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(-) Description

Title :  CRYSTAL STRUCTURE OF A TRIMERIC EXONUCLEASE PHOEXO I FROM PYROCOCCUS HORIKOSHII OT3 AT 2.20A 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 :  2.20
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:432 , HOH A:433 , HOH A:434 , HOH A:438binding site for residue MG A 301
2AC2SOFTWAREASP B:7 , ASP B:80 , HOH B:426 , HOH B:427binding site for residue MG B 301
3AC3SOFTWAREASP C:7 , GLU C:61 , ASP C:80 , HOH C:417 , HOH C:418 , HOH C:419 , HOH C:423binding site for residue MG C 301

(-) SS Bonds  (0, 0)

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

(-) 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 4YOU)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YOU)

(-) 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:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee.....eeeeeeeeeeee........eeeeee.hhhhh...hhhhhhhhhhhhhhhhhhhh..eee........hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.eee.hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee....eeeee...eeeeee.hhhhh..eeeee......eeeeeee.......eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4you A   1 MRIVAADTGGAVLDESFQPVGLIATVAVLVEKPYKTSKRFLVKYADPYNYDLSGRQAIRDEIELAIELAREVSPDVIHLDSTLGGIEVRKLDESTIDRGKEIWKELSKDLQPLAKKFWEETGIEIIAIGKSSVPVRIAEIYAGIFSVKWALDNVGGLLVGLPRYMEVEIKKDKIIGKSLDPREGGLYGEVKTEVPQGIKWELYPNPLVRRFMVFEITSKS 229
                                    10        20        30        40        50        60        70        80        90      |106       116       126       136       146       156   ||  169       179       189       199       209       219       229
                                                                                                                           97|                                                     160|                                                                 
                                                                                                                           104                                                      164                                                                 


Chain B from PDB  Type:PROTEIN  Length:199
                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee.....eeeeeeeeeeee........eeeeee......hhhhhhhhhhhhhhhh..eee........hhhhhhhhhhhhhhhhhhhhhhh.eee.hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.eeeee...eeeeee.hhhhh..eeeee......eeeeeee......eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4you B   1 MRIVAADTGGAVLDESFQPVGLIATVAVLVEKPYKTSKRFLVKYADPYNAIRDEIELAIELAREVSPDVIHLDSTLGGIEVRKLELSKDLQPLAKKFWEETGIEIIAIGKSSVPVRIAEIYAGIFSVKWALDNVGGLLVGLPRYMEVEIKKDKIIGKSLDPREGGLYGEVKTEVPQGIKWELYPNPLVRRFMVFEITSK 228
                                    10        20        30        40        57        67        77        87   ||  116       126       136       146       156   ||  169       179       189       199       209       219         
                                                                           49|                                91|                                              160|                                                                
                                                                            57                                111                                               164                                                                


Chain C from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee.....eeeeeeeeeeee........eeeeee.hhhhh...hhhhhhhhhhhhhhhhhhhh..eeee.......hhhhh......hhhhhh.hhhhhhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee.eeeee...eeeeee.hhhhh..eeeee.......eeeeee......eeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4you C   1 MRIVAADTGGAVLDESFQPVGLIATVAVLVEKPYKTSKRFLVKYADPYNYDLSGRQAIRDEIELAIELAREVSPDVIHLDSTLGGIEVRKLDESTIIWKELSKDLQPLAKKFWEETGIEIIAIGKSSVPVRIAEIYAGIFSVKWALDNVGLLVGLPRYMEVEIKKDKIIGKSLDPREGGLYGEVKTEVPQGIKWELYPNPLVRRFMVFEIT 226
                                    10        20        30        40        50        60        70        80        90     ||111       121       131       141       151       165       175       185       195       205       215       225 
                                                                                                                          96|                                                 160|                                                             
                                                                                                                          108                                                  165
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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 4YOU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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    Lys A:32 - Pro A:33   [ RasMol ]  
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  4you
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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 4yov 4yow 4yox 4yoy

(-) Related Entries Specified in the PDB File

4yor 4yot 4yov 4yow 4yox 4yoz