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(-) Description

Title :  4-FLUOROCATECHOL BOUND TO PROTOCATECHUATE 3,4-DIOXYGENASE (PSEUDOMONAS PUTIDA) AT PH 8.5
 
Authors :  C. J. Knoot, V. M. Purpero, J. D. Lipscomb
Date :  23 Sep 14  (Deposition) - 31 Dec 14  (Release) - 28 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
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
    ChainsA, E, C
    EC Number1.13.11.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPCE120K
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GenePCAG
    Organism ScientificPSEUDOMONAS PUTIDA
    Organism Taxid303
    Synonym3,4-PCD
 
Molecule 2 - PROTOCATECHUATE 3,4-DIOXYGENASE BETA CHAIN
    ChainsF, B
    EC Number1.13.11.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPCE120K
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GenePCAH
    Organism ScientificPSEUDOMONAS PUTIDA
    Organism Taxid303
    Synonym3,4-PCD
 
Molecule 3 - PROTOCATECHUATE 3,4-DIOXYGENASE BETA CHAIN
    ChainsD
    EC Number1.13.11.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPCE120K
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GenePCAH
    Organism ScientificPSEUDOMONAS PUTIDA
    Organism Taxid303
    Synonym3,4-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  (8, 25)

Asymmetric Unit (8, 25)
No.NameCountTypeFull Name
13N810Ligand/Ion4-FLUOROBENZENE-1,2-DIOL
2BME4Ligand/IonBETA-MERCAPTOETHANOL
3CL3Ligand/IonCHLORIDE ION
4CSO1Mod. Amino AcidS-HYDROXYCYSTEINE
5FE3Ligand/IonFE (III) ION
6MHO1Mod. Amino AcidS-OXYMETHIONINE
7MUC2Ligand/Ion[(2S)-5-OXO-2,5-DIHYDROFURAN-2-YL]ACETIC ACID
8SO41Ligand/IonSULFATE ION
Biological Unit 1 (6, 76)
No.NameCountTypeFull Name
13N840Ligand/Ion4-FLUOROBENZENE-1,2-DIOL
2BME16Ligand/IonBETA-MERCAPTOETHANOL
3CL-1Ligand/IonCHLORIDE ION
4CSO4Mod. Amino AcidS-HYDROXYCYSTEINE
5FE-1Ligand/IonFE (III) ION
6MHO4Mod. Amino AcidS-OXYMETHIONINE
7MUC8Ligand/Ion[(2S)-5-OXO-2,5-DIHYDROFURAN-2-YL]ACETIC ACID
8SO44Ligand/IonSULFATE ION

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:164 , ARG A:167 , GLU A:168 , ILE A:171 , HOH A:470binding site for residue 3N8 A 301
02AC2SOFTWAREASN A:37 , THR A:105 , HIS A:107binding site for residue SO4 A 302
03AC3SOFTWARETYR F:408 , TYR F:447 , HIS F:460 , HIS F:462 , 3N8 F:605binding site for residue FE F 601
04AC4SOFTWAREARG D:450 , PRO D:453 , MET D:516 , HOH D:762 , SER F:338 , HOH F:793binding site for residue 3N8 F 602
05AC5SOFTWAREHOH A:413 , HOH A:558 , MET F:488 , MET F:510 , HOH F:736binding site for residue BME F 603
06AC6SOFTWARELEU A:160 , SER B:338 , PRO B:340 , ARG F:450 , PRO F:453 , MET F:516 , HOH F:931binding site for residue 3N8 F 604
07AC7SOFTWAREPRO E:15 , TYR E:16 , HOH E:534 , TYR F:408 , TYR F:447 , TRP F:449 , ARG F:457 , HIS F:460 , HIS F:462 , FE F:601 , HOH F:763 , HOH F:889binding site for residue 3N8 F 605
08AC8SOFTWAREPRO F:418 , LEU F:419binding site for residue CL F 606
09AC9SOFTWAREPRO E:164 , ARG E:167 , GLU E:168 , ILE E:171 , HOH E:488binding site for residue 3N8 E 301
10AD1SOFTWAREGLU E:168 , THR E:169 , ILE E:171 , ARG E:184 , PHE E:185 , ASP E:186 , ARG E:188binding site for residue MUC E 302
11AD2SOFTWAREPRO C:164 , ARG C:167 , GLU C:168 , ILE C:171 , HOH C:449binding site for residue 3N8 C 301
12AD3SOFTWAREALA C:151 , HOH C:473 , HOH C:488 , HOH C:549 , HOH C:561binding site for residue BME C 302
13AD4SOFTWARE3N8 B:604 , ASN C:116 , HOH C:439 , HOH C:509 , HOH C:532 , PRO D:340binding site for residue BME C 303
14AD5SOFTWAREGLU C:168 , THR C:169 , ILE C:171 , ALA C:172 , ARG C:184 , PHE C:185 , ASP C:186 , HOH C:527binding site for residue MUC C 304
15AD6SOFTWARETYR D:408 , TYR D:447 , HIS D:460 , HIS D:462 , 3N8 D:602binding site for residue FE D 601
16AD7SOFTWAREPRO C:15 , TYR C:16 , HOH C:554 , TYR D:408 , TYR D:447 , TRP D:449 , ARG D:457 , HIS D:460 , HIS D:462 , FE D:601 , HOH D:891 , HOH D:914binding site for residue 3N8 D 602
17AD8SOFTWAREILE B:328 , ARG D:333 , HOH D:907binding site for residue 3N8 D 603
18AD9SOFTWARETYR B:408 , TYR B:447 , HIS B:460 , HIS B:462 , 3N8 B:603binding site for residue FE B 601
19AE1SOFTWAREMET B:488 , MET B:510 , HOH B:713 , HOH B:718 , HOH B:740 , PRO C:1 , ILE C:2 , GLU C:3binding site for residue BME B 602
20AE2SOFTWAREPRO A:15 , TYR A:16 , HOH A:556 , TYR B:408 , TYR B:447 , TRP B:449 , ARG B:457 , HIS B:460 , HIS B:462 , FE B:601 , HOH B:878 , HOH B:905 , HOH B:915 , HOH B:929binding site for residue 3N8 B 603
21AE3SOFTWAREARG B:450 , PRO B:453 , MET B:516 , HOH B:719 , LEU C:160 , BME C:303 , SER D:338binding site for residue 3N8 B 604
22AE4SOFTWAREARG B:409 , HIS B:410binding site for residue CL B 605
23AE5SOFTWARETRP B:449 , ARG B:450 , HOH B:881 , HOH B:915binding site for residue CL B 606

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WHS)

(-) 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 ...............hhhhhhhhhhhh....................eeeeeeeee..........eeeee....................eeeee......eeeeeee................eeeeee.......eeeeeee..hhhhhhh..hhhhh.hhhhhh..eeeeeee..eeeee..ee.........ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4whs 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
                                                                                                                                                                                                                                                                              
               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
                 4whs B 301 PAQDNSRFVIRDRNWHPKALTPDYKTSIARSPRQALVSIPQSISETTGPNFSHLGFGAHDHDLLLNFNNGGLPIGERIIVAGRVVDQYGKPVPNTLVEMWQANAGGRYRHKNDRYLAPLDPNFGGVGRCLTDSDGYYSFRTIKPGPYPWRNGPNDWRPAHIHFGISGPSIATKLITQLYFEGDPLIPMCPIVKSIANPEAVQQLIAKLDMNNANPMDCLAYRFDIVLRGQRKTHFENC 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
                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhh....................eeeeeeeee..........eeeee....................eeeee......eeeeeee................eeeeee.......eeeeeee..hhhhhhhh.hhhhh.hhhhhh..eeeeeee..eeeee..ee.........ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4whs 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
                                                                                                                                                                                                                                                                              
               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
                 4whs D 301 PAQDNSRFVIRDRNWHPKALTPDYKTSIARSPRQALVSIPQSISETTGPNFSHLGFGAHDHDLLLNFNNGGLPIGERIIVAGRVVDQYGKPVPNTLVEMWQANAGGRYRHKNDRYLAPLDPNFGGVGRcLTDSDGYYSFRTIKPGPYPWRNGPNDWRPAHIHFGISGPSIATKLITQLYFEGDPLIPmCPIVKSIANPEAVQQLIAKLDMNNANPMDCLAYRFDIVLRGQRKTHFENC 538
                                   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                                                    488-MHO                                              

Chain E from PDB  Type:PROTEIN  Length:200
                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhh....................eeeeeeeee..........eeeee....................eeeee......eeeeeee....ee.....ee...eeeeee.......eeeeeee..hhhhhhhh.hhhhh.hhhhhh..eeeeeee..eeeee..ee.........ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4whs 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
                                                                                                                                                                                                                                                                              
               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
                 4whs F 301 PAQDNSRFVIRDRNWHPKALTPDYKTSIARSPRQALVSIPQSISETTGPNFSHLGFGAHDHDLLLNFNNGGLPIGERIIVAGRVVDQYGKPVPNTLVEMWQANAGGRYRHKNDRYLAPLDPNFGGVGRCLTDSDGYYSFRTIKPGPYPWRNGPNDWRPAHIHFGISGPSIATKLITQLYFEGDPLIPMCPIVKSIANPEAVQQLIAKLDMNNANPMDCLAYRFDIVLRGQRKTHFENC 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)
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  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 4WHS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 24)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        PCXA_PSEPU | P004361ykk 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 4who 4whp 4whq 4whr
        PCXB_PSEPU | P004371ykk 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 4who 4whp 4whq 4whr

(-) Related Entries Specified in the PDB File

4who 4whp 4whq 4whr