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(-) Description

Title :  UBIX IN COMPLEX WITH A COVALENT ADDUCT BETWEEN DIMETHYLALLYL MONOPHOSPHATE AND REDUCED FMN
 
Authors :  M. D. White, D. Leys
Date :  14 Apr 15  (Deposition) - 17 Jun 15  (Release) - 01 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (12x)
Keywords :  Prenyl Transferase, Ubix, Fmn Binding, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. D. White, K. A. Payne, K. Fisher, S. A. Marshall, D. Parker, N. J. Rattray, D. K. Trivedi, R. Goodacre, S. E. Rigby, N. S. Scrutton, S. Hay, D. Leys
Ubix Is A Flavin Prenyltransferase Required For Bacterial Ubiquinone Biosynthesis.
Nature V. 522 497 2015
PubMed-ID: 26083743  |  Reference-DOI: 10.1038/NATURE14559

(-) Compounds

Molecule 1 - UBIX
    Chains: A
    EC Number: 4.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PA4019
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (12x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
14LS1Ligand/Ion1-DEOXY-1-[7,8-DIMETHYL-5-(3-METHYLBUT-2-EN-1-YL)-2,4-DIOXO-1,3,4,5-TETRAHYDROBENZO[G]PTERIDIN-10(2H)-YL]-5-O-PHOSPHONO-D-RIBITOL
2NA1Ligand/IonSODIUM ION
3PO41Ligand/IonPHOSPHATE ION
4SCN4Ligand/IonTHIOCYANATE ION
Biological Unit 1 (3, 72)
No.NameCountTypeFull Name
14LS12Ligand/Ion1-DEOXY-1-[7,8-DIMETHYL-5-(3-METHYLBUT-2-EN-1-YL)-2,4-DIOXO-1,3,4,5-TETRAHYDROBENZO[G]PTERIDIN-10(2H)-YL]-5-O-PHOSPHONO-D-RIBITOL
2NA-1Ligand/IonSODIUM ION
3PO412Ligand/IonPHOSPHATE ION
4SCN48Ligand/IonTHIOCYANATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:12 , GLY A:13 , ALA A:14 , SER A:15 , SER A:39 , ALA A:41 , LEU A:44 , VAL A:45 , TRP A:84 , ALA A:89 , SER A:104 , THR A:105 , THR A:107 , CYS A:116 , ARG A:122 , ARG A:139 , TYR A:169 , TRP A:200 , PO4 A:307 , HOH A:415 , HOH A:449 , HOH A:461 , HOH A:462 , HOH A:513 , HOH A:533 , HOH A:537binding site for residue 4LS A 301
2AC2SOFTWAREPRO A:95 , ASN A:96 , ALA A:97 , ARG A:132 , PRO A:133binding site for residue SCN A 302
3AC3SOFTWAREHIS A:170 , MET A:196 , PRO A:198binding site for residue SCN A 303
4AC4SOFTWAREGLU A:5 , ARG A:6 , ARG A:199binding site for residue SCN A 304
5AC5SOFTWAREGLN A:59 , ASP A:208 , HOH A:405 , HOH A:437 , HOH A:463binding site for residue SCN A 305
6AC6SOFTWAREASN A:117 , HOH A:407 , HOH A:454 , HOH A:461 , HOH A:513 , HOH A:537binding site for residue NA A 306
7AC7SOFTWARESER A:90 , GLY A:91 , ARG A:122 , LYS A:129 , ARG A:139 , GLU A:140 , TYR A:169 , ARG A:185 , 4LS A:301 , HOH A:435binding site for residue PO4 A 307

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Cys A:101 -Pro A:102
2Ala A:141 -Pro A:142

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZAV)

(-) 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:208
                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee....hhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhh......hhhhhhhhhhhhhh.....eee.......hhhhh......eeeeeeehhhhhhhhhhh...hhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhh..ee............hhhhhhhhhhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zav A   1 MSGPERITLAMTGASGAQYGLRLLDCLVQEEREVHFLISKAAQLVMATETDVALPAKPQAMQAFLTEYCGAAAGQIRVFGQNDWMAPPASGSSAPNAMVICPCSTGTLSAVATGACNNLIERAADVALKERRPLVLVPREAPFSSIHLENMLKLSNLGAVILPAAPGFYHQPQSVEDLVDFVVARILNTLGIPQDMLPRWGEQHLVSD 208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
   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 4ZAV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)

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  4zav
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  UBIX_PSEAE | Q9HX08
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  4.1.1.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        UBIX_PSEAE | Q9HX08: 3zqu 4zaf 4zag 4zal 4zan 4zaw 4zax 4zay 4zaz

(-) Related Entries Specified in the PDB File

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