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(-) Description

Title :  CRYSTAL STRUCTURE OF A TRIMERIC EXONUCLEASE PHOEXO I FROM PYROCOCCUS HORIKOSHII OT3 IN COMPLEX WITH POLY-DT
 
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 :  2.05
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(*TP*TP*TP*TP*TP*TP*T)-3'
    Chains: B, D, F
    Engineered: YES
    Organism Scientific: UNIDENTIFIED
    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 4YOX)

(-) Sites  (0, 0)

(no "Site" information available for 4YOX)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Lys A:32 -Pro A:33
2Lys C:32 -Pro C:33
3Ser C:53 -Gly C:54
4Lys E:32 -Pro E:33

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YOX)

(-) 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:226
                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee.....eeeeeeeeeeee........eeeeee.hhhhh....hhhhhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee.eeeee...eeeeee.hhhhh..eeeee......eeeeeee......eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yox A   1 MRIVAADTGGAVLDESFQPVGLIATVAVLVEKPYKTSKRFLVKYADPYNYDLSGRQAIRDEIELAIELAREVSPDVIHLNSTLGGIEVRKLDESTIDALQISDRGKEIWKELSKDLQPLAKKFWEETGIEIIAIGKSSVPVRIAEIYAGIFSVKWALDNVGGLLVGLPRYMEVEIKKDKIIGKSLDPREGGLYGEVKTEVPQGIKWELYPNPLVRRFMVFEITSKS 229
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160|      173       183       193       203       213       223      
                                                                                                                                                                                         160|                                                                 
                                                                                                                                                                                          164                                                                 


Chain B from PDB  Type:DNA  Length:4
                                    
                 4yox B   4 TTTT   7


Chain C from PDB  Type:PROTEIN  Length:226
                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee.....eeeeeeeeeeee........eeeeee.hhhhh....hhhhhhhhhhhhhhhhhhh..eee........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee....eeeee...eeeeee.hhhhh..eeeee......eeeeeee.......eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yox C   1 MRIVAADTGGAVLDESFQPVGLIATVAVLVEKPYKTSKRFLVKYADPYNYDLSGRQAIRDEIELAIELAREVSPDVIHLNSTLGGIEVRKLDESTIDALQISDRGKEIWKELSKDLQPLAKKFWEETGIEIIAIGKSSVPVRIAEIYAGIFSVKWALDNVGGLLVGLPRYMEVEIKKDKIIGKSLDPREGGLYGEVKTEVPQGIKWELYPNPLVRRFMVFEITSKS 229
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160|      173       183       193       203       213       223      
                                                                                                                                                                                         160|                                                                 
                                                                                                                                                                                          164                                                                 


Chain D from PDB  Type:DNA  Length:4
                                    
                 4yox D   4 TTTT   7


Chain E from PDB  Type:PROTEIN  Length:224
                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee.....eeeeeeeeeeee........eeeeee.hhhhh....hhhhhhhhhhhhhhhhhhh..eee........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.eee.hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee.eeeee...eeeeee.hhhhh..eeeee.......eeeeee......eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yox E   1 MRIVAADTGGAVLDESFQPVGLIATVAVLVEKPYKTSKRFLVKYADPYNYDLSGRQAIRDEIELAIELAREVSPDVIHLNSTLGGIEVRKLDESTIDALQISDRGKEIWKELSKDLQPLAKKFWEETGIEIIAIGKSSVPVRIAEIYAGIFSVKWALDNVGGLLVGLPRYMEVEIKKDKIIGKSLDPREGGLYGEVKTEVPQGIKWELYPNPLVRRFMVFEITS 227
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160|      173       183       193       203       213       223    
                                                                                                                                                                                         160|                                                               
                                                                                                                                                                                          164                                                               


Chain F from PDB  Type:DNA  Length:4
                                    
                 4yox F   4 TTTT   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 4YOX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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  Ligands, Modified Residues, Ions
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  Sites
(no "Sites" information available for 4yox)
 
  Cis Peptide Bonds
    Lys A:32 - Pro A:33   [ RasMol ]  
    Lys C:32 - Pro C:33   [ RasMol ]  
    Lys E:32 - Pro E:33   [ RasMol ]  
    Ser C:53 - Gly C:54   [ RasMol ]  
 

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  A0A060P168_P | A0A060P168
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

4yor 4yot 4you 4yov 4yow 4yoy