1P5C - JenaLib

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Title :   CIRCULAR PERMUTATION OF HELIX A IN T4 LYSOZYME

Authors :   M. Sagermann, L. Gay, W. A. Baase, B. W. Matthews

Date :   25 Apr 03 (Deposition) - 04 May 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Circular Permutation, Protein Design, Context Dependent Folding, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Sagermann, W. A. Baase, B. H. Mooers, L. Gay, B. W. Matthews
Relocation Or Duplication Of The Helix A Sequence Of T4 Lysozyme Causes Only Modest Changes In Structure But Can Increase Or Decrease The Rate Of Folding.
Biochemistry V. 43 1296 2004
PubMed-ID: 14756565 | Reference-DOI: 10.1021/BI035702Q
(for further references see the PDB file header)

Molecule 1 - LYSOZYME
	Chains	:	A, B, C, D
	EC Number	:	3.2.1.17
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PHS1403
	Expression System Strain	:	RR1
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	GENE E
	Mutation	:	YES
	Organism Scientific	:	ENTEROBACTERIA PHAGE T4
	Organism Taxid	:	10665
	Synonym	:	LYSIS PROTEIN, MURAMIDASE, ENDOLYSIN

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1P5C)

(no "Site" information available for 1P5C)

(no "SS Bond" information available for 1P5C)

(no "Cis Peptide Bond" information available for 1P5C)

(no "SAP(SNP)/Variant" information available for 1P5C)

(no "PROSITE Motif" information available for 1P5C)

(no "Exon" information available for 1P5C)

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:166
 aligned with ENLYS_BPT4 | P00720 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:166
                                                                                                                                                                                163        164    
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162|        - |    
           ENLYS_BPT4    13 LRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRCALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSIWYNQTPNRAKRVITTFRTGTWDAYKN----------L----   -
               SCOP domains d1p5ca_ A: Phage T4 lysozyme                                                                                                                                           SCOP domains
               CATH domains 1p5cA00 A:13-178  [code=1.10.530.40, no name defined]                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeee..eeee...hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhh......hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p5c A  13 LRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKNSGGAMNIFEMLRIDE 178
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172

Chain B from PDB  Type:PROTEIN  Length:166
 aligned with ENLYS_BPT4 | P00720 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:166
                                                                                                                                                                                163        164    
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162|        - |    
           ENLYS_BPT4    13 LRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRCALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSIWYNQTPNRAKRVITTFRTGTWDAYKN----------L----   -
               SCOP domains d1p5cb_ B: Phage T4 lysozyme                                                                                                                                           SCOP domains
               CATH domains 1p5cB00 B:13-178  [code=1.10.530.40, no name defined]                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.....eee...eeee...hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhh...hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p5c B  13 LRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKNSGGAMNIFEMLRIDE 178
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172

Chain C from PDB  Type:PROTEIN  Length:166
 aligned with ENLYS_BPT4 | P00720 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:166
                                                                                                                                                                                163        164    
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162|        - |    
           ENLYS_BPT4    13 LRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRCALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSIWYNQTPNRAKRVITTFRTGTWDAYKN----------L----   -
               SCOP domains d1p5cc_ C: Phage T4 lysozyme                                                                                                                                           SCOP domains
               CATH domains 1p5cC00 C:13-178  [code=1.10.530.40, no name defined]                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeee..eeee...hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhh...hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p5c C  13 LRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKNSGGAMNIFEMLRIDE 178
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172

Chain D from PDB  Type:PROTEIN  Length:166
 aligned with ENLYS_BPT4 | P00720 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:166
                                                                                                                                                                                163        164    
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162|        - |    
           ENLYS_BPT4    13 LRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRCALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSIWYNQTPNRAKRVITTFRTGTWDAYKN----------L----   -
               SCOP domains d1p5cd_ D: Phage T4 lysozyme                                                                                                                                           SCOP domains
               CATH domains 1p5cD00 D:13-178  [code=1.10.530.40, no name defined]                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeee..eeee...hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh...hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p5c D  13 LRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKNSGGAMNIFEMLRIDE 178
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Lysozyme-like (1361)

Superfamily: Lysozyme-like (1361)

Family: Phage lysozyme (550)

Protein domain: Phage T4 lysozyme (546)

Bacteriophage T4 [TaxId: 10665] (546)

1a	d1p5ca_	A:
1b	d1p5cb_	B:
1c	d1p5cc_	C:
1d	d1p5cd_	D:

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)

1a	1p5cA00	A:13-178
1b	1p5cB00	B:13-178
1c	1p5cC00	C:13-178
1d	1p5cD00	D:13-178

(no "Pfam Domain" information available for 1P5C)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (ENLYS_BPT4 | P00720)

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.
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: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: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:0030430	host cell cytoplasm	The cytoplasm of a host cell.

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1jtm	DUPLICATION EXTENSION OF THE B-SHEET SEQUENCE OF T4 LYSOZYME
1oyu	HELIX B TANDEM REPEAT, ALTERNATIVE CONFORMATION
1p56	DUPLICATION-EXTENSION OF HELIX A OF T4 LYSOZYME
262l	HELIX B TANDEM REPEAT

Description

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