenase; Chain A
(2)
Homologous Superfamily
:
Protocatechuate 4,5-dioxygenase; Chain A
(2)
Sphingomonas paucimobilis. Organism_taxid: 13689. Strain: syk-6.
(1)
2a
1b4uA00
A:8-139
2b
1b4uC00
C:8-139
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Pfam Domains
(0, 0)
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Asymmetric Unit 1
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