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(-) Description

Title :  RESTING PROTOCATECHUATE 3,4-DIOXYGENASE (PSEUDOMONAS PUTIDA) AT PH 8.5
 
Authors :  C. J. Knoot, J. D. Lipscomb
Date :  23 Sep 14  (Deposition) - 31 Dec 14  (Release) - 28 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.83
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C,D,E,F  (4x)
Keywords :  Dioxygen Activation, Non-Heme Iron, Intradiol Dioxygenase, Aromatic Ring Cleavage, Catalytic Intermediates, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. J. Knoot, V. M. Purpero, J. D. Lipscomb
Crystal Structures Of Alkylperoxo And Anhydride Intermediates In An Intradiol Ring-Cleaving Dioxygenase.
Proc. Natl. Acad. Sci. Usa V. 112 388 2015
PubMed-ID: 25548185  |  Reference-DOI: 10.1073/PNAS.1419118112

(-) Compounds

Molecule 1 - PROTOCATECHUATE 3,4-DIOXYGENASE ALPHA CHAIN
    Chains: A, E, C
    EC Number: 1.13.11.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCE120K
    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: B
    EC Number: 1.13.11.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCE120K
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PCAH
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 303
    Synonym: 3,4-PCD
 
Molecule 3 - PROTOCATECHUATE 3,4-DIOXYGENASE BETA CHAIN
    Chains: D, F
    EC Number: 1.13.11.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCE120K
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PCAH
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 303
    Synonym: 3,4-PCD

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
1BCT1Ligand/IonBICARBONATE ION
2BME2Ligand/IonBETA-MERCAPTOETHANOL
3CSO1Mod. Amino AcidS-HYDROXYCYSTEINE
4FE3Ligand/IonFE (III) ION
Biological Unit 1 (3, 16)
No.NameCountTypeFull Name
1BCT4Ligand/IonBICARBONATE ION
2BME8Ligand/IonBETA-MERCAPTOETHANOL
3CSO4Mod. Amino AcidS-HYDROXYCYSTEINE
4FE-1Ligand/IonFE (III) ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:37 , THR A:105 , HIS A:107binding site for residue BCT A 301
2AC2SOFTWARETYR B:408 , TYR B:447 , HIS B:460 , HIS B:462 , HOH B:868binding site for residue FE B 601
3AC3SOFTWAREPRO A:15 , HOH A:519 , TYR B:324 , THR B:326binding site for residue BME B 602
4AC4SOFTWARETYR D:408 , TYR D:447 , HIS D:460 , HIS D:462 , HOH D:889binding site for residue FE D 600
5AC5SOFTWAREPRO E:15 , ARG E:133 , TYR F:324 , THR F:326 , TRP F:449binding site for residue BME F 601
6AC6SOFTWARETYR F:408 , TYR F:447 , HIS F:460 , HIS F:462 , HOH F:859binding site for residue FE F 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4WHO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4WHO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4WHO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4WHO)

(-) Exons   (0, 0)

(no "Exon" information available for 4WHO)

(-) 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
                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4who 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:236
                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4who B 301 PAQDNSRFVIRDRNWHPKALTPDYKTSIARSPRQALVSIPQSISETTGPNFSHLGFGAHDHDLLLNFNNGGLPIGERIIVAGRVVDQYGKPVPNTLVEMWQANAGGRYRHKNDRYLAPLDPNFGGVGRcLTDSDGYYSFRTIKPGPYPWRNGPNDWRPAHIHFGISGPSIATKLITQLYFEGDPLIPMCPIVKSIANPEAVQQLIAKLDMNNANPMDCLAYRFDIVLRGQRKTHFE 536
                                   310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530      
                                                                                                                                                          429-CSO                                                                                                       


Chain C from PDB  Type:PROTEIN  Length:200
                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhh.........................eeeeee.ee..........eeeee....................eeeee.......eeeeee...............eeeeeee.......eeeeeee..hhhhhhhh.hhhhh.hhhhhh..eeeeeee..eeeee..ee.........ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4who 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:237
                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4who D 301 PAQDNSRFVIRDRNWHPKALTPDYKTSIARSPRQALVSIPQSISETTGPNFSHLGFGAHDHDLLLNFNNGGLPIGERIIVAGRVVDQYGKPVPNTLVEMWQANAGGRYRHKNDRYLAPLDPNFGGVGRCLTDSDGYYSFRTIKPGPYPWRNGPNDWRPAHIHFGISGPSIATKLITQLYFEGDPLIPMCPIVKSIANPEAVQQLIAKLDMNNANPMDCLAYRFDIVLRGQRKTHFEN 537
                                   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
                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhh.........................eeeeee.ee..........eeeee....................eeeee.......eeeeee....ee.....ee..eeeeeee.......eeeeeee..hhhhhhh..hhhhh.hhhhhh..eeeeeee..eeeee..ee.........ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4who 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:236
                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4who F 301 PAQDNSRFVIRDRNWHPKALTPDYKTSIARSPRQALVSIPQSISETTGPNFSHLGFGAHDHDLLLNFNNGGLPIGERIIVAGRVVDQYGKPVPNTLVEMWQANAGGRYRHKNDRYLAPLDPNFGGVGRCLTDSDGYYSFRTIKPGPYPWRNGPNDWRPAHIHFGISGPSIATKLITQLYFEGDPLIPMCPIVKSIANPEAVQQLIAKLDMNNANPMDCLAYRFDIVLRGQRKTHFE 536
                                   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  (0, 0)

(no "SCOP Domain" information available for 4WHO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4WHO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4WHO)

(-) Gene Ontology  (13, 24)

Asymmetric Unit(hide GO term definitions)

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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 1ykl 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 4whp 4whq 4whr 4whs
        PCXB_PSEPU | P00437: 1ykk 1ykl 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 4whp 4whq 4whr 4whs

(-) Related Entries Specified in the PDB File

4whp 4whq 4whr 4whs