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(-) Description

Title :  STRUCTURE OF A. NIGER FDC1 IN COMPLEX WITH A PHENYLPYRUVATE DERIVED ADDUCT TO THE PRENYLATED FLAVIN COFACTOR
 
Authors :  K. A. P. Payne, D. Leys
Date :  13 Apr 15  (Deposition) - 17 Jun 15  (Release) - 01 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.01
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Ubid-Enzyme, Prenylated Flavin, (De)Carboxylase, 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
    EC Number: 4.1.1.61
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: AN03G06590
    Organism Scientific: ASPERGILLUS NIGER
    Organism Taxid: 425011

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
14MJ1Ligand/Ion1-DEOXY-5-O-PHOSPHONO-1-[(1S)-3,3,4,5-TETRAMETHYL-9,11-DIOXO-1-(PHENYLACETYL)-2,3,8,9,10,11-HEXAHYDRO-1H,7H-QUINOLINO[1,8-FG]PTERIDIN-7-YL]-D-RIBITOL
2K2Ligand/IonPOTASSIUM ION
3MN1Ligand/IonMANGANESE (II) ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
14MJ2Ligand/Ion1-DEOXY-5-O-PHOSPHONO-1-[(1S)-3,3,4,5-TETRAMETHYL-9,11-DIOXO-1-(PHENYLACETYL)-2,3,8,9,10,11-HEXAHYDRO-1H,7H-QUINOLINO[1,8-FG]PTERIDIN-7-YL]-D-RIBITOL
2K-1Ligand/IonPOTASSIUM ION
3MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:153 , ASN A:168 , SER A:170 , ILE A:171 , ALA A:172 , ARG A:173 , LEU A:185 , GLN A:190 , HIS A:191 , SER A:223 , SER A:224 , MET A:225 , PRO A:226 , GLU A:233 , ILE A:327 , LYS A:391 , PHE A:437 , LEU A:439 , MN A:602 , K A:603 , HOH A:733 , HOH A:743 , HOH A:749 , HOH A:755 , HOH A:844 , HOH A:900 , HOH A:937binding site for residue 4MJ A 601
2AC2SOFTWAREASN A:168 , HIS A:191 , GLU A:233 , 4MJ A:601 , K A:603 , HOH A:733 , HOH A:823binding site for residue MN A 602
3AC3SOFTWARETRP A:169 , ALA A:222 , SER A:223 , MET A:225 , GLU A:233 , 4MJ A:601 , MN A:602binding site for residue K A 603
4AC4SOFTWAREARG A:421 , ASP A:427 , ASP A:459 , LEU A:461 , HOH A:1019 , HOH A:1083binding site for residue K A 604

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ZA9)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Leu A:63 -Phe A:64
2Pro A:188 -Pro A:189
3Gly A:278 -Pro A:279
4Leu A:319 -Thr A:320

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ZA9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ZA9)

(-) Exons   (0, 0)

(no "Exon" information available for 4ZA9)

(-) 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:497
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhh..eeee...........eeee............hhhhhh........hhhhhhhhhhhhhhh.....ee...hhhhheee.....hhhhh..................eeeee......eeee...eeeee..eeee.....hhhhhhhhhhhhhh...eeeeeee..hhhhhhhhh.......hhhhhhhhhhh...eeee......eee....eeeeeeeeeeeeeee...............eeeeeeeeeeeee....eeee.......hhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh..eeeeeehhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhh.....eeee........hhhhhh.........eeeee..hhhhhh........hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4za9 A   3 AQPAHLCFRSFVEALKVDNDLVEINTPIDPNLEAAAITRRVCETNDKAPLFNNLIGMKNGLFRILGAPGSLRKSSADRYGRLARHLALPPTASMREILDKMLSASDMPPIPPTIVPTGPCKENSLDDSEFDLTELPVPLIHKSDGGKYIQTYGMHIVQSPDGTWTNWSIARAMVHDKNHLTGLVIPPQHIWQIHQMWKKEGRSDVPWALAFGVPPAAIMASSMPIPDGVTEAGYVGAMTGSSLELVKCDTNDLYVPATSEIVLEGTLSISETGPEGPFGEMHGYIFPGDTHLGAKYKVNRITYRNNAIMPMSSCGRLTDETHTMIGSLAAAEIRKLCQQNDLPITDAFAPFESQVTWVALRVDTEKLRAMKTTSEGFRKRVGDVVFNHKAGYTIHRLVLVGDDIDVYEGKDVLWAFSTRCRPGMDETLFEDVRGFPLIPYMGHGNGPAHRGGKVVSDALMPTEYTTGRNWEAADFNQSYPEDLKQKVLDNWTKMGFS 499
                                    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       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492
   Legend:   → Mismatch (orange background)
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  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 4ZA9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ZA9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ZA9)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)

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  4.1.1.61
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 Related Entries

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

UniProtKB/Swiss-Prot
        FDC1_ASPNC | A2QHE5: 4za4 4za5 4za7 4za8 4zaa 4zab

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4ZA9)