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(-) Description

Title :  CRYSTAL STRUCTURE OF THE G2P (LARGE TERMINASE) NUCLEASE DOMAIN FROM THE BACTERIOPHAGE SPP1 WITH BOUND MN
 
Authors :  C. Smits, M. Chechik, O. V. Kovalevskiy, M. B. Shevtsov, A. W. Foster, J. A. A. Antson
Date :  10 Mar 09  (Deposition) - 24 Mar 09  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Viral Protein, Dna Translocation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Smits, M. Chechik, O. V. Kovalevskiy, M. B. Shevtsov, A. W. Foster, J. C. Alonso, A. A. Antson
Structural Basis For The Nuclease Activity Of A Bacteriophage Large Terminase.
Embo Rep. V. 10 592 2009
PubMed-ID: 19444313  |  Reference-DOI: 10.1038/EMBOR.2009.53

(-) Compounds

Molecule 1 - TERMINASE LARGE SUBUNIT
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PYM20
    Expression System Strain: B834 (DE3)
    Expression System Taxid: 562
    Expression System Vector: PET28A
    Fragment: NUCLEASE DOMAIN, RESIDUES 232-422
    Organism Common: BACTERIOPHAGE SPP1
    Organism Scientific: BACILLUS PHAGE SPP1
    Organism Taxid: 10724
    Synonym: G2P

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1MN2Ligand/IonMANGANESE (II) ION
2MSE1Mod. Amino AcidSELENOMETHIONINE
3SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:266 , HIS A:400BINDING SITE FOR RESIDUE MN A 1413
2AC2SOFTWAREASP A:266 , ASP A:321BINDING SITE FOR RESIDUE MN A 1414
3AC3SOFTWAREARG A:317 , ARG A:411BINDING SITE FOR RESIDUE SO4 A 1415

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WC9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2WC9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_TERL_BPSPP_004 *D412NTERL_BPSPP  ---  ---AD412N
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WC9)

(-) Exons   (0, 0)

(no "Exon" information available for 2WC9)

(-) 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:177
 aligned with TERL_BPSPP | P54308 from UniProtKB/Swiss-Prot  Length:422

    Alignment length:177
                                   246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       
           TERL_BPSPP   237 VVPFENLQIEEGIITDAEVARFDNIRQGLDFGYGPDPLAFVRWHYDKRKNRIYAIDELVDHKVSLKRTADFVRKNKYESARIIADSSEPRSIDALKLEHGINRIEGAKKGPDSVEHGERWLDELDAIVIDPLRTPNIAREFENIDYQTDKNGDPIPRLEDKDNHTIDATRYAFERDM 413
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Terminase_3-2wc9A01 A:237-411                                                                                                                                                  -- Pfam domains
         Sec.struct. author ......eee.....hhhhhhhh..eeeeee.......eeeeeeeee....eeeeeeeeee...hhhhhhhhhhhh......eee...hhhhhhhhhhh.....eee......hhhhhhhhhhh..eeee....hhhhhhhhhhh.eee.....eeeee....hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------N- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wc9 A 237 VVPFENLQIEEGIITDAEVARFDNIRQGLDFGYGPDPLAFVRWHYDKRKNRIYAIDELVDHKVSLKRTADFVRKNKYESARIIADSSEPRSIDALKLEHGINRIEGAKKGPDSVEHGERWLDELDAIVIDPLRTPNIAREFENIDYQTDKNGDPIPRLEDKDNHTIDATRYAFERDm 413
                                   246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406      |
                                                                                                                                                                                                          413-MSE
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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 2WC9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WC9)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TERL_BPSPP | P54308)
molecular function
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
biological process
    GO:0006323    DNA packaging    Any process in which DNA and associated proteins are formed into a compact, orderly structure.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0019073    viral DNA genome packaging    The packing of viral DNA into a capsid.
    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.
cellular component
    GO:0098009    viral terminase, large subunit    The part of the viral terminase complex that contains the translocase and endonuclease activities and allows the translocation of the phage DNA into the procapsid. The large subunit usually assembles as a heterooligomer with the small subunit.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TERL_BPSPP | P54308: 2wbn

(-) Related Entries Specified in the PDB File

2wbn CRYSTAL STRUCTURE OF THE G2P (LARGE TERMINASE) NUCLEASE DOMAIN FROM THE BACTERIOPHAGE SPP1