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(-) Description

Title :  CRYSTAL STRUCTURE OF PYRENE- AND PHENANTHRENE-MODIFIED DNA IN COMPLEX WITH THE BPUJ1 ENDONUCLEASE BINDING DOMAIN
 
Authors :  M. Probst, W. Aeschimann, T. -T. -H. Chau, S. M. Langenegger, A. Stocker
Date :  18 Jan 16  (Deposition) - 17 Aug 16  (Release) - 14 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.88
Chains :  Asym./Biol. Unit :  A,L,M
Keywords :  Phenanthrene, Pyrene, Dna, Endonuclease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Probst, W. Aeschimann, T. T. Chau, S. M. Langenegger, A. Stocker, R. Haner
Structural Insight Into Dna-Assembled Oligochromophores: Crystallographic Analysis Of Pyrene- And Phenanthrene-Modified Dna In Complex With Bpuji Endonuclease.
Nucleic Acids Res. V. 44 7079 2016
PubMed-ID: 27422870  |  Reference-DOI: 10.1093/NAR/GKW644

(-) Compounds

Molecule 1 - RESTRICTION ENDONUCLEASE R.BPUJI
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: BPUJIR
    Organism Scientific: BACILLUS PUMILUS
    Organism Taxid: 1408
 
Molecule 2 - DNA (5'-D(*GP*(YPY)P*AP*CP*CP*CP*GP*TP*GP*GP*A)-3')
    Chains: L
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*TP*CP*CP*AP*CP*GP*GP*GP*T*(YPY)*(YPY)*C)-3')
    Chains: M
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ALM

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1YPE3Mod. Nucleotide4-[8-(4-HYDROXYBUT-1-YN-1-YL)PYREN-1-YL]BUT-3-YN-1-YLDIHYDROGEN PHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 5HNH)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5HNH)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Cys A:37 -Pro A:38
2Phe A:115 -Pro A:116

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5HNH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5HNH)

(-) Exons   (0, 0)

(no "Exon" information available for 5HNH)

(-) 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:279
                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhhhhhhhhhhhhh.eehhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.......eeee..eeeehhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh....hhhhhhhhhhhhhhhh...eehhhhhhhh..hhhhhh...hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhh..eeee..eeee...hhhhhhhhhh........hhhhh...hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hnh A   2 NYNPEEQFRCTIIRGKAKNMLDNLLPAYANIIDDICPCDKASFVKDFNNRLIEILGEETTKKTLDNHRTEIAGKLFGMFYEDDEVIFPSGRTNKYIEDSDQPAFFKDICFKFQFPNGMDKLDKVIEKVGAKIQIRQFPYILQVLLTADNNNIQLSKDDIAYYVLNSLQVLQGKIKPIEVIEKIIEDRSNDITKKVRHPGKETSYSMQHIREQLNYLELANLIRIDGNLVKLNYREAENINYIAQFWGNKPEFNAYKYDFTSEDDKKSFFKDWQQYYSNV 280
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271         


Chain L from PDB  Type:DNA  Length:11
                                           
                 5hnh L 101 GxACCCGTGGA 111
                             |     110 
                           102-YPE     


Chain M from PDB  Type:DNA  Length:12
                                            
                 5hnh M 201 TCCACGGGTxxC 212
                                   210| 
                                   210-YPE
                                    211-YPE
   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 5HNH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5HNH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5HNH)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Cys A:37 - Pro A:38   [ RasMol ]  
    Phe A:115 - Pro A:116   [ RasMol ]  
 

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  5hnh
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 Related Entries

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

UniProtKB/TrEMBL
        A3FMN7_BACPU | A3FMN7: 2vla 5hlt 5hnf

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5HNH)