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(-) Description

Title :  CRYSTAL STRUCTURE OF A TRIMERIC EXONUCLEASE PHOEXO I FROM PYROCOCCUS HORIKOSHII OT3 AT 1.52A 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 :  1.52
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (3x)
Biol. Unit 2:  B  (3x)
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
    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

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): A 
Biological Unit 2 (3x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:7 , ASP A:80 , HOH A:587 , HOH A:588 , HOH A:589 , HOH A:590binding site for residue MG A 301
2AC2SOFTWAREASP B:7 , ASP B:80 , HOH B:565 , HOH B:566 , HOH B:567 , HOH B:568binding site for residue MG B 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys A:32 -Pro A:33
2Lys B:32 -Pro B:33

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YOR)

(-) 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:227
                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee.....eeeeeeeeeeee........eeeeee.hhhhh...hhhhhhhhhhhhhhhhhhhh..eee........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeee.eeeeee..eeeeee.hhhhh..eeeee.......eeeeee......eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yor A   1 MRIVAADTGGAVLDESFQPVGLIATVAVLVEKPYKTSKRFLVKYADPYNYDLSGRQAIRDEIELAIELAREVSPDVIHLDSTLGGIEVRKLDESTIDALQISDRGKEIWKELSKDLQPLAKKFWEETGIEIIAIGKSSVPVRIAEIYAGIFSVKWALDNVKEKGGLLVGLPRYMEVEIKKDKIIGKSLDPREGGLYGEVKTEVPQGIKWELYPNPLVRRFMVFEITS 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:PROTEIN  Length:222
                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeeee.....eeeeeeeeeeee........eeeeee.hhhhh.hhhhhhhhhhhhhhhhh..eee........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeee.eeeeee..eeeeee.hhhhh..eeeee.......eeeeee......eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4yor B   1 MRIVAADTGGAVLDESFQPVGLIATVAVLVEKPYKTSKRFLVKYADPYNYQAIRDEIELAIELAREVSPDVIHLDSTLGGIEVRKLDESTIDALQISDRGKEIWKELSKDLQPLAKKFWEETGIEIIAIGKSSVPVRIAEIYAGIFSVKWALDNVKEKGGLLVGLPRYMEVEIKKDKIIGKSLDPREGGLYGEVKTEVPQGIKWELYPNPLVRRFMVFEITS 227
                                    10        20        30        40        50|       65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225  
                                                                            50|                                                                                                                                                                           
                                                                             56
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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 4YOR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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  A0A060P168_P | A0A060P168
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 Related Entries

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

(-) Related Entries Specified in the PDB File

4yot 4you 4yov 4yow 4yox 4yoy