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(-) Description

Title :  STRUCTURE OF C. DUBLIENSIS FDC1 WITH THE PRENYLATED-FLAVIN COFACTOR IN THE IMINIUM FORM.
 
Authors :  S. S. Bailey, D. Leys
Date :  13 Apr 15  (Deposition) - 17 Jun 15  (Release) - 01 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.46
Chains :  Asym./Biol. Unit :  A,B
Keywords :  (De)Carboxylase, Prenylated Flavin Binding, Ubid-Type Enzyme, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. A. Payne, M. D. White, K. Fisher, B. Khara, S. S. Bailey, D. Parker, N. J. Rattray, D. K. Trivedi, R. Goodacre, R. Beveridge, P. Barran, S. E. Rigby, N. S. Scrutton, S. Hay, D. Leys
New Cofactor Supports Alpha , Beta-Unsaturated Acid Decarboxylation Via 1, 3-Dipolar Cycloaddition.
Nature V. 522 502 2015
PubMed-ID: 26083754  |  Reference-DOI: 10.1038/NATURE14560

(-) Compounds

Molecule 1 - FDC1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CD36_64160
    Organism Common: YEAST
    Organism Scientific: CANDIDA DUBLINIENSIS
    Organism Taxid: 42374

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
14LU2Ligand/Ion1-DEOXY-5-O-PHOSPHONO-1-(3,3,4,5-TETRAMETHYL-9,11-DIOXO-2,3,8,9,10,11-HEXAHYDRO-7H-QUINOLINO[1,8-FG]PTERIDIN-12-IUM-7-YL)-D-RIBITOL
2K2Ligand/IonPOTASSIUM ION
3MN2Ligand/IonMANGANESE (II) ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:174 , HIS A:197A , GLU A:240 , K A:602 , 4LU A:603 , HOH A:713 , HOH A:717binding site for residue MN A 601
2AC2SOFTWARETRP A:175 , VAL A:229 , SER A:230 , MET A:232 , GLU A:240 , MN A:601 , 4LU A:603binding site for residue K A 602
3AC3SOFTWARETHR A:159 , ASN A:174 , SER A:176 , ILE A:177 , ALA A:178 , ARG A:179 , LEU A:191 , GLN A:196 , HIS A:197A , SER A:230 , SER A:231 , MET A:232 , PRO A:233 , GLU A:240 , GLU A:289 , PRO A:323 , ILE A:334 , LYS A:404 , MN A:601 , K A:602 , HOH A:704 , HOH A:713 , HOH A:726 , HOH A:734binding site for residue 4LU A 603
4AC4SOFTWAREASN B:174 , HIS B:197 , GLU B:240 , 4LU B:603 , HOH B:706 , HOH B:710binding site for residue MN B 601
5AC5SOFTWARETRP B:175 , VAL B:229 , SER B:230 , MET B:232 , GLU B:240 , 4LU B:603binding site for residue K B 602
6AC6SOFTWARETHR B:159 , ASN B:174 , SER B:176 , ILE B:177 , ALA B:178 , ARG B:179 , LEU B:191 , GLN B:196 , HIS B:197 , SER B:230 , SER B:231 , MET B:232 , PRO B:233 , GLU B:240 , GLU B:289 , SER B:321 , PRO B:323 , THR B:330 , ILE B:334 , LYS B:404 , MN B:601 , K B:602 , HOH B:701 , HOH B:710binding site for residue 4LU B 603

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Leu A:67 -Phe A:68
2Asn A:194 -Pro A:195
3Cys A:326 -Thr A:327
4Leu B:67 -Phe B:68
5Asn B:194 -Pro B:195
6Cys B:326 -Thr B:327

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZAD)

(-) Sequences/Alignments

Asymmetric/Biological 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:511
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhh..eeee................eee............hhhhhhhh......hhhhhhhhhhhhhhhhhh...ee.hhhhhhhhheeee....hhhhh..................eeeee......eeee....eeee..eee......hhhhhhhhhhhhh.....eeeeeee..hhhhhhhhh.......hhhhhhhhhh....eeee......eee....eeeeeeeeeeeeeee........ee.....eeeeeeeeeeeee....eee........hhhhhhhhhhhhhhhhhhhhh..hhhhheeeee.hhhhh..eeeeeehhhhhhhh..hhhhhhhhhhhhhhhh...........eeeeee......hhhhhhhhhhhh......eeee........hhhhhh.hhhhhh...eeeeee.hhhhhh......ee.hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4zad A    3 LNPALKFRDFIQVLKNEGDLIEIDTEVDPNLEVGAITRKAYENKLAAPLFNNLKQDPENIDPKNLFRILGCPGGLRGFGNDHARIALHLGLDSQTPMKEIIDFLVANRNPKKYIPPVLVPNDQSPHKKHHLTKEQIDLTKLPVPLLHHGDGGKFIQTYGMWVLQTPDKSWTNWSIARGMVHDSKSITGLVINPQHVKQVSDAWVAAGKGDKIPFALCFGVPPAAILVSSMPIPDGATEAEYIGGLCNQAVPVVKCETNDLEVPADCEMVFEGYLDRDTLVREGPFGEMHGYCFPKDHHTQPLYRVNHISYRDQAIMPISNPGLCTDETHTLIGGLVSAETKYLISQHPVLSKIVEDVFTPYEAQALWLAVKINTHELVKLKTNAKELSNLVGDFLFRSKECYKVCSILHEIILVGDDIDIFDFKQLIWAYTTRHTPVQDQLYFDDVKPFALAPFASQGPLIKTRQGGKCVTTCIFPKQFTDPDFEFVTCNFNGYPEEVKNKISQNWDKYYK  512
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192    |  202       212       222       232       242       252       262       272       282       292       302       312       322       332       342      |351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511 
                                                                                                                                                                                                                           197A                                                                                                                                                    348A                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:511
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh..eeee.......hhhhhhhhhhhhh...eeee................eee............hhhhhhhh......hhhhhhhhhhhh.hhhhh...ee.hhhhhhhhheeee.hhhhhhhh.................eeeeee......eeee...eeeee..eeee.....hhhhhhhhhhhhh.....eeeeeee..hhhhhhhhh.......hhhhhhhhhhh...eeee......eee....eeeeeeeeeeeeee.........ee......eeeeeeeeeeee....eee........hhhhhhhhhhhhhhhhhhhhh..hhhhheeeee.hhhhh..eeeeeehhhhhhh...hhhhhhhhhhhhhhhh...........eeeeee......hhhhhhhhhhhhh.....eeee........hhhhhh.hhhhhh...eeeeee.hhhhhh......ee.hhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4zad B    3 LNPALKFRDFIQVLKNEGDLIEIDTEVDPNLEVGAITRKAYENKLAAPLFNNLKQDPENIDPKNLFRILGCPGGLRGFGNDHARIALHLGLDSQTPMKEIIDFLVANRNPKKYIPPVLVPNDQSPHKKHHLTKEQIDLTKLPVPLLHHGDGGKFIQTYGMWVLQTPDKSWTNWSIARGMVHDSKSITGLVINPQHVKQVSDAWVAAGKGDKIPFALCFGVPPAAILVSSMPIPDGATEAEYIGGLCNQAVPVVKCETNDLEVPADCEMVFEGYLDRDTLVREGPFGEMHGYCFPKDHHTQPLYRVNHISYRDQAIMPISNPGLCTDETHTLIGGLVSAETKYLISQHPVLSKIVEDVFTPYEAQALWLAVKINTHELVKLKTNAKELSNLVGDFLFRSKECYKVCSILHEIILVGDDIDIFDFKQLIWAYTTRHTPVQDQLYFDDVKPFALAPFASQGPLIKTRQGGKCVTTCIFPKQFTDPDFEFVTCNFNGYPEEVKNKISQNWDKYYK  512
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342      |351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511 
                                                                                                                                                                                                                                                                                                                                                                                   348A
   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 4ZAD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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