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(-) Description

Title :  PROTOCATECHUATE 3,4-DIOXYGENASE Y408C MUTANT BOUND TO DHB
 
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 :  2.25
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 :  Protocatechuate Catechol, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
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
PubMed-ID: 16101286  |  Reference-DOI: 10.1021/BI050902I

(-) Compounds

Molecule 1 - PROTOCATECHUATE 3,4-DIOXYGENASE ALPHA CHAIN
    Chains: A, C, E, G, I, K
    EC Number: 1.13.11.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PCAG
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 303
    Synonym: 3,4-PCD
 
Molecule 2 - PROTOCATECHUATE 3,4-DIOXYGENASE BETA CHAIN
    Chains: B, D, F, H, J, L
    EC Number: 1.13.11.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PCAH
    Mutation: YES
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 303
    Synonym: 3,4-PCD

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit : ABCDEFGHIJKL
Biological Unit 1 (2x): ABCDEFGHIJKL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1DHB6Ligand/Ion3,4-DIHYDROXYBENZOIC ACID
2FE6Ligand/IonFE (III) ION
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1DHB12Ligand/Ion3,4-DIHYDROXYBENZOIC ACID
2FE-1Ligand/IonFE (III) ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR B:447 , HIS B:460 , HIS B:462 , DHB B:550BINDING SITE FOR RESIDUE FE B 600
02AC2SOFTWARETYR D:447 , HIS D:460 , HIS D:462 , DHB D:1550BINDING SITE FOR RESIDUE FE D 600
03AC3SOFTWARETYR F:447 , HIS F:460 , HIS F:462 , DHB F:2550 , HOH F:2901BINDING SITE FOR RESIDUE FE F 600
04AC4SOFTWARETYR H:447 , HIS H:460 , HIS H:462 , DHB H:3550 , HOH H:3901BINDING SITE FOR RESIDUE FE H 600
05AC5SOFTWARETYR J:447 , HIS J:460 , HIS J:462 , DHB J:4550 , HOH J:4901BINDING SITE FOR RESIDUE FE J 600
06AC6SOFTWARETYR L:447 , HIS L:460 , HIS L:462 , DHB L:5550BINDING SITE FOR RESIDUE FE L 600
07AC7SOFTWAREGLY A:14 , PRO A:15 , ARG A:133 , TYR B:324 , TYR B:447 , TRP B:449 , ARG B:457 , HIS B:460 , HIS B:462 , GLN B:477 , FE B:600BINDING SITE FOR RESIDUE DHB B 550
08AC8SOFTWAREPRO C:15 , ARG C:133 , TYR D:324 , TYR D:447 , ARG D:457 , HIS D:460 , GLN D:477 , ILE D:491 , FE D:600BINDING SITE FOR RESIDUE DHB D 1550
09AC9SOFTWAREPRO E:15 , ARG E:133 , TYR F:324 , TYR F:447 , TRP F:449 , ARG F:457 , HIS F:462 , ILE F:491 , FE F:600BINDING SITE FOR RESIDUE DHB F 2550
10BC1SOFTWAREGLY G:14 , PRO G:15 , ARG G:133 , TYR H:324 , TYR H:447 , TRP H:449 , ARG H:457 , HIS H:460 , HIS H:462 , GLN H:477 , ILE H:491 , FE H:600BINDING SITE FOR RESIDUE DHB H 3550
11BC2SOFTWAREPRO I:15 , ARG I:133 , TYR J:324 , TYR J:447 , TRP J:449 , ARG J:457 , ILE J:491 , FE J:600BINDING SITE FOR RESIDUE DHB J 4550
12BC3SOFTWAREPRO K:15 , ARG K:133 , TYR L:324 , TYR L:447 , ARG L:457 , HIS L:460 , ILE L:491 , FE L:600BINDING SITE FOR RESIDUE DHB L 5550

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YKL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 12)

Asymmetric Unit (1, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1INTRADIOL_DIOXYGENASPS00083 Intradiol ring-cleavage dioxygenases signature.PCXA_PSEPU52-80
 
 
 
 
 		  6A:51-79
C:51-79
E:51-79
G:51-79
I:51-79
K:51-79
PCXB_PSEPU81-109
 
 
 
 
 		  6B:380-407
D:380-407
F:380-407
H:380-407
J:380-407
L:380-407
Biological Unit 1 (1, 24)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1INTRADIOL_DIOXYGENASPS00083 Intradiol ring-cleavage dioxygenases signature.PCXA_PSEPU52-80
 
 
 
 
 		  12A:51-79
C:51-79
E:51-79
G:51-79
I:51-79
K:51-79
PCXB_PSEPU81-109
 
 
 
 
 		  12B:380-407
D:380-407
F:380-407
H:380-407
J:380-407
L:380-407

(-) Exons   (0, 0)

(no "Exon" information available for 1YKL)

(-) Sequences/Alignments

Asymmetric 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:200
 aligned with PCXA_PSEPU | P00436 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:200
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201
           PCXA_PSEPU     2 PIELLPETPSQTAGPYVHIGLALEAAGNPTRDQEIWNRLAKPDAPGEHILLLGQVYDGNGHLVRDSFLEVWQADANGEYQDAYNLENAFNSFGRTATTFDAGEWTLHTVKPGVVNNAAGVPMAPHINISLFARGINIHLHTRLYFDDEAQANAKCPVLNLIEQPQRRETLIAKRCEVDGKTAYRFDIRIQGEGETVFFDF 201
               SCOP domains d1ykla_ A: Protocatechuate-3,4-dioxygenase, alpha chain                                                                                                                                                  SCOP domains
               CATH domains 1yklA00 A:1-200 Protocatechuate 3,4-Dioxygenase, subunit A                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhh.........................eeeeee.ee..........eeeee....................eeeee.......eeeeee....ee.....ee...eeeeee.......eeeeeee..hhhhhh...hhhhh.hhhhhh..eeeeeee..eeeee..ee.........ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------INTRADIOL_DIOXYGENAS         ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ykl A   1 PIELLPETPSQTAGPYVHIGLALEAAGNPTRDQEIWNRLAKPDAPGEHILLLGQVYDGNGHLVRDSFLEVWQADANGEYQDAYNLENAFNSFGRTATTFDAGEWTLHTVKPGVVNNAAGVPMAPHINISLFARGINIHLHTRLYFDDEAQANAKCPVLNLIEQPQRRETLIAKRCEVDGKTAYRFDIRIQGEGETVFFDF 200
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200


Chain B from PDB  Type:PROTEIN  Length:238
 aligned with PCXB_PSEPU | P00437 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:238
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231        
           PCXB_PSEPU     2 PAQDNSRFVIRDRNWHPKALTPDYKTSIARSPRQALVSIPQSISETTGPNFSHLGFGAHDHDLLLNFNNGGLPIGERIIVAGRVVDQYGKPVPNTLVEMWQANAGGRYRHKNDRYLAPLDPNFGGVGRCLTDSDGYYSFRTIKPGPYPWRNGPNDWRPAHIHFGISGPSIATKLITQLYFEGDPLIPMCPIVKSIANPEAVQQLIAKLDMNNANPMDCLAYRFDIVLRGQRKTHFENC 239
               SCOP domains d1yklb_ B: Protocatechuate-3,4-dioxygenase, beta chain                                                                                                                                                                                         SCOP domains
               CATH domains 1yklB00 B:301-538 Protocatechuate 3,4-Dioxygenase, subunit A                                                                                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee...............hhhhh........ee...hhhhhh.............................eeeeeeeeee.........eeeee.........................eeeee.....eeeeeee....eee.....eee...eeeee...hhhhheeeeeee....hhhhh.hhhhh.hhhhhhh.eeee..........eeee..eee..eee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------INTRADIOL_DIOXYGENAS         ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ykl B 301 PAQDNSRFVIRDRNWHPKALTPDYKTSIARSPRQALVSIPQSISETTGPNFSHLGFGAHDHDLLLNFNNGGLPIGERIIVAGRVVDQYGKPVPNTLVEMWQANAGGRCRHKNDRYLAPLDPNFGGVGRCLTDSDGYYSFRTIKPGPYPWRNGPNDWRPAHIHFGISGPSIATKLITQLYFEGDPLIPMCPIVKSIANPEAVQQLIAKLDMNNANPMDCLAYRFDIVLRGQRKTHFENC 538
                                   310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530        


Chain C from PDB  Type:PROTEIN  Length:200
 aligned with PCXA_PSEPU | P00436 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:200
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201
           PCXA_PSEPU     2 PIELLPETPSQTAGPYVHIGLALEAAGNPTRDQEIWNRLAKPDAPGEHILLLGQVYDGNGHLVRDSFLEVWQADANGEYQDAYNLENAFNSFGRTATTFDAGEWTLHTVKPGVVNNAAGVPMAPHINISLFARGINIHLHTRLYFDDEAQANAKCPVLNLIEQPQRRETLIAKRCEVDGKTAYRFDIRIQGEGETVFFDF 201
               SCOP domains d1yklc_ C: Protocatechuate-3,4-dioxygenase, alpha chain                                                                                                                                                  SCOP domains
               CATH domains 1yklC00 C:1-200 Protocatechuate 3,4-Dioxygenase, subunit A                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhh.........................eeeeee.ee..........eeeee....................eeeee.......eeeeee....ee.....ee..eeeeeee.......eeeeeee..hhhhhhhh.hhhhh.hhhhhh..eeeeee....eeee..ee.........ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------INTRADIOL_DIOXYGENAS         ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ykl C   1 PIELLPETPSQTAGPYVHIGLALEAAGNPTRDQEIWNRLAKPDAPGEHILLLGQVYDGNGHLVRDSFLEVWQADANGEYQDAYNLENAFNSFGRTATTFDAGEWTLHTVKPGVVNNAAGVPMAPHINISLFARGINIHLHTRLYFDDEAQANAKCPVLNLIEQPQRRETLIAKRCEVDGKTAYRFDIRIQGEGETVFFDF 200
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200


Chain D from PDB  Type:PROTEIN  Length:238
 aligned with PCXB_PSEPU | P00437 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:238
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231        
           PCXB_PSEPU     2 PAQDNSRFVIRDRNWHPKALTPDYKTSIARSPRQALVSIPQSISETTGPNFSHLGFGAHDHDLLLNFNNGGLPIGERIIVAGRVVDQYGKPVPNTLVEMWQANAGGRYRHKNDRYLAPLDPNFGGVGRCLTDSDGYYSFRTIKPGPYPWRNGPNDWRPAHIHFGISGPSIATKLITQLYFEGDPLIPMCPIVKSIANPEAVQQLIAKLDMNNANPMDCLAYRFDIVLRGQRKTHFENC 239
               SCOP domains d1ykld_ D: Protocatechuate-3,4-dioxygenase, beta chain                                                                                                                                                                                         SCOP domains
               CATH domains 1yklD00 D:301-538 Protocatechuate 3,4-Dioxygenase, subunit A                                                                                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee...............hhhhh........ee......................................eeeeeeeeee.........eeeee.........................eeeee.....eeeeeee....eee.....eee..eeeeee........eeeeeee....hhhhhhhhhh..hhhhhhh.eeee.hhhh.....eeee..eee..eee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------INTRADIOL_DIOXYGENAS         ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ykl D 301 PAQDNSRFVIRDRNWHPKALTPDYKTSIARSPRQALVSIPQSISETTGPNFSHLGFGAHDHDLLLNFNNGGLPIGERIIVAGRVVDQYGKPVPNTLVEMWQANAGGRCRHKNDRYLAPLDPNFGGVGRCLTDSDGYYSFRTIKPGPYPWRNGPNDWRPAHIHFGISGPSIATKLITQLYFEGDPLIPMCPIVKSIANPEAVQQLIAKLDMNNANPMDCLAYRFDIVLRGQRKTHFENC 538
                                   310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530        


Chain E from PDB  Type:PROTEIN  Length:200
 aligned with PCXA_PSEPU | P00436 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:200
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201
           PCXA_PSEPU     2 PIELLPETPSQTAGPYVHIGLALEAAGNPTRDQEIWNRLAKPDAPGEHILLLGQVYDGNGHLVRDSFLEVWQADANGEYQDAYNLENAFNSFGRTATTFDAGEWTLHTVKPGVVNNAAGVPMAPHINISLFARGINIHLHTRLYFDDEAQANAKCPVLNLIEQPQRRETLIAKRCEVDGKTAYRFDIRIQGEGETVFFDF 201
               SCOP domains d1ykle_ E: Protocatechuate-3,4-dioxygenase, alpha chain                                                                                                                                                  SCOP domains
               CATH domains 1yklE00 E:1-200 Protocatechuate 3,4-Dioxygenase, subunit A                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhh....................eeeeee.ee..........eeeee....................eeeee.......eeeeee...............eeeeeee.......eeeeeee..hhhhhhhh.hhhhh.hhhhhh..eeeeeee..eeeee..ee.........ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------INTRADIOL_DIOXYGENAS         ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ykl E   1 PIELLPETPSQTAGPYVHIGLALEAAGNPTRDQEIWNRLAKPDAPGEHILLLGQVYDGNGHLVRDSFLEVWQADANGEYQDAYNLENAFNSFGRTATTFDAGEWTLHTVKPGVVNNAAGVPMAPHINISLFARGINIHLHTRLYFDDEAQANAKCPVLNLIEQPQRRETLIAKRCEVDGKTAYRFDIRIQGEGETVFFDF 200
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200


Chain F from PDB  Type:PROTEIN  Length:238
 aligned with PCXB_PSEPU | P00437 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:238
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231        
           PCXB_PSEPU     2 PAQDNSRFVIRDRNWHPKALTPDYKTSIARSPRQALVSIPQSISETTGPNFSHLGFGAHDHDLLLNFNNGGLPIGERIIVAGRVVDQYGKPVPNTLVEMWQANAGGRYRHKNDRYLAPLDPNFGGVGRCLTDSDGYYSFRTIKPGPYPWRNGPNDWRPAHIHFGISGPSIATKLITQLYFEGDPLIPMCPIVKSIANPEAVQQLIAKLDMNNANPMDCLAYRFDIVLRGQRKTHFENC 239
               SCOP domains d1yklf_ F: Protocatechuate-3,4-dioxygenase, beta chain                                                                                                                                                                                         SCOP domains
               CATH domains 1yklF00 F:301-538 Protocatechuate 3,4-Dioxygenase, subunit A                                                                                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee...............hhhhh........ee...hhhhhh.............................eeeeeeeeee.........eeeee.........................eeeee.....eeeeeee....eee.....eee...eeeee........eeeeeee....hhhhhhhhhh..hhhhhhh.eeee.hhhh.....eeee..eee..eee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------INTRADIOL_DIOXYGENAS         ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ykl F 301 PAQDNSRFVIRDRNWHPKALTPDYKTSIARSPRQALVSIPQSISETTGPNFSHLGFGAHDHDLLLNFNNGGLPIGERIIVAGRVVDQYGKPVPNTLVEMWQANAGGRCRHKNDRYLAPLDPNFGGVGRCLTDSDGYYSFRTIKPGPYPWRNGPNDWRPAHIHFGISGPSIATKLITQLYFEGDPLIPMCPIVKSIANPEAVQQLIAKLDMNNANPMDCLAYRFDIVLRGQRKTHFENC 538
                                   310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530        


Chain G from PDB  Type:PROTEIN  Length:200
 aligned with PCXA_PSEPU | P00436 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:200
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201
           PCXA_PSEPU     2 PIELLPETPSQTAGPYVHIGLALEAAGNPTRDQEIWNRLAKPDAPGEHILLLGQVYDGNGHLVRDSFLEVWQADANGEYQDAYNLENAFNSFGRTATTFDAGEWTLHTVKPGVVNNAAGVPMAPHINISLFARGINIHLHTRLYFDDEAQANAKCPVLNLIEQPQRRETLIAKRCEVDGKTAYRFDIRIQGEGETVFFDF 201
               SCOP domains d1yklg_ G: Protocatechuate-3,4-dioxygenase, alpha chain                                                                                                                                                  SCOP domains
               CATH domains 1yklG00 G:1-200 Protocatechuate 3,4-Dioxygenase, subunit A                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhh.........................eeeeee.ee..........eeeee....................eeeee.......eeeeee................eeeeee.......eeeeeee..hhhhhh.hhhhhhh.hhhhhh..eeeeeee..eeeee..ee.........ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------INTRADIOL_DIOXYGENAS         ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ykl G   1 PIELLPETPSQTAGPYVHIGLALEAAGNPTRDQEIWNRLAKPDAPGEHILLLGQVYDGNGHLVRDSFLEVWQADANGEYQDAYNLENAFNSFGRTATTFDAGEWTLHTVKPGVVNNAAGVPMAPHINISLFARGINIHLHTRLYFDDEAQANAKCPVLNLIEQPQRRETLIAKRCEVDGKTAYRFDIRIQGEGETVFFDF 200
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200


Chain H from PDB  Type:PROTEIN  Length:238
 aligned with PCXB_PSEPU | P00437 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:238
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231        
           PCXB_PSEPU     2 PAQDNSRFVIRDRNWHPKALTPDYKTSIARSPRQALVSIPQSISETTGPNFSHLGFGAHDHDLLLNFNNGGLPIGERIIVAGRVVDQYGKPVPNTLVEMWQANAGGRYRHKNDRYLAPLDPNFGGVGRCLTDSDGYYSFRTIKPGPYPWRNGPNDWRPAHIHFGISGPSIATKLITQLYFEGDPLIPMCPIVKSIANPEAVQQLIAKLDMNNANPMDCLAYRFDIVLRGQRKTHFENC 239
               SCOP domains d1yklh_ H: Protocatechuate-3,4-dioxygenase, beta chain                                                                                                                                                                                         SCOP domains
               CATH domains 1yklH00 H:301-538 Protocatechuate 3,4-Dioxygenase, subunit A                                                                                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee...............hhhhh........ee...hhhhhh.............................eeeeeeeeee.........eeeeee........................eeeee.....eeeeeee....eee.....eee..eeeeee........eeeeeee....hhhhhhhhhh..hhhhhhh.eeee.hhhh.....eeee..eee..eee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------INTRADIOL_DIOXYGENAS         ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ykl H 301 PAQDNSRFVIRDRNWHPKALTPDYKTSIARSPRQALVSIPQSISETTGPNFSHLGFGAHDHDLLLNFNNGGLPIGERIIVAGRVVDQYGKPVPNTLVEMWQANAGGRCRHKNDRYLAPLDPNFGGVGRCLTDSDGYYSFRTIKPGPYPWRNGPNDWRPAHIHFGISGPSIATKLITQLYFEGDPLIPMCPIVKSIANPEAVQQLIAKLDMNNANPMDCLAYRFDIVLRGQRKTHFENC 538
                                   310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530        


Chain I from PDB  Type:PROTEIN  Length:200
 aligned with PCXA_PSEPU | P00436 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:200
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201
           PCXA_PSEPU     2 PIELLPETPSQTAGPYVHIGLALEAAGNPTRDQEIWNRLAKPDAPGEHILLLGQVYDGNGHLVRDSFLEVWQADANGEYQDAYNLENAFNSFGRTATTFDAGEWTLHTVKPGVVNNAAGVPMAPHINISLFARGINIHLHTRLYFDDEAQANAKCPVLNLIEQPQRRETLIAKRCEVDGKTAYRFDIRIQGEGETVFFDF 201
               SCOP domains d1ykli_ I: Protocatechuate-3,4-dioxygenase, alpha chain                                                                                                                                                  SCOP domains
               CATH domains 1yklI00 I:1-200 Protocatechuate 3,4-Dioxygenase, subunit A                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhh.........................eeeeee.ee..........eeeee....................eeeee.......eeeeee....ee.....ee..eeeeeee.......eeeeeee..hhhhhhhh.hhhhh.hhhhhh..eeeeeee..eeeee..ee.........ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------INTRADIOL_DIOXYGENAS         ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ykl I   1 PIELLPETPSQTAGPYVHIGLALEAAGNPTRDQEIWNRLAKPDAPGEHILLLGQVYDGNGHLVRDSFLEVWQADANGEYQDAYNLENAFNSFGRTATTFDAGEWTLHTVKPGVVNNAAGVPMAPHINISLFARGINIHLHTRLYFDDEAQANAKCPVLNLIEQPQRRETLIAKRCEVDGKTAYRFDIRIQGEGETVFFDF 200
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200


Chain J from PDB  Type:PROTEIN  Length:238
 aligned with PCXB_PSEPU | P00437 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:238
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231        
           PCXB_PSEPU     2 PAQDNSRFVIRDRNWHPKALTPDYKTSIARSPRQALVSIPQSISETTGPNFSHLGFGAHDHDLLLNFNNGGLPIGERIIVAGRVVDQYGKPVPNTLVEMWQANAGGRYRHKNDRYLAPLDPNFGGVGRCLTDSDGYYSFRTIKPGPYPWRNGPNDWRPAHIHFGISGPSIATKLITQLYFEGDPLIPMCPIVKSIANPEAVQQLIAKLDMNNANPMDCLAYRFDIVLRGQRKTHFENC 239
               SCOP domains d1yklj_ J: Protocatechuate-3,4-dioxygenase, beta chain                                                                                                                                                                                         SCOP domains
               CATH domains 1yklJ00 J:301-538 Protocatechuate 3,4-Dioxygenase, subunit A                                                                                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee...............hhhhh........ee......................................eeeeeeeeee.........eeeee.........................eeeee.....eeeeeee....eee.....eee...eeeee........eeeeeee....hhhhhhhhhh..hhhhhhhheeee.hhhh.....eeee..eee..eee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------INTRADIOL_DIOXYGENAS         ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ykl J 301 PAQDNSRFVIRDRNWHPKALTPDYKTSIARSPRQALVSIPQSISETTGPNFSHLGFGAHDHDLLLNFNNGGLPIGERIIVAGRVVDQYGKPVPNTLVEMWQANAGGRCRHKNDRYLAPLDPNFGGVGRCLTDSDGYYSFRTIKPGPYPWRNGPNDWRPAHIHFGISGPSIATKLITQLYFEGDPLIPMCPIVKSIANPEAVQQLIAKLDMNNANPMDCLAYRFDIVLRGQRKTHFENC 538
                                   310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530        


Chain K from PDB  Type:PROTEIN  Length:200
 aligned with PCXA_PSEPU | P00436 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:200
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201
           PCXA_PSEPU     2 PIELLPETPSQTAGPYVHIGLALEAAGNPTRDQEIWNRLAKPDAPGEHILLLGQVYDGNGHLVRDSFLEVWQADANGEYQDAYNLENAFNSFGRTATTFDAGEWTLHTVKPGVVNNAAGVPMAPHINISLFARGINIHLHTRLYFDDEAQANAKCPVLNLIEQPQRRETLIAKRCEVDGKTAYRFDIRIQGEGETVFFDF 201
               SCOP domains d1yklk_ K: Protocatechuate-3,4-dioxygenase, alpha chain                                                                                                                                                  SCOP domains
               CATH domains 1yklK00 K:1-200 Protocatechuate 3,4-Dioxygenase, subunit A                                                                                                                                               CATH domains
           Pfam domains (1) ----------------------Dioxygenase_C-1yklK01 K:23-192                                                                                                                                            -------- Pfam domains (1)
           Pfam domains (2) ----------------------Dioxygenase_C-1yklK02 K:23-192                                                                                                                                            -------- Pfam domains (2)
           Pfam domains (3) ----------------------Dioxygenase_C-1yklK03 K:23-192                                                                                                                                            -------- Pfam domains (3)
           Pfam domains (4) ----------------------Dioxygenase_C-1yklK04 K:23-192                                                                                                                                            -------- Pfam domains (4)
           Pfam domains (5) ----------------------Dioxygenase_C-1yklK05 K:23-192                                                                                                                                            -------- Pfam domains (5)
           Pfam domains (6) ----------------------Dioxygenase_C-1yklK06 K:23-192                                                                                                                                            -------- Pfam domains (6)
         Sec.struct. author ...............hhhhhhhhhhhh....................eeeeee.ee..........eeeee....................eeeee.......eeeeee...............eeeeeee.......eeeeeee..hhhhhhhh.hhhhh.hhhhhh..eeeeee....eeee..ee.........ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------INTRADIOL_DIOXYGENAS         ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ykl K   1 PIELLPETPSQTAGPYVHIGLALEAAGNPTRDQEIWNRLAKPDAPGEHILLLGQVYDGNGHLVRDSFLEVWQADANGEYQDAYNLENAFNSFGRTATTFDAGEWTLHTVKPGVVNNAAGVPMAPHINISLFARGINIHLHTRLYFDDEAQANAKCPVLNLIEQPQRRETLIAKRCEVDGKTAYRFDIRIQGEGETVFFDF 200
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200


Chain L from PDB  Type:PROTEIN  Length:238
 aligned with PCXB_PSEPU | P00437 from UniProtKB/Swiss-Prot  Length:239

    Alignment length:238
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231        
           PCXB_PSEPU     2 PAQDNSRFVIRDRNWHPKALTPDYKTSIARSPRQALVSIPQSISETTGPNFSHLGFGAHDHDLLLNFNNGGLPIGERIIVAGRVVDQYGKPVPNTLVEMWQANAGGRYRHKNDRYLAPLDPNFGGVGRCLTDSDGYYSFRTIKPGPYPWRNGPNDWRPAHIHFGISGPSIATKLITQLYFEGDPLIPMCPIVKSIANPEAVQQLIAKLDMNNANPMDCLAYRFDIVLRGQRKTHFENC 239
               SCOP domains d1ykll_ L: Protocatechuate-3,4-dioxygenase, beta chain                                                                                                                                                                                         SCOP domains
               CATH domains 1yklL00 L:301-538 Protocatechuate 3,4-Dioxygenase, subunit A                                                                                                                                                                                   CATH domains
           Pfam domains (1) -------PCDO_beta_N-1yklL07 L:308-343       --Dioxygenase_C-1yklL01 L:346-530                                                                                                                                                          -------- Pfam domains (1)
           Pfam domains (2) -------PCDO_beta_N-1yklL08 L:308-343       --Dioxygenase_C-1yklL02 L:346-530                                                                                                                                                          -------- Pfam domains (2)
           Pfam domains (3) -------PCDO_beta_N-1yklL09 L:308-343       --Dioxygenase_C-1yklL03 L:346-530                                                                                                                                                          -------- Pfam domains (3)
           Pfam domains (4) -------PCDO_beta_N-1yklL10 L:308-343       --Dioxygenase_C-1yklL04 L:346-530                                                                                                                                                          -------- Pfam domains (4)
           Pfam domains (5) -------PCDO_beta_N-1yklL11 L:308-343       --Dioxygenase_C-1yklL05 L:346-530                                                                                                                                                          -------- Pfam domains (5)
           Pfam domains (6) -------PCDO_beta_N-1yklL12 L:308-343       --Dioxygenase_C-1yklL06 L:346-530                                                                                                                                                          -------- Pfam domains (6)
         Sec.struct. author .....eee...............hhhhh........ee...hhhhhh.............................eeeeeeeeee.........eeeee.........................eeeee.....eeeeeee....eee.....eee...eeeee...hhhhheeeeeee....hhhhh.hhhhh.hhhhhhh.eeee.hhhh.....eeee..eee..eee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------INTRADIOL_DIOXYGENAS         ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ykl L 301 PAQDNSRFVIRDRNWHPKALTPDYKTSIARSPRQALVSIPQSISETTGPNFSHLGFGAHDHDLLLNFNNGGLPIGERIIVAGRVVDQYGKPVPNTLVEMWQANAGGRCRHKNDRYLAPLDPNFGGVGRCLTDSDGYYSFRTIKPGPYPWRNGPNDWRPAHIHFGISGPSIATKLITQLYFEGDPLIPMCPIVKSIANPEAVQQLIAKLDMNNANPMDCLAYRFDIVLRGQRKTHFENC 538
                                   310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530
   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, 12)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 12)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 18)

Asymmetric Unit
(-)
Clan: Transthyretin (88)
(-)
Clan: no clan defined [family: PCDO_beta_N] (26)

(-) Gene Ontology  (13, 24)

Asymmetric Unit(hide GO term definitions)
Chain A,C,E,G,I,K   (PCXA_PSEPU | P00436)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0008199    ferric iron binding    Interacting selectively and non-covalently with ferric iron, Fe(III).
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    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:0016702    oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from one donor, and two oxygen atoms is incorporated into a donor.
    GO:0018578    protocatechuate 3,4-dioxygenase activity    Catalysis of the reaction: 3,4-dihydroxybenzoate + O2 = 3-carboxy-cis,cis-muconate.
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:0042952    beta-ketoadipate pathway    A pathway of aromatic compound degradation by ortho-cleavage; one branch converts protocatechuate, derived from phenolic compounds, to beta-ketoadipate, and the other branch converts catechol, generated from various aromatic hydrocarbons, amino aromatics, and lignin monomers, also to beta-ketoadipate. Two additional steps accomplish the conversion of beta-ketoadipate to tricarboxylic acid cycle intermediates.
    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.

Chain B,D,F,H,J,L   (PCXB_PSEPU | P00437)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0008199    ferric iron binding    Interacting selectively and non-covalently with ferric iron, Fe(III).
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0016702    oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from one donor, and two oxygen atoms is incorporated into a donor.
    GO:0018578    protocatechuate 3,4-dioxygenase activity    Catalysis of the reaction: 3,4-dihydroxybenzoate + O2 = 3-carboxy-cis,cis-muconate.
biological process
    GO:0019619    3,4-dihydroxybenzoate catabolic process    The chemical reactions and pathways resulting in the breakdown of 3,4-dihydroxybenzoate.
    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:0042952    beta-ketoadipate pathway    A pathway of aromatic compound degradation by ortho-cleavage; one branch converts protocatechuate, derived from phenolic compounds, to beta-ketoadipate, and the other branch converts catechol, generated from various aromatic hydrocarbons, amino aromatics, and lignin monomers, also to beta-ketoadipate. Two additional steps accomplish the conversion of beta-ketoadipate to tricarboxylic acid cycle intermediates.
    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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  PCXB_PSEPU | P00437
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  1.13.11.3
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 Related Entries

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

UniProtKB/Swiss-Prot
        PCXA_PSEPU | P00436: 1ykk 1ykm 1ykn 1yko 1ykp 2pcd 3lkt 3lmx 3lxv 3mfl 3mi1 3mi5 3mv4 3mv6 3pca 3pcb 3pcc 3pcd 3pce 3pcf 3pcg 3pch 3pci 3pcj 3pck 3pcl 3pcm 3pcn 3t63 3t67 4who 4whp 4whq 4whr 4whs
        PCXB_PSEPU | P00437: 1ykk 1ykm 1ykn 1yko 1ykp 2pcd 3lkt 3lmx 3lxv 3mfl 3mi1 3mi5 3mv4 3mv6 3pca 3pcb 3pcc 3pcd 3pce 3pcf 3pcg 3pch 3pci 3pcj 3pck 3pcl 3pcm 3pcn 3t63 3t67 4who 4whp 4whq 4whr 4whs

(-) Related Entries Specified in the PDB File

1ykk 1ykm 1ykn 1yko 1ykp 2pcd 3pca