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(-) Description

Title :  CRYSTAL STRUCTURE OF A TRIMERIC EXONUCLEASE PHOEXO I FROM PYROCOCCUS HORIKOSHII OT3 AT 2.15A RESOLUTION
 
Authors :  K. Miyazono, K. Tsutsumi, M. Tanokura
Date :  12 Mar 15  (Deposition) - 15 Jul 15  (Release) - 16 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Exonuclease, Hydrolase (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, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET26B
    Expression System Strain: ROSETTA(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1MG3Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:7 , ASP A:80 , HOH A:468 , HOH A:472 , HOH A:481 , HOH A:502binding site for residue MG A 301
2AC2SOFTWAREASP B:7 , ASP B:80 , HOH B:453binding site for residue MG B 301
3AC3SOFTWAREASP C:7 , ASP C:80 , HOH C:432 , HOH C:437 , HOH C:439 , HOH C:454binding site for residue MG C 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YOT)

(-) 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:225
                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee.....eeeeeeeeeeee........eeeeee.hhhhh.hhhhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee....eeeee...eeeeee.hhhhh..eeeee......eeeeeee.......eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yot A   1 MRIVAADTGGAVLDESFQPVGLIATVAVLVEKPYKTSKRFLVKYADPYNYRQAIRDEIELAIELAREVSPDVIHLDSTLGGIEVRKLDESTIDALQISDRGKEIWKELSKDLQPLAKKFWEETGIEIIAIGKSSVPVRIAEIYAGIFSVKWALDNVKEKGGLLVGLPRYMEVEIKKDKIIGKSLDPREGGLYGEVKTEVPQGIKWELYPNPLVRRFMVFEITSKS 229
                                    10        20        30        40        50|       64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224     
                                                                            50|                                                                                                                                                                              
                                                                             55                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee.....eeeeeeeeeeee........eeeeee.......hhhhhhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee.eeeeee..eeeeee.hhhhh..eeeee......eeeeeee......eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yot B   1 MRIVAADTGGAVLDESFQPVGLIATVAVLVEKPYKTSKRFLVKYADPYNYSGRQAIRDEIELAIELAREVSPDVIHLDSTLGGIEVRKLDESTIDAKEIWKELSKDLQPLAKKFWEETGIEIIAIGKSSVPVRIAEIYAGIFSVKWALDNVKEKGGLLVGLPRYMEVEIKKDKIIGKSLDPREGGLYGEVKTEVPQGIKWELYPNPLVRRFMVFEITSKS 229
                                    10        20        30        40        50|       62        72        82        92     ||109       119       129       139       149       159       169       179       189       199       209       219       229
                                                                            50|                                           98|                                                                                                                           
                                                                             53                                           106                                                                                                                           


Chain C from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee.....eeeeeeeeeeee........eeeeee.hhhhh.hhhhhhhhhhhhhhhhh..eee........hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeee....eeeeee..eeeeee.hhhhh..eeeee.......eeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yot C   1 MRIVAADTGGAVLDESFQPVGLIATVAVLVEKPYKTSKRFLVKYADPYNYQAIRDEIELAIELAREVSPDVIHLDSTLGGIEVRKLDESTIDADRGKEIWKELSKDLQPLAKKFWEETGIEIIAIGKSSVPVRIAEIYAGIFSVKWALDNVKEKGGLLVGLPRYMEVEIKKDKIIGKSLDPREGGLYGEVKTEVPQGIKWELYPNPLVRRFMVFEITS 227
                                    10        20        30        40        50|       65        75        85        95  ||   109       119       129       139       149       159       169       179       189       199       209       219        
                                                                            50|                                        98|                                                                                                                            
                                                                             56                                        103
   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 4YOT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

4yor 4you 4yov 4yow 4yox 4yoy