Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  AXIAL LIGAND SWAPPING IN DOUBLE MUTANT MAINTAINS INTRADIOL-CLEAVAGE CHEMISTRY IN PROTOCATECHUATE 3,4-DIOXYGENASE
 
Authors :  V. M. Purpero, J. D. Lipscomb
Date :  09 Apr 10  (Deposition) - 27 Apr 11  (Release) - 27 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.74
Chains :  Asym. Unit :  A,B,C,M,N,O
Biol. Unit 1:  A,B,C,M,N,O  (4x)
Keywords :  Dioxygenase, Non-Heme, Iron, Homoprotocatechuate, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. M. Purpero, J. D. Lipscomb
Axial Ligand Swapping In Double Mutant Maintains Intradiol-Cleavage Chemistry In Protocatechuate 3, 4-Dioxygenase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROTOCATECHUATE 3,4-DIOXYGENASE ALPHA CHAIN
    Chains: A, B, C
    EC Number: 1.13.11.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCE VECTOR, PT7-7
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PCAG
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 303
    Synonym: 3,4-PCD
 
Molecule 2 - PROTOCATECHUATE 3,4-DIOXYGENASE BETA CHAIN
    Chains: M, N, O
    EC Number: 1.13.11.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCE VECTOR, PT7-7
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PCAH
    Mutation: YES
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 303
    Synonym: 3,4-PCD

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCMNO
Biological Unit 1 (4x): ABCMNO

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 29)

Asymmetric Unit (5, 29)
No.NameCountTypeFull Name
1BME9Ligand/IonBETA-MERCAPTOETHANOL
2CL3Ligand/IonCHLORIDE ION
3FE3Ligand/IonFE (III) ION
4GOL6Ligand/IonGLYCEROL
5SO48Ligand/IonSULFATE ION
Biological Unit 1 (3, 92)
No.NameCountTypeFull Name
1BME36Ligand/IonBETA-MERCAPTOETHANOL
2CL-1Ligand/IonCHLORIDE ION
3FE-1Ligand/IonFE (III) ION
4GOL24Ligand/IonGLYCEROL
5SO432Ligand/IonSULFATE ION

(-) Sites  (28, 28)

Asymmetric Unit (28, 28)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:37 , THR A:105 , HIS A:107 , HOH A:258 , HOH A:631BINDING SITE FOR RESIDUE SO4 A 201
02AC2SOFTWARETHR A:169 , ILE A:171 , ARG A:184 , PHE A:185 , ASP A:186 , ARG A:188 , HOH A:235 , HOH A:885 , HOH A:1033BINDING SITE FOR RESIDUE GOL A 202
03AC3SOFTWARETHR A:12 , GLY A:14 , HOH A:1055 , ARG M:457 , TYR M:462 , GLN M:477 , HOH M:1067BINDING SITE FOR RESIDUE FE M 600
04AC4SOFTWAREARG A:133 , HOH A:1055 , HOH A:1084 , HOH A:1163 , TYR M:324 , THR M:326 , TRP M:449 , HOH M:552BINDING SITE FOR RESIDUE SO4 A 203
05AC5SOFTWAREILE B:2 , GLN M:503 , LYS M:507 , ARG M:522 , PHE M:523 , ASP M:524BINDING SITE FOR RESIDUE GOL M 1
06AC6SOFTWAREARG M:409 , PRO M:421BINDING SITE FOR RESIDUE BME M 541
07AC7SOFTWAREPHE M:535 , HIS O:361BINDING SITE FOR RESIDUE BME M 542
08AC8SOFTWAREASN B:37 , ARG B:38 , THR B:105 , HIS B:107 , HOH B:450BINDING SITE FOR RESIDUE SO4 B 201
09AC9SOFTWAREARG B:133 , HOH B:557 , HOH B:1060 , HOH N:226 , TYR N:324 , THR N:326 , TRP N:449 , HOH N:1198BINDING SITE FOR RESIDUE SO4 B 202
10BC1SOFTWARETHR B:12 , GLY B:14 , HOH B:1060 , ARG N:457 , TYR N:462 , GLN N:477 , HOH N:1077BINDING SITE FOR RESIDUE FE N 600
11BC2SOFTWAREARG N:414 , ARG N:450 , HOH N:1219BINDING SITE FOR RESIDUE SO4 N 8
12BC3SOFTWAREGLN N:503 , ILE N:505 , LYS N:507 , ARG N:522 , PHE N:523 , ASP N:524BINDING SITE FOR RESIDUE GOL N 539
13BC4SOFTWAREARG N:407 , LEU N:419BINDING SITE FOR RESIDUE BME N 540
14BC5SOFTWAREASN C:37 , THR C:105 , HIS C:107 , HOH C:669BINDING SITE FOR RESIDUE SO4 C 201
15BC6SOFTWAREARG C:133 , HOH C:665 , HOH C:1058 , HOH C:1242 , HOH O:236 , TYR O:324 , THR O:326 , TRP O:449BINDING SITE FOR RESIDUE SO4 C 202
16BC7SOFTWARETHR C:169 , ILE C:171 , ARG C:184 , PHE C:185 , ASP C:186 , ARG C:188 , HOH C:673 , HOH C:1028BINDING SITE FOR RESIDUE GOL C 203
17BC8SOFTWAREPRO C:164 , ARG C:167 , HOH C:679BINDING SITE FOR RESIDUE BME C 204
18BC9SOFTWARELEU C:23 , ASN C:28 , PRO C:29 , HOH C:530 , PHE O:367BINDING SITE FOR RESIDUE BME C 205
19CC1SOFTWARETHR C:12 , GLY C:14 , HOH C:1058 , ARG O:457 , TYR O:462 , GLN O:477 , HOH O:1078BINDING SITE FOR RESIDUE FE O 600
20CC2SOFTWAREGLN O:503 , ILE O:505 , ARG O:522 , PHE O:523 , ASP O:524BINDING SITE FOR RESIDUE GOL O 1
21CC3SOFTWAREARG O:407 , LEU O:419BINDING SITE FOR RESIDUE BME O 539
22CC4SOFTWARETHR O:321 , PRO O:322 , ASP O:323 , LYS O:493 , HOH O:551BINDING SITE FOR RESIDUE BME O 540
23CC5SOFTWAREARG O:383BINDING SITE FOR RESIDUE CL O 541
24CC6SOFTWAREGLU B:168 , THR B:169 , ILE B:171 , ARG B:184 , PHE B:185 , ASP B:186 , ARG B:188 , HOH B:564 , HOH B:973BINDING SITE FOR RESIDUE GOL B 203
25CC7SOFTWAREASN O:412 , ARG O:414 , ARG O:450BINDING SITE FOR RESIDUE SO4 O 3
26CC8SOFTWAREHOH M:87 , ARG M:407 , LEU M:419BINDING SITE FOR RESIDUE CL M 540
27CC9SOFTWAREHIS N:534 , PHE N:535 , GLU N:536BINDING SITE FOR RESIDUE BME N 1
28DC1SOFTWAREHIS O:534 , PHE O:535BINDING SITE FOR RESIDUE BME O 542

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MI1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MI1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MI1)

(-) PROSITE Motifs  (1, 6)

Asymmetric Unit (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1INTRADIOL_DIOXYGENASPS00083 Intradiol ring-cleavage dioxygenases signature.PCXA_PSEPU52-80
 
 		  3A:51-79
B:51-79
C:51-79
PCXB_PSEPU81-109
 
 		  3M:380-408
N:380-408
O:380-408
Biological Unit 1 (1, 24)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1INTRADIOL_DIOXYGENASPS00083 Intradiol ring-cleavage dioxygenases signature.PCXA_PSEPU52-80
 
 		  12A:51-79
B:51-79
C:51-79
PCXB_PSEPU81-109
 
 		  12M:380-408
N:380-408
O:380-408

(-) Exons   (0, 0)

(no "Exon" information available for 3MI1)

(-) 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 d3mi1a_ A: Protocatechuate-3,4-dioxygenase, alpha chain                                                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhh.........................eeeeee.ee..........eeeee....................eeeee.......eeeeee....ee.....ee...eeeeee.......eeeeeee..hhhhhhh..hhhhh.hhhhhh..eeeeeee..eeeee..ee.........ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------INTRADIOL_DIOXYGENAS         ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mi1 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: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 d3mi1b_ B: Protocatechuate-3,4-dioxygenase, alpha chain                                                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhh.........................eeeeee.ee..........eeeee....................eeeee.......eeeeee................eeeeee.......eeeeeee..hhhhhhh..hhhhh.hhhhhh..eeeeeee..eeeee..ee.........ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------INTRADIOL_DIOXYGENAS         ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mi1 B   1 PIELLPETPSQTAGPYVHIGLALEAAGNPTRDQEIWNRLAKPDAPGEHILLLGQVYDGNGHLVRDSFLEVWQADANGEYQDAYNLENAFNSFGRTATTFDAGEWTLHTVKPGVVNNAAGVPMAPHINISLFARGINIHLHTRLYFDDEAQANAKCPVLNLIEQPQRRETLIAKRCEVDGKTAYRFDIRIQGEGETVFFDF 200
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200


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 d3mi1c_ C: Protocatechuate-3,4-dioxygenase, alpha chain                                                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------Dioxygenase_C-3mi1C01 C:23-192                                                                                                                                            -------- Pfam domains (1)
           Pfam domains (2) ----------------------Dioxygenase_C-3mi1C02 C:23-192                                                                                                                                            -------- Pfam domains (2)
           Pfam domains (3) ----------------------Dioxygenase_C-3mi1C03 C:23-192                                                                                                                                            -------- Pfam domains (3)
         Sec.struct. author ...............hhhhhhh.........................eeeeee.ee..........eeeee....................eeeee.......eeeeee....ee.....ee...eeeeee.......eeeeeee..hhhhhhhh.hhhhh.hhhhhh..eeeeeee..eeeee..ee.........ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------INTRADIOL_DIOXYGENAS         ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mi1 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 M 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 d3mi1m_ M: Protocatechuate-3,4-dioxygenase, beta chain                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee...............hhhhh........ee...hhhhhh.............................eeeeeeeeee.........eeeee.........................eeeee.....eeeeeee....eee.....eee..eeeeee........eeeeeee....hhhhh.hhhhh.hhhhhhh.eeee.hhhh.....eeee..eee..eee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------INTRADIOL_DIOXYGENAS         ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mi1 M 301 PAQDNSRFVIRDRNWHPKALTPDYKTSIARSPRQALVSIPQSISETTGPNFSHLGFGAHDHDLLLNFNNGGLPIGERIIVAGRVVDQYGKPVPNTLVEMWQANAGGRYRHKNDRYLAPLDPNFGGVGRCLTDSDGYYSFRTIKPGPYPWRNGPNDWRPAHIYFGISGPSIATKLITQLYFEGDPLIPMCPIVKSIANPEAVQQLIAKLDMNNANPMDCLAYRFDIVLRGQRKTHFENC 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 N 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 d3mi1n_ N: Protocatechuate-3,4-dioxygenase, beta chain                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee...............hhhhh........ee...hhhhhh.............................eeeeeeeeee.........eeeee.........................eeeee.....eeeeeee....eee.....eee...eeeee........eeeeeee....hhhhh.hhhhh.hhhhhhh.eeee.hhhh.....eeee..eee..eee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------INTRADIOL_DIOXYGENAS         ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mi1 N 301 PAQDNSRFVIRDRNWHPKALTPDYKTSIARSPRQALVSIPQSISETTGPNFSHLGFGAHDHDLLLNFNNGGLPIGERIIVAGRVVDQYGKPVPNTLVEMWQANAGGRYRHKNDRYLAPLDPNFGGVGRCLTDSDGYYSFRTIKPGPYPWRNGPNDWRPAHIYFGISGPSIATKLITQLYFEGDPLIPMCPIVKSIANPEAVQQLIAKLDMNNANPMDCLAYRFDIVLRGQRKTHFENC 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 O 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 d3mi1o_ O: Protocatechuate-3,4-dioxygenase, beta chain                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------PCDO_beta_N-3mi1O04 O:308-343       --Dioxygenase_C-3mi1O01 O:346-530                                                                                                                                                          -------- Pfam domains (1)
           Pfam domains (2) -------PCDO_beta_N-3mi1O05 O:308-343       --Dioxygenase_C-3mi1O02 O:346-530                                                                                                                                                          -------- Pfam domains (2)
           Pfam domains (3) -------PCDO_beta_N-3mi1O06 O:308-343       --Dioxygenase_C-3mi1O03 O:346-530                                                                                                                                                          -------- Pfam domains (3)
         Sec.struct. author .....eee...............hhhhh........ee...hhhhhh.............................eeeeeeeeee.........eeeee.........................eeeee.....eeeeeee....eee.....eee...eeeee........eeeeeee....hhhhh.hhhhh.hhhhhhh.eeee.hhhh.....eeee..eee..eee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------INTRADIOL_DIOXYGENAS         ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mi1 O 301 PAQDNSRFVIRDRNWHPKALTPDYKTSIARSPRQALVSIPQSISETTGPNFSHLGFGAHDHDLLLNFNNGGLPIGERIIVAGRVVDQYGKPVPNTLVEMWQANAGGRYRHKNDRYLAPLDPNFGGVGRCLTDSDGYYSFRTIKPGPYPWRNGPNDWRPAHIYFGISGPSIATKLITQLYFEGDPLIPMCPIVKSIANPEAVQQLIAKLDMNNANPMDCLAYRFDIVLRGQRKTHFENC 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, 6)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MI1)

(-) Pfam Domains  (2, 9)

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,B,C   (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 M,N,O   (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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    BME  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
    CC2  [ RasMol ]  +environment [ RasMol ]
    CC3  [ RasMol ]  +environment [ RasMol ]
    CC4  [ RasMol ]  +environment [ RasMol ]
    CC5  [ RasMol ]  +environment [ RasMol ]
    CC6  [ RasMol ]  +environment [ RasMol ]
    CC7  [ RasMol ]  +environment [ RasMol ]
    CC8  [ RasMol ]  +environment [ RasMol ]
    CC9  [ RasMol ]  +environment [ RasMol ]
    DC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3mi1)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3mi1
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PCXA_PSEPU | P00436
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  PCXB_PSEPU | P00437
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.13.11.3
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PCXA_PSEPU | P00436
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  PCXB_PSEPU | P00437
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PCXA_PSEPU | P00436: 1ykk 1ykl 1ykm 1ykn 1yko 1ykp 2pcd 3lkt 3lmx 3lxv 3mfl 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 1ykl 1ykm 1ykn 1yko 1ykp 2pcd 3lkt 3lmx 3lxv 3mfl 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

2pcd WT 3,4-PCD