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(-) Description

Title :  AN ATOMIC VIEW OF THE NONAMERIC SMALL TERMINASE SUBUNIT OF BACTERIOPHAGE P22
 
Authors :  A. Bhardwaj, A. Roy, G. Cingolani
Date :  17 Oct 10  (Deposition) - 09 May 12  (Release) - 29 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,I
Keywords :  Terminase Small Subunit, Dna Packaging, Bacteriophage P22, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Roy, A. Bhardwaj, P. Datta, G. C. Lander, G. Cingolani
Small Terminase Couples Viral Dna Binding To Genome-Packaging Atpase Activity.
Structure V. 20 1403 2012
PubMed-ID: 22771211  |  Reference-DOI: 10.1016/J.STR.2012.05.014

(-) Compounds

Molecule 1 - DNA-PACKAGING PROTEIN GP3
    Chains: A, B, C, D, E, F, G, H, I
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMAL-2CE
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: 3
    Organism Common: BACTERIOPHAGE P22
    Organism Scientific: ENTEROBACTERIA PHAGE P22
    Organism Taxid: 10754
    Synonym: TERMINASE SMALL SUBUNIT

 Structural Features

(-) Chains, Units

  123456789
Asymmetric/Biological Unit : ABCDEFGHI

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3P9A)

(-) Sites  (0, 0)

(no "Site" information available for 3P9A)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3P9A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3P9A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3P9A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3P9A)

(-) Exons   (0, 0)

(no "Exon" information available for 3P9A)

(-) 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:139
 aligned with TERS_BPP22 | P04893 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:139
                                    10        20        30        40        50        60        70        80        90       100       110       120       130         
           TERS_BPP22     1 MAAPKGNRFWEARSSHGRNPKFESPEALWAACCEYFEWVEANPLWEMKAFSYQGEVIQEPIAKMRAMTITGLTLFIDVTLETWRTYRLREDLSEVVTRAEQVIYDQKFSGAAADLLNANIIARDLGLKEQSQVEDVTPD 139
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh...........hhhhhhhhhhhhhhhhhhh.eeeeeeee....eeeeeeee....hhhhhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p9a A   1 MAAPKGNRFWEARSSHGRNPKFESPEALWAACCEYFEWVEANPLWEMKAFSYQGEVIQEPIAKMRAMTITGLTLFIDVTLETWRTYRLREDLSEVVTRAEQVIYDQKFSGAAADLLNANIIARDLGLKEQSQVEDVTPD 139
                                    10        20        30        40        50        60        70        80        90       100       110       120       130         


Chain B from PDB  Type:PROTEIN  Length:132
 aligned with TERS_BPP22 | P04893 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:132
                                    17        27        37        47        57        67        77        87        97       107       117       127       137  
           TERS_BPP22     8 RFWEARSSHGRNPKFESPEALWAACCEYFEWVEANPLWEMKAFSYQGEVIQEPIAKMRAMTITGLTLFIDVTLETWRTYRLREDLSEVVTRAEQVIYDQKFSGAAADLLNANIIARDLGLKEQSQVEDVTPD 139
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhh...........hhhhhhhhhhhhhhhhhhh.eeeeeeee....eeeeeeee....hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3p9a B   8 RFWEARSSHGRNPKFESPEALWAACCEYFEWVEANPLWEMKAFSYQGEVIQEPIAKMRAMTITGLTLFIDVTLETWRTYRLREDLSEVVTRAEQVIYDQKFSGAAADLLNANIIARDLGLKEQSQVEDVTPD 139
                                    17        27        37        47        57        67        77        87        97       107       117       127       137  


Chain C from PDB  Type:PROTEIN  Length:133
 aligned with TERS_BPP22 | P04893 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:133
                                    16        26        36        46        56        66        76        86        96       106       116       126       136   
           TERS_BPP22     7 NRFWEARSSHGRNPKFESPEALWAACCEYFEWVEANPLWEMKAFSYQGEVIQEPIAKMRAMTITGLTLFIDVTLETWRTYRLREDLSEVVTRAEQVIYDQKFSGAAADLLNANIIARDLGLKEQSQVEDVTPD 139
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh...........hhhhhhhhhhhhhhhhhhh.eeeeeeeee..eeeeeeeee....hhhhhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p9a C   7 NRFWEARSSHGRNPKFESPEALWAACCEYFEWVEANPLWEMKAFSYQGEVIQEPIAKMRAMTITGLTLFIDVTLETWRTYRLREDLSEVVTRAEQVIYDQKFSGAAADLLNANIIARDLGLKEQSQVEDVTPD 139
                                    16        26        36        46        56        66        76        86        96       106       116       126       136   


Chain D from PDB  Type:PROTEIN  Length:135
 aligned with TERS_BPP22 | P04893 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:135
                                    14        24        34        44        54        64        74        84        94       104       114       124       134     
           TERS_BPP22     5 KGNRFWEARSSHGRNPKFESPEALWAACCEYFEWVEANPLWEMKAFSYQGEVIQEPIAKMRAMTITGLTLFIDVTLETWRTYRLREDLSEVVTRAEQVIYDQKFSGAAADLLNANIIARDLGLKEQSQVEDVTPD 139
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh...........hhhhhhhhhhhhhhhhhhh.eeeeeeeee..eeeeeeeee....hhhhhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..eeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p9a D   5 KGNRFWEARSSHGRNPKFESPEALWAACCEYFEWVEANPLWEMKAFSYQGEVIQEPIAKMRAMTITGLTLFIDVTLETWRTYRLREDLSEVVTRAEQVIYDQKFSGAAADLLNANIIARDLGLKEQSQVEDVTPD 139
                                    14        24        34        44        54        64        74        84        94       104       114       124       134     


Chain E from PDB  Type:PROTEIN  Length:132
 aligned with TERS_BPP22 | P04893 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:132
                                    17        27        37        47        57        67        77        87        97       107       117       127       137  
           TERS_BPP22     8 RFWEARSSHGRNPKFESPEALWAACCEYFEWVEANPLWEMKAFSYQGEVIQEPIAKMRAMTITGLTLFIDVTLETWRTYRLREDLSEVVTRAEQVIYDQKFSGAAADLLNANIIARDLGLKEQSQVEDVTPD 139
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ................hhhhhhhhhhhhhhhhhhh.eeeeeeeee..eeeeeeeee....hhhhhhhhhh.hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3p9a E   8 RFWEARSSHGRNPKFESPEALWAACCEYFEWVEANPLWEMKAFSYQGEVIQEPIAKMRAMTITGLTLFIDVTLETWRTYRLREDLSEVVTRAEQVIYDQKFSGAAADLLNANIIARDLGLKEQSQVEDVTPD 139
                                    17        27        37        47        57        67        77        87        97       107       117       127       137  


Chain F from PDB  Type:PROTEIN  Length:134
 aligned with TERS_BPP22 | P04893 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:134
                                    15        25        35        45        55        65        75        85        95       105       115       125       135    
           TERS_BPP22     6 GNRFWEARSSHGRNPKFESPEALWAACCEYFEWVEANPLWEMKAFSYQGEVIQEPIAKMRAMTITGLTLFIDVTLETWRTYRLREDLSEVVTRAEQVIYDQKFSGAAADLLNANIIARDLGLKEQSQVEDVTPD 139
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhh.eeeeeeeee..eeeeeeeee....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..eeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p9a F   6 GNRFWEARSSHGRNPKFESPEALWAACCEYFEWVEANPLWEMKAFSYQGEVIQEPIAKMRAMTITGLTLFIDVTLETWRTYRLREDLSEVVTRAEQVIYDQKFSGAAADLLNANIIARDLGLKEQSQVEDVTPD 139
                                    15        25        35        45        55        65        75        85        95       105       115       125       135    


Chain G from PDB  Type:PROTEIN  Length:133
 aligned with TERS_BPP22 | P04893 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:133
                                    16        26        36        46        56        66        76        86        96       106       116       126       136   
           TERS_BPP22     7 NRFWEARSSHGRNPKFESPEALWAACCEYFEWVEANPLWEMKAFSYQGEVIQEPIAKMRAMTITGLTLFIDVTLETWRTYRLREDLSEVVTRAEQVIYDQKFSGAAADLLNANIIARDLGLKEQSQVEDVTPD 139
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh...........hhhhhhhhhhhhhhhhhhh.eeeeeeeee..eeeeeeeee....hhhhhhhhhh.hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p9a G   7 NRFWEARSSHGRNPKFESPEALWAACCEYFEWVEANPLWEMKAFSYQGEVIQEPIAKMRAMTITGLTLFIDVTLETWRTYRLREDLSEVVTRAEQVIYDQKFSGAAADLLNANIIARDLGLKEQSQVEDVTPD 139
                                    16        26        36        46        56        66        76        86        96       106       116       126       136   


Chain H from PDB  Type:PROTEIN  Length:132
 aligned with TERS_BPP22 | P04893 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:132
                                    17        27        37        47        57        67        77        87        97       107       117       127       137  
           TERS_BPP22     8 RFWEARSSHGRNPKFESPEALWAACCEYFEWVEANPLWEMKAFSYQGEVIQEPIAKMRAMTITGLTLFIDVTLETWRTYRLREDLSEVVTRAEQVIYDQKFSGAAADLLNANIIARDLGLKEQSQVEDVTPD 139
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhh...........hhhhhhhhhhhhhhhhhhh.eeeeeeeee..eeeeeeeee....hhhhhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3p9a H   8 RFWEARSSHGRNPKFESPEALWAACCEYFEWVEANPLWEMKAFSYQGEVIQEPIAKMRAMTITGLTLFIDVTLETWRTYRLREDLSEVVTRAEQVIYDQKFSGAAADLLNANIIARDLGLKEQSQVEDVTPD 139
                                    17        27        37        47        57        67        77        87        97       107       117       127       137  


Chain I from PDB  Type:PROTEIN  Length:132
 aligned with TERS_BPP22 | P04893 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:132
                                    17        27        37        47        57        67        77        87        97       107       117       127       137  
           TERS_BPP22     8 RFWEARSSHGRNPKFESPEALWAACCEYFEWVEANPLWEMKAFSYQGEVIQEPIAKMRAMTITGLTLFIDVTLETWRTYRLREDLSEVVTRAEQVIYDQKFSGAAADLLNANIIARDLGLKEQSQVEDVTPD 139
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhh...........hhhhhhhhhhhhhhhhhhh.eeeeeeeee..eeeeeeeee....hhhhhhhhhh.hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3p9a I   8 RFWEARSSHGRNPKFESPEALWAACCEYFEWVEANPLWEMKAFSYQGEVIQEPIAKMRAMTITGLTLFIDVTLETWRTYRLREDLSEVVTRAEQVIYDQKFSGAAADLLNANIIARDLGLKEQSQVEDVTPD 139
                                    17        27        37        47        57        67        77        87        97       107       117       127       137
   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 3P9A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3P9A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3P9A)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H,I   (TERS_BPP22 | P04893)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    GO:0019076    viral release from host cell    The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane.

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  3p9a
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  TERS_BPP22 | P04893
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 Related Entries

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