P15057 (LYS_BPCP1) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Lysozyme
EC=3.2.1.17

Alternative name(s):
CP-1 lysin
Endolysin
Muramidase

Gene names

Name:	CPL1
Synonyms:	22

Organism

Streptococcus phage Cp-1 (Bacteriophage Cp-1) [Complete proteome]

Taxonomic identifier

10747 [NCBI]

Taxonomic lineage

Viruses › dsDNA viruses, no RNA stage › Caudovirales › Podoviridae › Picovirinae › unassigned Picovirinae

Virus host

Streptococcus pneumoniae [TaxID: 1313]

Protein attributes

Sequence length	339 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Responsible for the separation of the host daughter cells at the end of cell division and participates in the liberation of progeny bacteriophage into the medium. Strictly depends on the presence of choline-containing cell walls for activity.
Catalytic activity	Hydrolysis of (1->4)-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrins.
Domain	The C-terminal domain comprising the repeats is involved in choline binding.
Sequence similarities	Belongs to the glycosyl hydrolase 25 family. Contains 6 cell wall-binding repeats.

Ontologies

Keywords
Domain	Repeat
Molecular function	Antimicrobial Bacteriolytic enzyme Glycosidase Hydrolase
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological_process	carbohydrate metabolic process Inferred from electronic annotation. Source: InterPro cell wall macromolecule catabolic process Inferred from electronic annotation. Source: InterPro cytolysis Inferred from electronic annotation. Source: UniProtKB-KW defense response to bacterium Inferred from electronic annotation. Source: UniProtKB-KW peptidoglycan catabolic process Inferred from electronic annotation. Source: InterPro
Molecular_function	lysozyme activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 339

339

Lysozyme

PRO_0000208259

Regions

Repeat

200 – 219

20

Cell wall-binding 1

Repeat

220 – 239

20

Cell wall-binding 2

Repeat

241 – 260

20

Cell wall-binding 3

Repeat

261 – 280

20

Cell wall-binding 4

Repeat

281 – 300

20

Cell wall-binding 5

Repeat

303 – 322

20

Cell wall-binding 6

Sites

Active site

10

1

Active site

94

1

Experimental info

Mutagenesis

10

1

D → A, E, H, K or N: Almost complete loss of activity. Ref.3

Mutagenesis

37

1

E → A: 95% loss of activity. Ref.3

Mutagenesis

37

1

E → D: 63% loss of activity. Ref.3

Mutagenesis

37

1

E → K: Almost complete loss of activity. Ref.3

Mutagenesis

37

1

E → Q: 13% loss of activity. Ref.3

Mutagenesis

92

1

D → A: Almost complete loss of activity. Ref.4

Mutagenesis

94

1

E → A or Q: Almost complete loss of activity. Ref.4

Mutagenesis

182

1

D → A: Almost complete loss of activity. Ref.4

Sequence conflict

44

1

P → R in AAA32204. Ref.2

Secondary structure

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339

Helix Strand Turn

Details...

Beta strand

7 – 11

5

Helix

13 – 15

3

Helix

20 – 26

7

Beta strand

30 – 37

8

Turn

38 – 40

3

Helix

46 – 51

6

Beta strand

53 – 61

9

Helix

68 – 80

13

Beta strand

87 – 92

6

Helix

101 – 117

17

Beta strand

120 – 127

8

Helix

128 – 134

7

Helix

137 – 143

7

Beta strand

148 – 151

4

Beta strand

157 – 159

3

Helix

162 – 164

3

Beta strand

171 – 177

7

Beta strand

179 – 188

10

Beta strand

200 – 204

5

Beta strand

209 – 213

5

Beta strand

221 – 226

6

Beta strand

229 – 233

5

Beta strand

242 – 247

6

Beta strand

250 – 254

5

Beta strand

263 – 267

5

Beta strand

270 – 274

5

Beta strand

283 – 287

5

Beta strand

290 – 295

6

Helix

297 – 299

3

Beta strand

302 – 309

8

Beta strand

312 – 316

5

Turn

318 – 320

3

Beta strand

327 – 330

4

Beta strand

335 – 337

3

Sequences

	Sequence		Length	Mass (Da)
	P15057 [UniParc]. Last modified January 31, 2002. Version 2. Checksum: E2947566AC676B05	FASTA	339	39,190
	10 20 30 40 50 60 MVKKNDLFVD VSSHNGYDIT GILEQMGTTN TIIKISESTT YLNPCLSAQV EQSNPIGFYH 70 80 90 100 110 120 FARFGGDVAE AEREAQFFLD NVPMQVKYLV LDYEDDPSGD AQANTNACLR FMQMIADAGY 130 140 150 160 170 180 KPIYYSYKPF THDNVDYQQI LAQFPNSLWI AGYGLNDGTA NFEYFPSMDG IRWWQYSSNP 190 200 210 220 230 240 FDKNIVLLDD EEDDKPKTAG TWKQDSKGWW FRRNNGSFPY NKWEKIGGVW YYFDSKGYCL 250 260 270 280 290 300 TSEWLKDNEK WYYLKDNGAM ATGWVLVGSE WYYMDDSGAM VTGWVKYKNN WYYMTNERGN 310 320 330 MVSNEFIKSG KGWYFMNTNG ELADNPSFTK EPDGLITVA

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Molecular evolution of lytic enzymes of Streptococcus pneumoniae and its bacteriophages." Garcia E., Garcia J.L., Garcia P., Arraras A., Sanchez-Puelles J.M., Lopez R. Proc. Natl. Acad. Sci. U.S.A. 85:914-918(1988) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Analysis of the complete nucleotide sequence and functional organization of the genome of Streptococcus pneumoniae bacteriophage Cp-1." Martin A.C., Lopez R., Garcia P. J. Virol. 70:3678-3687(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]	"Role of Asp-9 and Glu-36 in the active site of the pneumococcal CPL1 lysozyme: an evolutionary perspective of lysozyme mechanism." Sanz J.M., Garcia P., Garcia J.L. Biochemistry 31:8495-8499(1992) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF ASP-10 AND GLU-37.
[4]	"Structural basis for selective recognition of pneumococcal cell wall by modular endolysin from phage Cp-1." Hermoso J.A., Monterroso B., Albert A., Galan B., Ahrazem O., Garcia P., Martinez-Ripoll M., Garcia J.L., Menendez M. Structure 11:1239-1249(2003) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF NATIVE PROTEIN AND COMPLEX WITH CHOLINE, MUTAGENESIS OF ASP-92; GLU-94 AND ASP-182.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

J03586 Genomic DNA. Translation: AAA32204.1.
Z47794 Genomic DNA. Translation: CAA87744.1.

PIR

MUBPCP. A31086.

RefSeq

NP_044837.1. NC_001825.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1H09	X-ray	2.10	A	2-339	[»]
1OBA	X-ray	2.45	A	1-339	[»]
2IXU	X-ray	2.28	A	1-339	[»]
2IXV	X-ray	1.96	A	1-339	[»]
2J8F	X-ray	1.84	A	1-339	[»]
2J8G	X-ray	1.69	A	1-339	[»]

ProteinModelPortal

P15057.

SMR

P15057. Positions 2-339.

ModBase

Search...

Protein family/group databases

CAZy

GH25. Glycoside Hydrolase Family 25.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

1261221.

Phylogenomic databases

ProtClustDB

CLSP2513893.

Family and domain databases

Gene3D

3.20.20.80. 1 hit.

InterPro

IPR018337. Cell_wall/Cho-bd_repeat.
IPR002053. Glyco_hydro_25.
IPR008270. Glyco_hydro_25_AS.
IPR013781. Glyco_hydro_catalytic_dom.
IPR018077. Glyco_hydro_fam25_subgr.
IPR017853. Glycoside_hydrolase_SF.
[Graphical view]

Pfam

PF01473. CW_binding_1. 5 hits.
PF01183. Glyco_hydro_25. 1 hit.
[Graphical view]

SMART

SM00641. Glyco_25. 1 hit.
[Graphical view]

SUPFAM

SSF51445. Glyco_hydro_cat. 1 hit.

PROSITE

PS51170. CW. 5 hits.
PS00953. GLYCOSYL_HYDROL_F25. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P15057.

Entry information

Entry name

LYS_BPCP1

Accession

Primary (citable) accession number: P15057
Secondary accession number(s): Q38009

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1990
Last sequence update:	January 31, 2002
Last modified:	May 1, 2013
This is version 101 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program