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(-) Description

Title :  STRUCTURE OF A. NIGER FDC1 IN COMPLEX WITH 4-VINYL GUAIACOL
 
Authors :  K. A. P. Payne, D. Leys
Date :  13 Apr 15  (Deposition) - 17 Jun 15  (Release) - 08 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.24
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
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
    EC Number: 4.1.1.61
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: AN03G06590
    Organism Scientific: ASPERGILLUS NIGER
    Organism Taxid: 5061

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 8)

Asymmetric Unit (6, 8)
No.NameCountTypeFull Name
14LU1Ligand/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
24M42Ligand/Ion2-METHOXY-4-VINYLPHENOL
3CO21Ligand/IonCARBON DIOXIDE
4FZZ1Ligand/Ion1-DEOXY-5-O-PHOSPHONO-1-[(10AR)-2,2,3,4-TETRAMETHYL-8,10-DIOXO-1,2,8,9,10,10A-HEXAHYDRO-6H-INDENO[1,7-EF]PYRIMIDO[4,5-B][1,4]DIAZEPIN-6-YL]-D-RIBITOL
5K2Ligand/IonPOTASSIUM ION
6MN1Ligand/IonMANGANESE (II) ION
Biological Unit 1 (4, 10)
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
24M44Ligand/Ion2-METHOXY-4-VINYLPHENOL
3CO22Ligand/IonCARBON DIOXIDE
4FZZ2Ligand/Ion1-DEOXY-5-O-PHOSPHONO-1-[(10AR)-2,2,3,4-TETRAMETHYL-8,10-DIOXO-1,2,8,9,10,10A-HEXAHYDRO-6H-INDENO[1,7-EF]PYRIMIDO[4,5-B][1,4]DIAZEPIN-6-YL]-D-RIBITOL
5K-1Ligand/IonPOTASSIUM ION
6MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
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 , FZZ A:602 , MN A:603 , K A:604 , 4M4 A:606 , CO2 A:608 , HOH A:724 , HOH A:726 , HOH A:742 , HOH A:746 , HOH A:747binding site for residue 4LU A 601
2AC2SOFTWARETHR 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 , THR A:323 , ILE A:327 , LYS A:391 , 4LU A:601 , MN A:603 , K A:604 , 4M4 A:606 , CO2 A:608 , HOH A:724 , HOH A:726 , HOH A:740 , HOH A:742 , HOH A:746binding site for residue FZZ A 602
3AC3SOFTWAREASN A:168 , HIS A:191 , GLU A:233 , 4LU A:601 , FZZ A:602 , K A:604 , HOH A:724 , HOH A:816binding site for residue MN A 603
4AC4SOFTWARETRP A:169 , ALA A:222 , SER A:223 , MET A:225 , GLU A:233 , 4LU A:601 , FZZ A:602 , MN A:603binding site for residue K A 604
5AC5SOFTWAREARG A:421 , ASP A:427 , ASP A:459 , LEU A:461 , HOH A:1014 , HOH A:1077binding site for residue K A 605
6AC6SOFTWARELEU A:185 , ILE A:187 , GLN A:190 , TYR A:394 , THR A:395 , PHE A:437 , LEU A:439 , 4LU A:601 , FZZ A:602 , HOH A:1055binding site for residue 4M4 A 606
7AC7SOFTWAREALA A:6 , GLU A:15 , ALA A:16 , VAL A:19 , ASP A:20 , PRO A:29 , ARG A:86 , HOH A:820 , HOH A:1027 , HOH A:1162binding site for residue 4M4 A 607
8AC8SOFTWAREARG A:173 , MET A:283 , LEU A:439 , 4LU A:601 , FZZ A:602binding site for residue CO2 A 608

(-) SS Bonds  (0, 0)

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

(-) 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 4ZAA)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZAA)

(-) 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:496
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhh..eeee...........eeee............hhhhhh........hhhhhhhhhhhhhhh.....ee...hhhhheeee...........................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
                 4zaa A   4 QPAHLCFRSFVEALKVDNDLVEINTPIDPNLEAAAITRRVCETNDKAPLFNNLIGMKNGLFRILGAPGSLRKSSADRYGRLARHLALPPTASMREILDKMLSASDMPPIPPTIVPTGPCKENSLDDSEFDLTELPVPLIHKSDGGKYIQTYGMHIVQSPDGTWTNWSIARAMVHDKNHLTGLVIPPQHIWQIHQMWKKEGRSDVPWALAFGVPPAAIMASSMPIPDGVTEAGYVGAMTGSSLELVKCDTNDLYVPATSEIVLEGTLSISETGPEGPFGEMHGYIFPGDTHLGAKYKVNRITYRNNAIMPMSSCGRLTDETHTMIGSLAAAEIRKLCQQNDLPITDAFAPFESQVTWVALRVDTEKLRAMKTTSEGFRKRVGDVVFNHKAGYTIHRLVLVGDDIDVYEGKDVLWAFSTRCRPGMDETLFEDVRGFPLIPYMGHGNGPAHRGGKVVSDALMPTEYTTGRNWEAADFNQSYPEDLKQKVLDNWTKMGFS 499
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493
   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 4ZAA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)

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UniProtKB/Swiss-Prot
        FDC1_ASPNC | A2QHE5: 4za4 4za5 4za7 4za8 4za9 4zab

(-) Related Entries Specified in the PDB File

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