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(-) Description

Title :  CRYSTAL STRUCTURE OF UBIX, AN AROMATIC ACID DECARBOXYLASE FROM THE COLWELLIA PSYCHRERYTHRAEA 34H
 
Authors :  H. Do, S. J. Kim, C. W. Lee, H. -W. Kim, H. H. Park, H. M. Kim, H. Park, H. J. Pa J. H. Lee
Date :  02 Oct 14  (Deposition) - 18 Feb 15  (Release) - 18 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C,D,E,F  (2x)
Keywords :  Rossmann Fold, Decarboxylase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Do, S. J. Kim, C. W. Lee, H. W. Kim, H. H. Park, H. M. Kim, H. Park, H. Park J. H. Lee
Crystal Structure Of Ubix, An Aromatic Acid Decarboxylase From The Psychrophilic Bacterium Colwellia Psychrerythraea That Undergoes Fmn-Induced Conformational Changes.
Sci Rep V. 5 8196 2015
PubMed-ID: 25645665  |  Reference-DOI: 10.1038/SREP08196

(-) Compounds

Molecule 1 - 3-OCTAPRENYL-4-HYDROXYBENZOATE CARBOXY-LYASE
    ChainsA, B, C, D, E, F
    EC Number4.1.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28A
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneUBIX, CPS_0408
    Organism ScientificCOLWELLIA PSYCHRERYTHRAEA 34H
    Organism Taxid167879

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (2x)ABCDEF

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1FMN6Ligand/IonFLAVIN MONONUCLEOTIDE
2SO46Ligand/IonSULFATE ION
Biological Unit 1 (2, 24)
No.NameCountTypeFull Name
1FMN12Ligand/IonFLAVIN MONONUCLEOTIDE
2SO412Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:14 , GLY A:15 , ALA A:16 , SER A:17 , SER A:41 , ALA A:43 , SER A:106 , THR A:107 , THR A:109 , ARG A:141 , GLU A:142 , TYR D:204 , TRP E:86 , SER E:118 , ARG E:124BINDING SITE FOR RESIDUE FMN A 301
02AC2SOFTWARETYR A:171 , PHE A:183 , ARG A:187 , TYR A:204 , HOH A:425 , SER C:92 , GLY C:93 , ARG C:124 , LYS C:131 , ARG D:141 , GLU D:142BINDING SITE FOR RESIDUE SO4 A 302
03AC3SOFTWARESER A:92 , GLY A:93 , ARG A:124 , LYS A:131 , ARG F:141 , GLU F:142 , TYR F:171 , PHE F:183 , ARG F:187 , TYR F:204 , HOH F:411BINDING SITE FOR RESIDUE SO4 A 303
04AC4SOFTWARETHR B:14 , GLY B:15 , ALA B:16 , SER B:17 , SER B:41 , ALA B:43 , VAL B:47 , SER B:106 , THR B:107 , THR B:109 , ARG B:141 , GLU B:142 , TYR B:204 , HOH B:437 , TRP D:86 , SER D:118 , ARG D:124 , HOH D:417 , HOH D:434BINDING SITE FOR RESIDUE FMN B 301
05AC5SOFTWAREARG B:141 , GLU B:142 , TYR B:171 , PHE B:183 , ARG B:187 , TYR B:204 , HOH B:431 , SER D:92 , GLY D:93 , ARG D:124 , LYS D:131BINDING SITE FOR RESIDUE SO4 B 302
06AC6SOFTWARESER B:92 , GLY B:93 , ARG B:124 , LYS B:131 , ARG C:141 , GLU C:142 , HOH C:421 , TYR E:171 , PHE E:183 , ARG E:187 , TYR E:204BINDING SITE FOR RESIDUE SO4 B 303
07AC7SOFTWARETRP B:86 , SER B:118 , ARG B:124 , HOH B:406 , HOH B:418 , THR C:14 , GLY C:15 , ALA C:16 , SER C:17 , SER C:41 , ALA C:43 , VAL C:47 , SER C:106 , THR C:107 , THR C:109 , ARG C:141 , GLU C:142 , HOH C:407 , HOH C:409 , TYR E:204BINDING SITE FOR RESIDUE FMN C 301
08AC8SOFTWARETYR C:171 , PHE C:183 , ARG C:187 , TYR C:204 , HOH C:403 , ARG E:141 , GLU E:142 , SER F:92 , GLY F:93 , ARG F:124 , LYS F:131BINDING SITE FOR RESIDUE SO4 C 302
09AC9SOFTWARETYR A:204 , TRP C:86 , SER C:118 , ARG C:124 , HOH C:405 , HOH C:427 , THR D:14 , GLY D:15 , ALA D:16 , SER D:17 , SER D:41 , ALA D:43 , SER D:106 , THR D:107 , THR D:109 , ARG D:141 , GLU D:142 , HOH D:421 , HOH D:433BINDING SITE FOR RESIDUE FMN D 301
10BC1SOFTWARETYR C:204 , THR E:14 , GLY E:15 , ALA E:16 , SER E:17 , SER E:41 , ALA E:43 , SER E:106 , THR E:107 , THR E:109 , ARG E:141 , GLU E:142 , HOH E:418 , TRP F:86 , SER F:118 , ARG F:124 , HOH F:413 , HOH F:422BINDING SITE FOR RESIDUE FMN E 301
11BC2SOFTWAREARG A:141 , GLU A:142 , TYR D:171 , PHE D:183 , ARG D:187 , TYR D:204 , SER E:92 , GLY E:93 , ARG E:124 , LYS E:131 , HOH E:401BINDING SITE FOR RESIDUE SO4 E 302
12BC3SOFTWARETRP A:86 , SER A:118 , ARG A:124 , HOH A:407 , THR F:14 , GLY F:15 , ALA F:16 , SER F:17 , SER F:41 , ALA F:43 , SER F:106 , THR F:107 , THR F:109 , ARG F:141 , GLU F:142 , TYR F:204 , HOH F:405 , HOH F:409 , HOH F:423BINDING SITE FOR RESIDUE FMN F 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Cys A:103 -Pro A:104
2Thr A:143 -Pro A:144
3Cys B:103 -Pro B:104
4Thr B:143 -Pro B:144
5Cys C:103 -Pro C:104
6Thr C:143 -Pro C:144
7Cys D:103 -Pro D:104
8Thr D:143 -Pro D:144
9Cys E:103 -Pro E:104
10Thr E:143 -Pro E:144
11Cys F:103 -Pro F:104
12Thr F:143 -Pro F:144

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RHE)

(-) 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:202
                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee....hhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhh.....hhhhhhhhhhhhhh.....eee.......hhhhh......eeeeeeehhhhhhhhhhh...hhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhh..ee............hhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rhe A   4 DFNGKITLAITGASGASYAMRLIECLIAANYQLYILCSSAGRIVLDTEVGVKIPSSPDAASKFLTEKYQAKDQQITVFGKEQWFSPVASGSSAPKQMVVCPCSTGTMAAICHGMSDNLIERAADVVIKERGQLILMVRETPFSTLHLQNMLSLSQQGVTIMPASPGFYHKVETIEDLIDFMVGRVLDHLGIEQDIMPRWGYN 205
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203  

Chain B from PDB  Type:PROTEIN  Length:203
                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee....hhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhh.....hhhhhhhhhhhhhh.....eeee......hhhhh......eeeeeeehhhhhhhhhhh...hhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhh..ee............hhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rhe B   3 NDFNGKITLAITGASGASYAMRLIECLIAANYQLYILCSSAGRIVLDTEVGVKIPSSPDAASKFLTEKYQAKDQQITVFGKEQWFSPVASGSSAPKQMVVCPCSTGTMAAICHGMSDNLIERAADVVIKERGQLILMVRETPFSTLHLQNMLSLSQQGVTIMPASPGFYHKVETIEDLIDFMVGRVLDHLGIEQDIMPRWGYN 205
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202   

Chain C from PDB  Type:PROTEIN  Length:201
                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee....hhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhh.....hhhhhhhhhhhhh......eee.......hhhhh......eeeeeeehhhhhhhhhh....hhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhh..ee............hhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rhe C   4 DFNGKITLAITGASGASYAMRLIECLIAANYQLYILCSSAGRIVLDTEVGVKIPSSPDAASKFLTEKYQAKDQQITVFGKEQWFSPVASGSSAPKQMVVCPCSTGTMAAICHGMSDNLIERAADVVIKERGQLILMVRETPFSTLHLQNMLSLSQQGVTIMPASPGFYHKVETIEDLIDFMVGRVLDHLGIEQDIMPRWGY 204
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203 

Chain D from PDB  Type:PROTEIN  Length:202
                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee....hhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhh.....hhhhhhhhhhhhhh.....eee.......hhhhh......eeeeeeehhhhhhhhhhh...hhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhh..ee............hhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rhe D   4 DFNGKITLAITGASGASYAMRLIECLIAANYQLYILCSSAGRIVLDTEVGVKIPSSPDAASKFLTEKYQAKDQQITVFGKEQWFSPVASGSSAPKQMVVCPCSTGTMAAICHGMSDNLIERAADVVIKERGQLILMVRETPFSTLHLQNMLSLSQQGVTIMPASPGFYHKVETIEDLIDFMVGRVLDHLGIEQDIMPRWGYN 205
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203  

Chain E from PDB  Type:PROTEIN  Length:202
                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee....hhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhh.....hhhhhhhhhhhhh......eee.......hhhhh......eeeeeeehhhhhhhhhhh...hhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhh..ee............hhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rhe E   4 DFNGKITLAITGASGASYAMRLIECLIAANYQLYILCSSAGRIVLDTEVGVKIPSSPDAASKFLTEKYQAKDQQITVFGKEQWFSPVASGSSAPKQMVVCPCSTGTMAAICHGMSDNLIERAADVVIKERGQLILMVRETPFSTLHLQNMLSLSQQGVTIMPASPGFYHKVETIEDLIDFMVGRVLDHLGIEQDIMPRWGYN 205
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203  

Chain F from PDB  Type:PROTEIN  Length:202
                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee....hhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhh.....hhhhhhhhhhhhhh.....eeee......hhhhh......eeeeeeehhhhhhhhhhh...hhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhh..ee............hhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rhe F   4 DFNGKITLAITGASGASYAMRLIECLIAANYQLYILCSSAGRIVLDTEVGVKIPSSPDAASKFLTEKYQAKDQQITVFGKEQWFSPVASGSSAPKQMVVCPCSTGTMAAICHGMSDNLIERAADVVIKERGQLILMVRETPFSTLHLQNMLSLSQQGVTIMPASPGFYHKVETIEDLIDFMVGRVLDHLGIEQDIMPRWGYN 205
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203  

   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 4RHE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

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 Related Entries

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

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        Q489U8_COLP3 | Q489U84rhf

(-) Related Entries Specified in the PDB File

4rhf CRYSTAL STRUCTURE OF UBIX MUTANT V47S