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(-) Description

Title :  CRYSTAL STRUCTURE OF A TRIMERIC EXONUCLEASE PHOEXO I FROM PYROCOCCUS HORIKOSHII OT3 IN COMPLEX WITH POLY-DC
 
Authors :  K. Miyazono, T. Ito, M. Tanokura
Date :  12 Mar 15  (Deposition) - 15 Jul 15  (Release) - 16 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Exonuclease, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Miyazono, S. Ishino, K. Tsutsumi, T. Ito, Y. Ishino, M. Tanokura
Structural Basis For Substrate Recognition And Processive Cleavage Mechanisms Of The Trimeric Exonuclease Phoexo I
Nucleic Acids Res. V. 43 7122 2015
PubMed-ID: 26138487  |  Reference-DOI: 10.1093/NAR/GKV654

(-) Compounds

Molecule 1 - 3-5 EXONUCLEASE PHOEXO I
    Chains: A, C, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET26B
    Expression System Strain: ROSETTA(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953
 
Molecule 2 - 5'-D(*CP*CP*CP*CP*CP*CP*C)-3'
    Chains: B, D, F
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32644
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4YOW)

(-) Sites  (0, 0)

(no "Site" information available for 4YOW)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Lys A:32 -Pro A:33
2Lys C:32 -Pro C:33
3Lys E:32 -Pro E:33

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YOW)

(-) 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:227
                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee.....eeeeeeeeeeeee.......eeeeee.hhhhh....hhhhhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.eeeee...eeeeee.hhhhh..eeeee.......eeeeee......eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yow A   1 MRIVAADTGGAVLDESFQPVGLIATVAVLVEKPYKTSKRFLVKYADPYNYDLSGRQAIRDEIELAIELAREVSPDVIHLNSTLGGIEVRKLDESTIDALQISDRGKEIWKELSKDLQPLAKKFWEETGIEIIAIGKSSVPVRIAEIYAGIFSVKWALDNVKEKGGLLVGLPRYMEVEIKKDKIIGKSLDPREGGLYGEVKTEVPQGIKWELYPNPLVRRFMVFEITS 227
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       


Chain B from PDB  Type:DNA  Length:4
                                    
                 4yow B   4 CCCC   7


Chain C from PDB  Type:PROTEIN  Length:227
                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee.....eeeeeeeeeeeee.......eeeeee.hhhhh....hhhhhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.eeeee...eeeeee.hhhhh..eeeee.......eeeeee......eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yow C   1 MRIVAADTGGAVLDESFQPVGLIATVAVLVEKPYKTSKRFLVKYADPYNYDLSGRQAIRDEIELAIELAREVSPDVIHLNSTLGGIEVRKLDESTIDALQISDRGKEIWKELSKDLQPLAKKFWEETGIEIIAIGKSSVPVRIAEIYAGIFSVKWALDNVKEKGGLLVGLPRYMEVEIKKDKIIGKSLDPREGGLYGEVKTEVPQGIKWELYPNPLVRRFMVFEITS 227
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       


Chain D from PDB  Type:DNA  Length:4
                                    
                 4yow D   4 CCCC   7


Chain E from PDB  Type:PROTEIN  Length:227
                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee.....eeeeeeeeeeee........eeeeee.hhhhh....hhhhhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.eeeee...eeeeee.hhhhh..eeeee.......eeeeee......eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yow E   1 MRIVAADTGGAVLDESFQPVGLIATVAVLVEKPYKTSKRFLVKYADPYNYDLSGRQAIRDEIELAIELAREVSPDVIHLNSTLGGIEVRKLDESTIDALQISDRGKEIWKELSKDLQPLAKKFWEETGIEIIAIGKSSVPVRIAEIYAGIFSVKWALDNVKEKGGLLVGLPRYMEVEIKKDKIIGKSLDPREGGLYGEVKTEVPQGIKWELYPNPLVRRFMVFEITS 227
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       


Chain F from PDB  Type:DNA  Length:4
                                    
                 4yow F   4 CCCC   7
   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 4YOW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4YOW)

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  Sites
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  Cis Peptide Bonds
    Lys A:32 - Pro A:33   [ RasMol ]  
    Lys C:32 - Pro C:33   [ RasMol ]  
    Lys E:32 - Pro E:33   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/TrEMBL
        A0A060P168_P | A0A060P168: 4yor 4yot 4you 4yov 4yox 4yoy

(-) Related Entries Specified in the PDB File

4yor 4yot 4you 4yov 4yox 4yoy