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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF (GP27-GP5)3 CONJUGATED WITH FE(III) PROTOPORPHYRIN
 
Authors :  T. Koshiyama, N. Yokoi, T. Ueno, S. Kanamaru, S. Nagano, Y. Shiro, F. Arisaka, Y. Watanabe
Date :  28 Jul 07  (Deposition) - 15 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.11
Chains :  Asym. Unit :  A,D
Biol. Unit 1:  A,D  (3x)
Keywords :  Protein Containing Metal Complexes, Antimicrobial, Bacteriolytic Enzyme, Glycosidase, Hydrolase, Late Protein, Virion, Hydrolase/Structural Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Koshiyama, N. Yokoi, T. Ueno, S. Kanamaru, S. Nagano, Y. Shiro, F. Arisaka, Y. Watanabe
Molecular Design Of Heteroprotein Assemblies Providing A Bionanocup As A Chemical Reactor.
Small V. 4 50 2008
PubMed-ID: 18098245  |  Reference-DOI: 10.1002/SMLL.200700855
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TAIL-ASSOCIATED LYSOZYME
    Chains: A
    EC Number: 3.2.1.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET29A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: 5
    Mutation: YES
    Organism Scientific: ENTEROBACTERIA PHAGE T4
    Organism Taxid: 10665
    Synonym: PROTEIN GP5
 
Molecule 2 - BASEPLATE STRUCTURAL PROTEIN GP27
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET29A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: 27
    Organism Scientific: ENTEROBACTERIA PHAGE T4
    Organism Taxid: 10665
    Synonym: HUB PROTEIN 27

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AD
Biological Unit 1 (3x): AD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NEN1Ligand/Ion1-ETHYL-PYRROLIDINE-2,5-DIONE
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1NEN3Ligand/Ion1-ETHYL-PYRROLIDINE-2,5-DIONE

(-) Sites  (0, 0)

(no "Site" information available for 2Z6B)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z6B)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr A:121 -Pro A:122
2Tyr A:387 -Pro A:388

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z6B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Z6B)

(-) Exons   (0, 0)

(no "Exon" information available for 2Z6B)

(-) Sequences/Alignments

Asymmetric 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:573
 aligned with BP5_BPT4 | P16009 from UniProtKB/Swiss-Prot  Length:575

    Alignment length:573
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   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       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---   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------2z6bA03 A:174-342  [code=1.10.530.40, no name defined]                                                                                                                   -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee.........eeeee................hhhhh.eeee.......................eeeeee.......eeeeeee..ee.....................ee..hhhhhhhhhhhhhhhhhhhhh...eee..................hhhhhhhhhhh.eeeeee.....eeee..ee.......hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......................................eeee............eeeee.....eeeee......eeeee.....eeee.....eeee................................................................................................................................................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z6b A   6 NCLNWFVGVVEDRMDPLKLGRVRVRVVGLHPPQRAQGDVMGIPTEKLPWMSVIQPITSAAMSGIGGSVTGPVEGTRVYGHFLDKWKTNGIVLGTYGGIVREKPNRLEGFSDPTGQYPRRLGNDTNVLNQGGEVGYDSSSNVIQDSNLDTAINPDDRPLSEIPTDDNPNMSMAEMLRRDEGLRLKVYWDTEGYPTIGIGHLIMKQPVRDMAQINKVLSKQVGREITGNPGSITMEEATTLFERDLADMQRDIKSHSKVGPVWQAVNRSRQMALENMAFQMGVGGVAKFNTMLTAMLAGDWEKAYKAGRDSLWYQQTKGRASRVTMIILTGNLESYGVEVKTPARSLLAMAATVAKSSDPADPPIPNDSRILFKEPVSSYKGEYPYVHTMETESGHIQEFDDTPGQERYRLVHPTGTYEEVSPSGRRTRKTVDNLYDITNADGNFLVAGDKKTNVGGSEIYYNMDNRLHQIDGSNTIFVRGDETKTVEGNGTILVKGNVTIIVEGNADITVKGDATTLVEGNQTNTVNGNLSWKVAGTVDWDVGGDWTEKMASMSSISSGQYTIDGSRIDIGSVD 578
                                    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   


Chain D from PDB  Type:PROTEIN  Length:368
 aligned with BP27_BPT4 | P17172 from UniProtKB/Swiss-Prot  Length:391

    Alignment length:374
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373    
            BP27_BPT4     4 LQRPGYPNLSVKLFDSYDAWSNNRFVELAATITTLTMRDSLYGRNEGMLQFYDSKNIHTKMDGNEIIQISVANANDINNVKTRIYGCKHFSVSVDSKGDNIIAIELGTIHSIENLKFGRPFFPDAGESIKEMLGVIYQDRTLLTPAINAINAYVPDIPWTSTFENYLSYVREVALAVGSDKFVFVWQDIMGVNMMDYDMMINQEPYPMIVGEPSLIGQFIQELKYPLAYDFVWLTKSNPHKRDPMKNATIYAHSFLDSSIPMITTGKGENSIVVSRSGAYSEMTYRNGYEEAIRLQTMAQYDGYAKCSTIGNFNLTPGVKIIFNDSKNQFKTEFYVDEVIHELSNNNSVTHLYMFTNATKLETIDPVKVKNEFK 377
               SCOP domains d2z6bd1 D:4-200 Baseplate structural protein gp27                                                                                                                                                    d2z6bd2 D:201-377       Baseplate structural protein gp27                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee.hhhhhh..........eeeeeeeee....eeeeeee..............eeeeee.........eeeeeeeeee...........eeeeee................hhhhhhhhhhhhhh.........ee...ee........hhhhhhhhhhh..ee......eeeeee..eeeeeehhhhhh....eeee....------......eeeeeeeee...hhhhhhhh.eeeeee........eee.....eeeeee.hhhhhhh....hhhhhhhhhhhhh..eeeeeeee.........eeeee.........eeeeeeeeee.....eeeeeeee.................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z6b D   4 LQRPGYPNLSVKLFDSYDAWSNNRFVELAATITTLTMRDSLYGRNEGMLQFYDSKNIHTKMDGNEIIQISVANANDINNVKTRIYGCKHFSVSVDSKGDNIIAIELGTIHSIENLKFGRPFFPDAGESIKEMLGVIYQDRTLLTPAINAINAYVPDIPWTSTFENYLSYVREVALAVGSDKFVFVWQDIMGVNMMDYDMMINQEPYPMIVGEPS------QELKYPLAYDFVWLTKSNPHKRDPMKNATIYAHSFLDSSIPMITTGKGENSIVVSRSGAYSEMTYRNGYEEAIRLQTMAQYDGYAKCSTIGNFNLTPGVKIIFNDSKNQFKTEFYVDEVIHELSNNNSVTHLYMFTNATKLETIDPVKVKNEFK 377
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213   |     -|      233       243       253       263       273       283       293       303       313       323       333       343       353       363       373    
                                                                                                                                                                                                                                               217    224
   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, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Z6B)

(-) Gene Ontology  (16, 19)

Asymmetric Unit(hide GO term definitions)
Chain A   (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.

Chain D   (BP27_BPT4 | P17172)
molecular function
    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: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.

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  2z6b
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 Related Entries

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

UniProtKB/Swiss-Prot
        BP27_BPT4 | P17172: 1k28 1pdj 1wth 5iv5
        BP5_BPT4 | P16009: 1k28 1pdl 1wth 3a1m 4jiv 4jiw 4jj2 4ku0 4osd 5iv5

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2Z6B)