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(-) Description

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./Biol. Unit :  A,B,C,D
Keywords :  Extradiol Type Dioxygenase, Protocatechuate, Non-Heme Iron Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
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
PubMed-ID: 10467151  |  Reference-DOI: 10.1016/S0969-2126(99)80122-1
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTOCATECHUATE 4,5-DIOXYGENASE
    Chains: A, C
    EC Number: 1.13.11.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: CHAIN A, C, ALPHA CHAIN, CHAIN B, D, BETA CHAIN
    Organism Scientific: SPHINGOMONAS PAUCIMOBILIS
    Organism Taxid: 13689
    Strain: SYK-6
    Synonym: LIGA, LIGB
 
Molecule 2 - PROTOCATECHUATE 4,5-DIOXYGENASE
    Chains: B, D
    EC Number: 1.13.11.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: CHAIN A, C, ALPHA CHAIN, CHAIN B, D, BETA CHAIN
    Organism Scientific: SPHINGOMONAS PAUCIMOBILIS
    Organism Taxid: 13689
    Strain: SYK-6
    Synonym: LIGA, LIGB

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1DHB2Ligand/Ion3,4-DIHYDROXYBENZOIC ACID
2FE2Ligand/IonFE (III) ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:12 , HIS B:61 , GLU B:242 , DHB B:503BINDING SITE FOR RESIDUE FE B 501
2AC2SOFTWAREHIS D:12 , HIS D:61 , GLU D:242 , DHB D:504BINDING SITE FOR RESIDUE FE D 502
3AC3SOFTWAREPHE 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:513BINDING SITE FOR RESIDUE DHB B 503
4AC4SOFTWAREPHE 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:519BINDING SITE FOR RESIDUE DHB D 504
5FE1UNKNOWNFE B:501NON-HEME IRON SITE
6FE2UNKNOWNFE D:502NON-HEME IRON SITE

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1B4U)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Tyr B:157 -Pro B:158
2Gly B:192 -Met B:193
3Ile B:266 -Pro B:267
4Glu B:289 -Pro B:290
5Tyr D:157 -Pro D:158
6Gly D:192 -Met D:193
7Ile D:266 -Pro D:267
8Glu D:289 -Pro D:290

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1B4U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1B4U)

(-) Exons   (0, 0)

(no "Exon" information available for 1B4U)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:132
 aligned with PCYA_SPHPI | P22635 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:132
                                    17        27        37        47        57        67        77        87        97       107       117       127       137  
           PCYA_SPHPI     8 IDVHAYLAEFDDIPGTRVFTAQRARKGYNLNQFAMSLMKAENRERFKADESAYLDEWNLTPAAKAAVLARDYNAMIDEGGNVYFLSKLFSTDGKSFQFAAGSMTGMTQEEYAQMMIDGGRSPAGVRSIKGGY 139
               SCOP domains d1b4ua_ A: LigA subunit of an aromatic-ring-opening dioxygenase LigAB                                                                SCOP domains
               CATH domains 1b4uA00 A:8-139 Protocatechuate 4,5-dioxygenase; Chain A                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhh........hhhhhh.hhhhhhhhhhh.hhhhhhhhh.hhhhhhhh...hhhhhhhh...hhhhhh....hhhhhhhhhh....hhhhhhhh....hhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1b4u A   8 IDVHAYLAEFDDIPGTRVFTAQRARKGYNLNQFAMSLMKAENRERFKADESAYLDEWNLTPAAKAAVLARDYNAMIDEGGNVYFLSKLFSTDGKSFQFAAGSMTGMTQEEYAQMMIDGGRSPAGVRSIKGGY 139
                                    17        27        37        47        57        67        77        87        97       107       117       127       137  


Chain B from PDB  Type:PROTEIN  Length:298
 aligned with PCYB_SPHPI | P22636 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:298
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291        
           PCYB_SPHPI     2 ARVTTGITSSHIPALGAAIQTGTSDNDYWGPVFKGYQPIRDWIKQPGNMPDVVILVYNDHASAFDMNIIPTFAIGCAETFKPADEGWGPRPVPDVKGHPDLAWHIAQSLILDEFDMTIMNQMDVDHGCTVPLSMIFGEPEEWPCKVIPFPVNVVTYPPPSGKRCFALGDSIRAAVESFPEDLNVHVWGTGGMSHQLQGPRAGLINKEFDLNFIDKLISDPEELSKMPHIQYLRESGSEGVELVMWLIMRGALPEKVRDLYTFYHIPASNTALGAMILQPEETAGTPLEPRKVMSGHSL 299
               SCOP domains d1b4ub_ B: LigB subunit of an aromatic-ring-opening dioxygenase LigAB                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1b4uB00 B:2-299 Protocatechuate 4,5-dioxygenase; Chain B                                                                                                                                                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee...hhhhhhhhh........hhhhhhhhhhhhhh........eeeeee...............eee.......................hhhhhhhhhhhhh.....eee......hhhhhhhhhhh........eeeeee..........hhhhhhhhhhhhhhhh......eeeeeee................hhhhhhhhhhhhh.hhhhhh..hhhhhhhh...hhhhhhhhhhhhh....eeeeeeeee.......eeeeeeeehhh........eeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b4u B   2 ARVTTGITSSHIPALGAAIQTGTSDNDYWGPVFKGYQPIRDWIKQPGNMPDVVILVYNDHASAFDMNIIPTFAIGCAETFKPADEGWGPRPVPDVKGHPDLAWHIAQSLILDEFDMTIMNQMDVDHGCTVPLSMIFGEPEEWPCKVIPFPVNVVTYPPPSGKRCFALGDSIRAAVESFPEDLNVHVWGTGGMSHQLQGPRAGLINKEFDLNFIDKLISDPEELSKMPHIQYLRESGSEGVELVMWLIMRGALPEKVRDLYTFYHIPASNTALGAMILQPEETAGTPLEPRKVMSGHSL 299
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291        


Chain C from PDB  Type:PROTEIN  Length:132
 aligned with PCYA_SPHPI | P22635 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:132
                                    17        27        37        47        57        67        77        87        97       107       117       127       137  
           PCYA_SPHPI     8 IDVHAYLAEFDDIPGTRVFTAQRARKGYNLNQFAMSLMKAENRERFKADESAYLDEWNLTPAAKAAVLARDYNAMIDEGGNVYFLSKLFSTDGKSFQFAAGSMTGMTQEEYAQMMIDGGRSPAGVRSIKGGY 139
               SCOP domains d1b4uc_ C: LigA subunit of an aromatic-ring-opening dioxygenase LigAB                                                                SCOP domains
               CATH domains 1b4uC00 C:8-139 Protocatechuate 4,5-dioxygenase; Chain A                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhh........hhhhhh.hhhhhhhhhhh.hhhhhhhhh.hhhhhhhh...hhhhhhhh...hhhhhh....hhhhhhhhhh....hhhhhhhh....hhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1b4u C   8 IDVHAYLAEFDDIPGTRVFTAQRARKGYNLNQFAMSLMKAENRERFKADESAYLDEWNLTPAAKAAVLARDYNAMIDEGGNVYFLSKLFSTDGKSFQFAAGSMTGMTQEEYAQMMIDGGRSPAGVRSIKGGY 139
                                    17        27        37        47        57        67        77        87        97       107       117       127       137  


Chain D from PDB  Type:PROTEIN  Length:298
 aligned with PCYB_SPHPI | P22636 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:298
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291        
           PCYB_SPHPI     2 ARVTTGITSSHIPALGAAIQTGTSDNDYWGPVFKGYQPIRDWIKQPGNMPDVVILVYNDHASAFDMNIIPTFAIGCAETFKPADEGWGPRPVPDVKGHPDLAWHIAQSLILDEFDMTIMNQMDVDHGCTVPLSMIFGEPEEWPCKVIPFPVNVVTYPPPSGKRCFALGDSIRAAVESFPEDLNVHVWGTGGMSHQLQGPRAGLINKEFDLNFIDKLISDPEELSKMPHIQYLRESGSEGVELVMWLIMRGALPEKVRDLYTFYHIPASNTALGAMILQPEETAGTPLEPRKVMSGHSL 299
               SCOP domains d1b4ud_ D: LigB subunit of an aromatic-ring-opening dioxygenase LigAB                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1b4uD00 D:2-299 Protocatechuate 4,5-dioxygenase; Chain B                                                                                                                                                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee...hhhhhhhh.........hhhhhhhhhhhhhhh.......eeeeee...............eee.......................hhhhhhhhhhhhh.....eee......hhhhhhhhhhh........eeeeee..........hhhhhhhhhhhhhhhhh.....eeeeeee................hhhhhhhhhhhhh.hhhhhh..hhhhhhhh.hhhhhhhhhhhhhhh....eeeeeeeee.......eeeeeeee...........eeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b4u D   2 ARVTTGITSSHIPALGAAIQTGTSDNDYWGPVFKGYQPIRDWIKQPGNMPDVVILVYNDHASAFDMNIIPTFAIGCAETFKPADEGWGPRPVPDVKGHPDLAWHIAQSLILDEFDMTIMNQMDVDHGCTVPLSMIFGEPEEWPCKVIPFPVNVVTYPPPSGKRCFALGDSIRAAVESFPEDLNVHVWGTGGMSHQLQGPRAGLINKEFDLNFIDKLISDPEELSKMPHIQYLRESGSEGVELVMWLIMRGALPEKVRDLYTFYHIPASNTALGAMILQPEETAGTPLEPRKVMSGHSL 299
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1B4U)

(-) Gene Ontology  (7, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,C   (PCYA_SPHPI | P22635)
molecular function
    GO:0051213    dioxygenase activity    Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0018579    protocatechuate 4,5-dioxygenase activity    Catalysis of the reaction: protocatechuate + O2 = 4-carboxy-2-hydroxymuconate semialdehyde.
biological process
    GO:0019439    aromatic compound catabolic process    The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

Chain B,D   (PCYB_SPHPI | P22636)
molecular function
    GO:0051213    dioxygenase activity    Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
    GO:0008198    ferrous iron binding    Interacting selectively and non-covalently with ferrous iron, Fe(II).
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0018579    protocatechuate 4,5-dioxygenase activity    Catalysis of the reaction: protocatechuate + O2 = 4-carboxy-2-hydroxymuconate semialdehyde.
biological process
    GO:0019439    aromatic compound catabolic process    The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
    GO:0006725    cellular aromatic compound metabolic process    The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PCYA_SPHPI | P22635: 1bou
        PCYB_SPHPI | P22636: 1bou

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1B4U)