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(-) Description

Title :  CRYSTAL STRUCTURE OF T4 GP17
 
Authors :  S. Sun, M. G. Rossmann
Date :  31 Mar 08  (Deposition) - 13 Jan 09  (Release) - 13 Jan 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Large Terminase, Alternative Initiation, Atp-Binding, Dna- Binding, Hydrolase, Nuclease, Nucleotide-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Sun, K. Kondabagil, B. Draper, T. I. Alam, V. D. Bowman, Z. Zhang, S. Hegde, A. Fokine, M. G. Rossmann, V. B. Rao
The Structure Of The Phage T4 Dna Packaging Motor Suggests A Mechanism Dependent On Electrostatic Forces
Cell(Cambridge, Mass. ) V. 135 1251 2008
PubMed-ID: 19109896  |  Reference-DOI: 10.1016/J.CELL.2008.11.015
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA PACKAGING PROTEIN GP17
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28
    Expression System StrainBL21(DE3) PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 1-567
    Gene17
    MutationYES
    Organism ScientificBACTERIOPHAGE T4
    SynonymTERMINASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION
2PO42Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:385 , TYR A:410 , HIS A:430 , ASN A:432 , HIS A:516 , ALA A:518 , HOH A:686 , HOH A:716BINDING SITE FOR RESIDUE PO4 A 568
2AC2SOFTWAREARG A:406 , SER A:435 , HIS A:436BINDING SITE FOR RESIDUE PO4 A 569

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ser A:276 -Gly A:277
2Glu A:404 -Gly A:405
3Gly A:407 -Gln A:408
4Gly A:530 -Val A:531

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3CPE)

(-) 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:553
 aligned with TERL_BPT4 | P17312 from UniProtKB/Swiss-Prot  Length:610

    Alignment length:553
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559   
            TERL_BPT4    10 DFHPLNEAGKILIKHPSLAERKDEDGIHWIKSQWDGKWYPEKFSDYLRLHKIVKIPNNSDKPELFQTYKDKNNKRSRYMGLPNLKRANIKTQWTREMVEEWKKCRDDIVYFAETYCAITHIDYGVIKVQLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFNKDKAVGILAHKGSMSAEVLDRTKQAIELLPDFLQPGIVEWNKGSIELDNGSSIGAYASSPDAVRGNSFAMIYIDECAFIPNFHDSWLAIQPVISSGRRSKIIITTTPNGLNHFYDIWTAAVEGKSGFEPYTAIWNSVKERLYNDEDIFDDGWQWSIQTINGSSLAQFRQEHTAAFEGTSGTLISGMKLAVMDFIEVTPDDHGFHQFKKPEPDRKYIATLDCSEGRGQDYHALHIIDVTDDVWEQVGVLHSNTISHLILPDIVMRYLVEYNECPVYIELNSTGVSVAKSLYMDLEYEGVICDSYTDLGMKQTKRTKAVGCSTLKDLIEKDKLIIHHRATIQEFRTFSEKGVSWAAEEGYHDDLVMSLVIFGWLSTQSKFIDY 562
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhh.eeee..eeeee......eee.hhhhhhh............................hhhhh............hhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhh.........eeee...eeee....eeeeee.hhhhhhhh...eeeee.hhhh.hhhhhhhhhhhhhh.....eeeeee.....hhhhhhhhhhhh.....eeeeehhhhhhhhhh........hhhhhhhhhh..hhhhhhhhhh...........hhhhhh.............eee.........eeeeee.........eeeeeee.....eeeeeeeee......hhhhhhhhhhhhh....eeeeehhhhhhhhhhhhh......ee........ee.hhhhhhhhhhhhhhhhhh..ee..hhhhhhhhh.eeee..eeee.....hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cpe A  10 DFHPLNEAGKILIKHPSLAERKDEDGIHWIKSQWDGKWYPEKFSDYLRLHKIVKIPNNSDKPELFQTYKDKNNKRSRYMGLPNLKRANIKTQWTREMVEEWKKCRDDIVYFAETYCAITHIDYGVIKVQLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFNKDKAVGILAHKGSMSAEVLDRTKQAIELLPDFLQPGIVEWNKGSIELDNGSSIGAYASSPDAVRGNSFAMIYIEDCAFIPNFHDSWLAIQPVISSGRRSKIIITTTPNGLNHFYDIWTAAVEGKSGFEPYTAIWNSVKERLYNDEDIFDDGWQWSIQTINGSSLAQFRQEHTAAFEGTSGTLISGMKLAVMDFIEVTPDDHGFHQFKKPEPDRKYIATLDCSEGRGQDYHALHIIDVTDDVWEQVGVLHSNTISHLILPDIVMRYLVEYNECPVYIELNSTGVSVAKSLYMDLEYEGVICDSYTDLGMKQTKRTKAVGCSTLKDLIEKDKLIIHHRATIQEFRTFSEKGVSWAAEEGYHDDLVMSLVIFGWLSTQSKFIDY 562
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559   

   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 3CPE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TERL_BPT4 | P17312)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0019072    viral genome packaging    The encapsulation of the viral genome within the capsid.
    GO:0046797    viral procapsid maturation    The refolding and structural rearrangements of individual capsid subunits to transition from the intermediate procapsid, to the more stable capsid structure.
    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_BPT4 | P173122o0h 2o0j 2o0k 3ezk

(-) Related Entries Specified in the PDB File

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