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(-) Description

Title :  FITTING OF GP5 IN THE CRYOEM RECONSTRUCTION OF THE BACTERIOPHAGE T4 BASEPLATE
 
Authors :  V. A. Kostyuchenko, P. G. Leiman, P. R. Chipman, S. Kanamaru, M. J. Van Raaij, F. Arisaka, V. V. Mesyanzhinov, M. G. Rossmann
Date :  19 May 03  (Deposition) - 09 Sep 03  (Release) - 24 Feb 09  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  12.00
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. A. Kostyuchenko, P. G. Leiman, P. R. Chipman, S. Kanamaru, M. J. Van Raaij, F. Arisaka, V. V. Mesyanzhinov, M. G. Rossmann
Three-Dimensional Structure Of The Bacteriophage T4 Baseplate
Nat. Struct. Biol. V. 10 688 2003
PubMed-ID: 12923574  |  Reference-DOI: 10.1038/NSB970
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TAIL-ASSOCIATED LYSOZYME
    Chains: A, B, C
    EC Number: 3.2.1.17
    Organism Scientific: ENTEROBACTERIA PHAGE T4
    Organism Taxid: 10665
    Synonym: PROTEIN GP5

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1PDL)

(-) Sites  (0, 0)

(no "Site" information available for 1PDL)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PDL)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1PDL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PDL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1PDL)

(-) Exons   (0, 0)

(no "Exon" information available for 1PDL)

(-) 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:554
 aligned with BP5_BPT4 | P16009 from UniProtKB/Swiss-Prot  Length:575

    Alignment length:570
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575
             BP5_BPT4     6 NNLNWFVGVVEDRMDPLKLGRVRVRVVGLHPPQRAQGDVMGIPTEKLPWMSVIQPITSAAMSGIGGSVTGPVEGTRVYGHFLDKWKTNGIVLGTYGGIVREKPNRLEGFSDPTGQYPRRLGNDTNVLNQGGEVGYDSSSNVIQDSNLDTAINPDDRPLSEIPTDDNPNMSMAEMLRRDEGLRLKVYWDTEGYPTIGIGHLIMKQPVRDMAQINKVLSKQVGREITGNPGSITMEEATTLFERDLADMQRDIKSHSKVGPVWQAVNRSRQMALENMAFQMGVGGVAKFNTMLTAMLAGDWEKAYKAGRDSLWYQQTKGRASRVTMIILTGNLESYGVEVKTPARSLSAMAATVAKSSDPADPPIPNDSRILFKEPVSSYKGEYPYVHTMETESGHIQEFDDTPGQERYRLVHPTGTYEEVSPSGRRTRKTVDNLYDITNADGNFLVAGDKKTNVGGSEIYYNMDNRLHQIDGSNTIFVRGDETKTVEGNGTILVKGNVTIIVEGNADITVKGDATTLVEGNQTNTVNGNLSWKVAGTVDWDVGGDWTEKMASMSSISSGQYTIDGSRIDIG 575
               SCOP domains d1pdla_ A: Bacteriophage T4 3D cryo-EM reconstruction                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....................................................................................................................................................................................................................................................................................................................................................----------------...................................................................................................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1pdl A   6 NNLNWFVGVVEDRMDPLKLGRVRVRVVGLHPPQRAQGDVMGIPTEKLPWMSVIQPITSAAMSGIGGSVTGPVEGTRVYGHFLDKWKTNGIVLGTYGGIVREKPNRLEGFSDPTGQYPRRLGNDTNVLNQGGEVGYDSSSNVIQDSNLDTAINPDDRPLSEIPTDDNPNMSMAEMLRRDEGLRLKVYWDTEGYPTIGIGHLIMKQPVRDMAQINKVLSKQVGREITGNPGSITMEEATTLFERDLADMQRDIKSHSKVGPVWQAVNRSRQMALENMAFQMGVGGVAKFNTMLTAMLAGDWEKAYKAGRDSLWYQQTKGRASRVTMIILTGNLESYGVEVKT----------------DPADPPIPNDSRILFKEPVSSYKGEYPYVHTMETESGHIQEFDDTPGQERYRLVHPTGTYEEVSPSGRRTRKTVDNLYDITNADGNFLVAGDKKTNVGGSEIYYNMDNRLHQIDGSNTIFVRGDETKTVEGNGTILVKGNVTIIVEGNADITVKGDATTLVEGNQTNTVNGNLSWKVAGTVDWDVGGDWTEKMASMSSISSGQYTIDGSRIDIG 575
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345         -      |365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575
                                                                                                                                                                                                                                                                                                                                                                             345              362                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:554
 aligned with BP5_BPT4 | P16009 from UniProtKB/Swiss-Prot  Length:575

    Alignment length:570
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575
             BP5_BPT4     6 NNLNWFVGVVEDRMDPLKLGRVRVRVVGLHPPQRAQGDVMGIPTEKLPWMSVIQPITSAAMSGIGGSVTGPVEGTRVYGHFLDKWKTNGIVLGTYGGIVREKPNRLEGFSDPTGQYPRRLGNDTNVLNQGGEVGYDSSSNVIQDSNLDTAINPDDRPLSEIPTDDNPNMSMAEMLRRDEGLRLKVYWDTEGYPTIGIGHLIMKQPVRDMAQINKVLSKQVGREITGNPGSITMEEATTLFERDLADMQRDIKSHSKVGPVWQAVNRSRQMALENMAFQMGVGGVAKFNTMLTAMLAGDWEKAYKAGRDSLWYQQTKGRASRVTMIILTGNLESYGVEVKTPARSLSAMAATVAKSSDPADPPIPNDSRILFKEPVSSYKGEYPYVHTMETESGHIQEFDDTPGQERYRLVHPTGTYEEVSPSGRRTRKTVDNLYDITNADGNFLVAGDKKTNVGGSEIYYNMDNRLHQIDGSNTIFVRGDETKTVEGNGTILVKGNVTIIVEGNADITVKGDATTLVEGNQTNTVNGNLSWKVAGTVDWDVGGDWTEKMASMSSISSGQYTIDGSRIDIG 575
               SCOP domains d1pdlb_ B: Bacteriophage T4 3D cryo-EM reconstruction                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....................................................................................................................................................................................................................................................................................................................................................----------------...................................................................................................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1pdl B   6 NNLNWFVGVVEDRMDPLKLGRVRVRVVGLHPPQRAQGDVMGIPTEKLPWMSVIQPITSAAMSGIGGSVTGPVEGTRVYGHFLDKWKTNGIVLGTYGGIVREKPNRLEGFSDPTGQYPRRLGNDTNVLNQGGEVGYDSSSNVIQDSNLDTAINPDDRPLSEIPTDDNPNMSMAEMLRRDEGLRLKVYWDTEGYPTIGIGHLIMKQPVRDMAQINKVLSKQVGREITGNPGSITMEEATTLFERDLADMQRDIKSHSKVGPVWQAVNRSRQMALENMAFQMGVGGVAKFNTMLTAMLAGDWEKAYKAGRDSLWYQQTKGRASRVTMIILTGNLESYGVEVKT----------------DPADPPIPNDSRILFKEPVSSYKGEYPYVHTMETESGHIQEFDDTPGQERYRLVHPTGTYEEVSPSGRRTRKTVDNLYDITNADGNFLVAGDKKTNVGGSEIYYNMDNRLHQIDGSNTIFVRGDETKTVEGNGTILVKGNVTIIVEGNADITVKGDATTLVEGNQTNTVNGNLSWKVAGTVDWDVGGDWTEKMASMSSISSGQYTIDGSRIDIG 575
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345         -      |365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575
                                                                                                                                                                                                                                                                                                                                                                             345              362                                                                                                                                                                                                                     


Chain C from PDB  Type:PROTEIN  Length:554
 aligned with BP5_BPT4 | P16009 from UniProtKB/Swiss-Prot  Length:575

    Alignment length:570
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575
             BP5_BPT4     6 NNLNWFVGVVEDRMDPLKLGRVRVRVVGLHPPQRAQGDVMGIPTEKLPWMSVIQPITSAAMSGIGGSVTGPVEGTRVYGHFLDKWKTNGIVLGTYGGIVREKPNRLEGFSDPTGQYPRRLGNDTNVLNQGGEVGYDSSSNVIQDSNLDTAINPDDRPLSEIPTDDNPNMSMAEMLRRDEGLRLKVYWDTEGYPTIGIGHLIMKQPVRDMAQINKVLSKQVGREITGNPGSITMEEATTLFERDLADMQRDIKSHSKVGPVWQAVNRSRQMALENMAFQMGVGGVAKFNTMLTAMLAGDWEKAYKAGRDSLWYQQTKGRASRVTMIILTGNLESYGVEVKTPARSLSAMAATVAKSSDPADPPIPNDSRILFKEPVSSYKGEYPYVHTMETESGHIQEFDDTPGQERYRLVHPTGTYEEVSPSGRRTRKTVDNLYDITNADGNFLVAGDKKTNVGGSEIYYNMDNRLHQIDGSNTIFVRGDETKTVEGNGTILVKGNVTIIVEGNADITVKGDATTLVEGNQTNTVNGNLSWKVAGTVDWDVGGDWTEKMASMSSISSGQYTIDGSRIDIG 575
               SCOP domains d1pdlc_ C: Bacteriophage T4 3D cryo-EM reconstruction                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....................................................................................................................................................................................................................................................................................................................................................----------------...................................................................................................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1pdl C   6 NNLNWFVGVVEDRMDPLKLGRVRVRVVGLHPPQRAQGDVMGIPTEKLPWMSVIQPITSAAMSGIGGSVTGPVEGTRVYGHFLDKWKTNGIVLGTYGGIVREKPNRLEGFSDPTGQYPRRLGNDTNVLNQGGEVGYDSSSNVIQDSNLDTAINPDDRPLSEIPTDDNPNMSMAEMLRRDEGLRLKVYWDTEGYPTIGIGHLIMKQPVRDMAQINKVLSKQVGREITGNPGSITMEEATTLFERDLADMQRDIKSHSKVGPVWQAVNRSRQMALENMAFQMGVGGVAKFNTMLTAMLAGDWEKAYKAGRDSLWYQQTKGRASRVTMIILTGNLESYGVEVKT----------------DPADPPIPNDSRILFKEPVSSYKGEYPYVHTMETESGHIQEFDDTPGQERYRLVHPTGTYEEVSPSGRRTRKTVDNLYDITNADGNFLVAGDKKTNVGGSEIYYNMDNRLHQIDGSNTIFVRGDETKTVEGNGTILVKGNVTIIVEGNADITVKGDATTLVEGNQTNTVNGNLSWKVAGTVDWDVGGDWTEKMASMSSISSGQYTIDGSRIDIG 575
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345         -      |365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575
                                                                                                                                                                                                                                                                                                                                                                             345              362
   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  (1, 3)

Asymmetric/Biological Unit
(-)
Class: Low resolution protein structures (283)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1PDL)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1PDL)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (BP5_BPT4 | P16009)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0003796    lysozyme activity    Catalysis of the hydrolysis of the beta-(1->4) linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan.
    GO:0033922    peptidoglycan beta-N-acetylmuramidase activity    Catalysis of the hydrolysis of terminal, non-reducing N-acetylmuramic residues.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0016998    cell wall macromolecule catabolic process    The chemical reactions and pathways resulting in the breakdown of macromolecules that form part of a cell wall.
    GO:0019835    cytolysis    The rupture of cell membranes and the loss of cytoplasm.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0085027    entry into host via enzymatic degradation of host anatomical structure    Penetration by symbiont of a host anatomical structure which provides a barrier to symbiont entry, mediated by symbiont degradative enzymes.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0009253    peptidoglycan catabolic process    The chemical reactions and pathways resulting in the breakdown of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    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:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0098025    virus tail, baseplate    Multiprotein component at the distal (head) end of the virus tail to which fibers of tailed viruses may be attached.

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 Related Entries

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

UniProtKB/Swiss-Prot
        BP5_BPT4 | P16009: 1k28 1wth 2z6b 3a1m 4jiv 4jiw 4jj2 4ku0 4osd 5iv5

(-) Related Entries Specified in the PDB File

1k28 GP27 IS A PART OF THE CELL-PUNCTURING DEVICE, PART OF THE BASEPLATE RELATED ID: EMD-1048 RELATED DB: EMDB