1EL1 - JenaLib

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Title :   X-RAY CRYSTAL STRUCTURE ANALYSIS OF CANINE MILK LYSOZYME (HOLO-TYPE)

Authors :   T. Koshiba, M. Yao, I. Tanaka, K. Nitta

Date :   13 Mar 00 (Deposition) - 13 Mar 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Calcium Binding Lysozyme, Holo-Form, C-Type Lysozyme, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Koshiba, M. Yao, I. Tanaka, K. Nitta
Calcium Induced Conformational Changes Of Canine Milk Lysozyme Revealed By Structural And Thermodynamical Evidences
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - LYSOZYME C
	Chains	:	A, B
	EC Number	:	3.2.1.17
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PSCREEN 1-B(+)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	DOG
	Organism Scientific	:	CANIS LUPUS FAMILIARIS
	Organism Taxid	:	9615
	Strain	:	FAMILIARIS

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:82 , ASP A:85 , ASN A:87 , ASP A:90 , ASP A:91 , HOH A:133 , HOH A:202	BINDING SITE FOR RESIDUE CA A 130
2	AC2	SOFTWARE	LYS B:82 , ASP B:85 , ASN B:87 , ASP B:90 , ASP B:91 , HOH B:144 , HOH B:185	BINDING SITE FOR RESIDUE CA B 130

Asymmetric Unit

No.	Residues
1	A:6	-	A:127
2	A:30	-	A:115
3	A:65	-	A:80
4	A:76	-	A:94
5	B:6	-	B:127
6	B:30	-	B:115
7	B:65	-	B:80
8	B:76	-	B:94

(no "Cis Peptide Bond" information available for 1EL1)

(no "SAP(SNP)/Variant" information available for 1EL1)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LACTALBUMIN_LYSOZYME_2	PS51348	Alpha-lactalbumin / lysozyme C family profile.	LYSC1_CANLF	1-129	2	A:1-129 B:1-129
2	LACTALBUMIN_LYSOZYME_1	PS00128	Alpha-lactalbumin / lysozyme C signature.	LYSC1_CANLF	76-94	2	A:76-94 B:76-94

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LACTALBUMIN_LYSOZYME_2	PS51348	Alpha-lactalbumin / lysozyme C family profile.	LYSC1_CANLF	1-129	1	A:1-129 -
2	LACTALBUMIN_LYSOZYME_1	PS00128	Alpha-lactalbumin / lysozyme C signature.	LYSC1_CANLF	76-94	1	A:76-94 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LACTALBUMIN_LYSOZYME_2	PS51348	Alpha-lactalbumin / lysozyme C family profile.	LYSC1_CANLF	1-129	1	- B:1-129
2	LACTALBUMIN_LYSOZYME_1	PS00128	Alpha-lactalbumin / lysozyme C signature.	LYSC1_CANLF	76-94	1	- B:76-94

(no "Exon" information available for 1EL1)

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:130
 aligned with LYSC1_CANLF | P81708 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:130
                             1                                                                                                                                
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129
          LYSC1_CANLF     - -KIFSKCELARKLKSMGMDGFHGYSLANWVCMAEYESNFNTQAFNGRNSNGSSDYGIFQLNSKWWCKSNSHSSANACNIMCSKFLDDNIDDDIACAKRVVKDPNGMSAWVAWVKHCKGKDLSKYLASCNL 129
               SCOP domains d1el1a_ A: Lysozyme                                                                                                                SCOP domains
               CATH domains 1el1A00 A:-1-129  [code=1.10.530.10, no name defined]                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhh.........hhhhhhhhhhhhh......ee........ee....ee...................hhhhh...hhhhhhhhhhhhh..hhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -LACTALBUMIN_LYSOZYME_2  PDB: A:1-129 UniProt: 1-129                                                                               PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------LACTALBUMIN_LYSOZYM----------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1el1 A  -1 SKIFSKCELARKLKSMGMDGFHGYSLANWVCMAEYESNFNTQAFNGRNSNGSSDYGIFQLNSKWWCKSNSHSSANACNIMCSKFLDDNIDDDIACAKRVVKDPNGMSAWVAWVKHCKGKDLSKYLASCNL 129
                            ||       9        19        29        39        49        59        69        79        89        99       109       119       129
                            ||                                                                                                                                
                           -1|                                                                                                                                
                             1

Chain B from PDB  Type:PROTEIN  Length:130
 aligned with LYSC1_CANLF | P81708 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:130
                             1                                                                                                                                
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129
          LYSC1_CANLF     - -KIFSKCELARKLKSMGMDGFHGYSLANWVCMAEYESNFNTQAFNGRNSNGSSDYGIFQLNSKWWCKSNSHSSANACNIMCSKFLDDNIDDDIACAKRVVKDPNGMSAWVAWVKHCKGKDLSKYLASCNL 129
               SCOP domains d1el1b_ B: Lysozyme                                                                                                                SCOP domains
               CATH domains 1el1B00 B:-1-129  [code=1.10.530.10, no name defined]                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....ee........ee....ee...................hhhhh...hhhhhhhhhhhh...hhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -LACTALBUMIN_LYSOZYME_2  PDB: B:1-129 UniProt: 1-129                                                                               PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------LACTALBUMIN_LYSOZYM----------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1el1 B  -1 SKIFSKCELARKLKSMGMDGFHGYSLANWVCMAEYESNFNTQAFNGRNSNGSSDYGIFQLNSKWWCKSNSHSSANACNIMCSKFLDDNIDDDIACAKRVVKDPNGMSAWVAWVKHCKGKDLSKYLASCNL 129
                            ||       9        19        29        39        49        59        69        79        89        99       109       119       129
                           -1|                                                                                                                                
                             1

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: C-type lysozyme (738)

Protein domain: Lysozyme (696)

Dog (Canis familiaris), milk [TaxId: 9615] (4)

1a	d1el1a_	A:
1b	d1el1b_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Lysozyme (1131)

Homologous Superfamily: [code=1.10.530.10, no name defined] (605)

Dog (Canis lupus familiaris) (5)

1a	1el1A00	A:-1-129
1b	1el1B00	B:-1-129

(no "Pfam Domain" information available for 1EL1)

Asymmetric Unit(hide GO term definitions)

Chain A,B (LYSC1_CANLF | P81708)

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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	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.

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	LYSC1_CANLF \| P81708	:	1i56 1qqy 2cwi 2z2e

1qqy	1QQY IS A CALCIUM FREE FORM OF CANINE MILK LYSOZYME.

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