1K28 - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   THE STRUCTURE OF THE BACTERIOPHAGE T4 CELL-PUNCTURING DEVICE

Authors :   S. Kanamaru, P. G. Leiman, V. A. Kostyuchenko, P. R. Chipman, V. V. Mesya F. Arisaka, M. G. Rossmann

Date :   26 Sep 01 (Deposition) - 06 Feb 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym. Unit : A,D
Biol. Unit 1: A,D  (3x)

Keywords :   Triple-Stranded Beta-Helix, Ob Fold, Pseudohexamer, T4 Tail Lysozyme, Hub, Gp27-Gp5*-Gp5C, Hydrolase-Structural Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Kanamaru, P. G. Leiman, V. A. Kostyuchenko, P. R. Chipman, V. V. Mesyanzhinov, F. Arisaka, M. G. Rossmann
Structure Of The Cell-Puncturing Device Of Bacteriophage T4
Nature V. 415 553 2002
PubMed-ID: 11823865 | Reference-DOI: 10.1038/415553A

Molecule 1 - TAIL-ASSOCIATED LYSOZYME
	Chains	:	A
	EC Number	:	3.2.1.17
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET-29A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	5
	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
	Expression System Plasmid	:	PET-29B
	Expression System Strain	:	B834 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	27
	Organism Scientific	:	ENTEROBACTERIA PHAGE T4
	Organism Taxid	:	10665

		1	2
Asymmetric Unit	:	A	D
Biological Unit 1 (3x)	:	A	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 17)

No.	Name	Count	Type	Full Name
1	K	1	Ligand/Ion	POTASSIUM ION
2	MSE	15	Mod. Amino Acid	SELENOMETHIONINE
3	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (2, 48)

No.	Name	Count	Type	Full Name
1	K	-1	Ligand/Ion	POTASSIUM ION
2	MSE	45	Mod. Amino Acid	SELENOMETHIONINE
3	PO4	3	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:799 , HOH A:885	BINDING SITE FOR RESIDUE K A 585
2	AC2	SOFTWARE	LYS A:454 , HOH A:634	BINDING SITE FOR RESIDUE PO4 A 586

(no "SS Bond" information available for 1K28)

Asymmetric Unit

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

(no "SAP(SNP)/Variant" information available for 1K28)

(no "PROSITE Motif" information available for 1K28)

(no "Exon" information available for 1K28)

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:557
 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 d1k28a1 A:6-129 Tail-associated lysozyme gp5, N-terminal domain                                                             d1k28a3 A:130-345 Tail-associated lysozyme gp5, catalytic domain                                                                                                                                                                        d1k28a2 A:362-584 Tail-associated lysozyme gp5, C-terminal domain                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------1k28A03 A:174-342  [code=1.10.530.40, no name defined]                                                                                                                   -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee.........eeeee................hhhhh.eeee.......................eeeeee.......eeeeee...ee.....................ee..hhhhhhhhhhhhhhhhhhhhh...eee.....hhhhh........hhhhhhhhhhh.eeeeee.....eeee..ee.......hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.....----------------............eeee..............eee.....eeeee......eeeee.....eeee.....eeee................................................................................................................................................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k28 A   6 NNLNWFVGVVEDRMDPLKLGRVRVRVVGLHPPQRAQGDVMGIPTEKLPWMSVIQPITSAAMSGIGGSVTGPVEGTRVYGHFLDKWKTNGIVLGTYGGIVREKPNRLEGFSDPTGQYPRRLGNDTNVLNQGGEVGYDSSSNVIQDSNLDTAINPDDRPLSEIPTDDNPNMSMAEMLRRDEGLRLKVYWDTEGYPTIGIGHLIMKQPVRDMAQINKVLSKQVGREITGNPGSITMEEATTLFERDLADMQRDIKSHSKVGPVWQAVNRSRQMALENMAFQMGVGGVAKFNTMLTAMLAGDWEKAYKAGRDSLWYQQTKGRASRVTMIILTGNLESYGVEVKT----------------DPADPPIPNDSRILFKEPVSSYKGEYPYVHTMETESGHIQEFDDTPGQERYRLVHPTGTYEEVSPSGRRTRKTVDNLYDITNADGNFLVAGDKKTNVGGSEIYYNMDNRLHQIDGSNTIFVRGDETKTVEGNGTILVKGNVTIIVEGNADITVKGDATTLVEGNQTNTVNGNLSWKVAGTVDWDVGGDWTEKMASMSSISSGQYTIDGSRIDIGSHH 584
                                    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                                                                                                                                                                                                                   576| 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     583

Chain D from PDB  Type:PROTEIN  Length:364
 aligned with BP27_BPT4 | P17172 from UniProtKB/Swiss-Prot  Length:391

    Alignment length:373
                                    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 LQRPGYPNLSVKLFDSYDAWSNNRFVELAATITTLTMRDSLYGRNEGMLQFYDSKNIHTKMDGNEIIQISVANANDINNVKTRIYGCKHFSVSVDSKGDNIIAIELGTIHSIENLKFGRPFFPDAGESIKEMLGVIYQDRTLLTPAINAINAYVPDIPWTSTFENYLSYVREVALAVGSDKFVFVWQDIMGVNMMDYDMMINQEPYPMIVGEPSLIGQFIQELKYPLAYDFVWLTKSNPHKRDPMKNATIYAHSFLDSSIPMITTGKGENSIVVSRSGAYSEMTYRNGYEEAIRLQTMAQYDGYAKCSTIGNFNLTPGVKIIFNDSKNQFKTEFYVDEVIHELSNNNSVTHLYMFTNATKLETIDPVKVKNEF 376
               SCOP domains d1k28d1 D:4-200 Baseplate structural protein gp27                                                                                                                                                    d1k28d2 D:201-376          Baseplate structural protein gp27                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee..hhhhhh...ee....eeeeeeeee....eeeeeeeee............eeeee...........eeeeeeeeeeee......eeeeeeeehhhhhh..........hhhhhhhhhhhhhh..hhhhh.eee...ee........hhhhhhhhhhhhhee......eeeee...eeeeeehhhhhh.....ee.....---------..............hhhhhh....eeeeee..........ee....eeeeee.hhhhhhh....hhhhhhhhhhhhhh.eeeeeee..........ee.ee.........eeeeeeeeeee...eeeeeeeee................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k28 D   4 LQRPGYPNLSVKLFDSYDAWSNNRFVELAATITTLTmRDSLYGRNEGmLQFYDSKNIHTKmDGNEIIQISVANANDINNVKTRIYGCKHFSVSVDSKGDNIIAIELGTIHSIENLKFGRPFFPDAGESIKEmLGVIYQDRTLLTPAINAINAYVPDIPWTSTFENYLSYVREVALAVGSDKFVFVWQDImGVNmmDYDmmINQEPYPmIVGEPS---------KYPLAYDFVWLTKSNPHKRDPmKNATIYAHSFLDSSIPmITTGKGENSIVVSRSGAYSEmTYRNGYEEAIRLQTmAQYDGYAKCSTIGNFNLTPGVKIIFNDSKNQFKTEFYVDEVIHELSNNNSVTHLYmFTNATKLETIDPVKVKNEF 376
                                    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   
                                                               40-MSE     51-MSE       64-MSE                                                                135-MSE                                                   193-MSE|   ||     211-MSE17       227                  248-MSE          265-MSE              286-MSE        301-MSE                                                 357-MSE               
                                                                                                                                                                                                                           197-MSE||                                                                                                                                                                             
                                                                                                                                                                                                                            198-MSE|                                                                                                                                                                             
                                                                                                                                                                                                                                202-MSE                                                                                                                                                                          
                                                                                                                                                                                                                                 203-MSE

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 '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Lysozyme (1131)

Homologous Superfamily: [code=1.10.530.40, no name defined] (526)

Enterobacteria phage t4. Organism_taxid: 10665. (237)

1k28A03

A:174-342

(no "Pfam Domain" information available for 1K28)

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.

Asymmetric Unit
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	Cis Peptide Bonds
		Tyr A:121 - Pro A:122	[ RasMol ]
		Tyr A:387 - Pro A:388	[ RasMol ]

Biological Unit
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		Biological Unit 1	[ Jena3D ]

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	1k28
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	BP5_BPT4 \| P16009
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	3.2.1.17
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UniProtKB/Swiss-Prot
	BP27_BPT4 \| P17172	:	1pdj 1wth 2z6b 5iv5
	BP5_BPT4 \| P16009	:	1pdl 1wth 2z6b 3a1m 4jiv 4jiw 4jj2 4ku0 4osd 5iv5

(no "Related Entries Specified in the PDB File" available for 1K28)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 17)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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SCOP Domains (4, 5)

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Gene Ontology (16, 19)

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