1H8G - JenaLib

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Title :   C-TERMINAL DOMAIN OF THE MAJOR AUTOLYSIN (C-LYTA) FROM STREPTOCOCCUS PNEUMONIAE

Authors :   C. Fernandez-Tornero, E. Garcia, R. Lopez, G. Gimenez-Gallego, A. Romero

Date :   06 Feb 01 (Deposition) - 31 Jan 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Choline-Binding Domain, Cell Wall Attachment (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Fernandez-Tornero, R. Lopez, E. Garcia, G. Gimenez-Gallego, A. Romero
A Novel Solenoid Fold In The Cell Wall Anchoring Domain Of The Pneumococcal Virulence Factor Lyta
Nat. Struct. Biol. V. 8 1020 2001
PubMed-ID: 11694890 | Reference-DOI: 10.1038/NSB724
(for further references see the PDB file header)

Molecule 1 - MAJOR AUTOLYSIN
	Cellular Location	:	EXTRACELLULAR
	Chains	:	A, B
	EC Number	:	3.5.1.28
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cellular Location	:	CYTOPLASM
	Expression System Plasmid	:	PCE17
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	CHOLINE-BINDING DOMAIN
	Gene	:	LYTA
	Organism Scientific	:	STREPTOCOCCUS PNEUMONIAE
	Organism Taxid	:	1313
	Synonym	:	C-LYTA, CELL WALL BINDING DOMAIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 12)

No.	Name	Count	Type	Full Name
1	CHT	6	Ligand/Ion	CHOLINE ION
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 24)

No.	Name	Count	Type	Full Name
1	CHT	12	Ligand/Ion	CHOLINE ION
2	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:261 , TYR A:293	BINDING SITE FOR RESIDUE CHT A 401
2	AC2	SOFTWARE	TRP A:248 , TYR A:269 , ASP A:298	BINDING SITE FOR RESIDUE CHT A 402
3	AC3	SOFTWARE	TYR A:229	BINDING SITE FOR RESIDUE CHT A 403
4	AC4	SOFTWARE	THR A:224 , ASP A:312 , LYS B:242 , TRP B:261 , LEU B:301	BINDING SITE FOR RESIDUE CHT B 404
5	AC5	SOFTWARE	LYS A:274 , GLU A:275 , TYR B:249	BINDING SITE FOR RESIDUE CHT B 405
6	AC6	SOFTWARE	TYR B:229	BINDING SITE FOR RESIDUE CHT B 406

(no "SS Bond" information available for 1H8G)

(no "Cis Peptide Bond" information available for 1H8G)

(no "SAP(SNP)/Variant" information available for 1H8G)

Asymmetric Unit (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CW	PS51170	Cell wall-binding repeat profile.	ALYS_STRPN	175-194 196-215 217-237 238-257 258-277 280-301	6	- - - A:238-257 B:238-257 A:258-277 B:258-277 A:280-301 B:280-301

Biological Unit 1 (1, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CW	PS51170	Cell wall-binding repeat profile.	ALYS_STRPN	175-194 196-215 217-237 238-257 258-277 280-301	12	- - - A:238-257 B:238-257 A:258-277 B:258-277 A:280-301 B:280-301

(no "Exon" information available for 1H8G)

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
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Chain A from PDB  Type:PROTEIN  Length:95
 aligned with ALYS_STRPN | P06653 from UniProtKB/Swiss-Prot  Length:318

    Alignment length:95
                                   233       243       253       263       273       283       293       303       313     
           ALYS_STRPN   224 TDGNWYWFDNSGEMATGWKKIADKWYYFNEEGAMKTGWVKYKDTWYYLDAKEGAMVSNAFIQSADGTGWYYLKPDGTLADKPEFTVEPDGLITVK 318
               SCOP domains d1h8ga_ A: Choline binding domain of autolysin C-LytA                                           SCOP domains
               CATH domains 1h8gA00 A:224-318 Cholin Binding                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee........eeeee..eeeee........eeeee..eeeee..........eeeee....eeeee..........eeeee...eeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE CW  PDB: -    CW  PDB: A:238-257  CW  PDB: A:258-277  --CW  PDB: A:280-301    ----------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 1h8g A 224 TDGNWYWFDNSGEmATGWKKIADKWYYFNEEGAmKTGWVKYKDTWYYLDAKEGAmVSNAFIQSADGTGWYYLKPDGTLADRPEFTVEPDGLITVK 318
                                   233   |   243       253   |   263       273    |  283       293       303       313     
                                       237-MSE             257-MSE              278-MSE

Chain B from PDB  Type:PROTEIN  Length:94
 aligned with ALYS_STRPN | P06653 from UniProtKB/Swiss-Prot  Length:318

    Alignment length:94
                                   234       244       254       264       274       284       294       304       314    
           ALYS_STRPN   225 DGNWYWFDNSGEMATGWKKIADKWYYFNEEGAMKTGWVKYKDTWYYLDAKEGAMVSNAFIQSADGTGWYYLKPDGTLADKPEFTVEPDGLITVK 318
               SCOP domains d1h8gb_ B: Choline binding domain of autolysin C-LytA                                          SCOP domains
               CATH domains 1h8gB00 B:225-318 Cholin Binding                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee........eeeee..eeeee........eeeee..eeeee..........eeeee....eeeee..........eeeee...eeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE CW  PDB: -   CW  PDB: B:238-257  CW  PDB: B:258-277  --CW  PDB: B:280-301    ----------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 1h8g B 225 DGNWYWFDNSGEmATGWKKIADKWYYFNEEGAmKTGWVKYKDTWYYLDAKEGAmVSNAFIQSADGTGWYYLKPDGTLADRPEFTVEPDGLITVK 318
                                   234  |    244       254  |    264       274   |   284       294       304       314    
                                      237-MSE             257-MSE              278-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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All beta proteins (24004)

Fold: beta-hairpin stack (12)

Superfamily: Cell wall binding repeat (12)

Family: Cell wall binding repeat (12)

Protein domain: Choline binding domain of autolysin C-LytA (4)

Pneumococcus (Streptococcus pneumoniae) [TaxId: 1313] (4)

1a	d1h8ga_	A:
1b	d1h8gb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Ribbon (789)

Topology: left handed beta-beta-3-solenoid (10)

Homologous Superfamily: Cholin Binding (10)

Streptococcus pneumoniae. Organism_taxid: 1313. (2)

1a	1h8gA00	A:224-318
1b	1h8gB00	B:225-318

(no "Pfam Domain" information available for 1H8G)

Asymmetric Unit(hide GO term definitions)

Chain A,B (ALYS_STRPN | P06653)

molecular function
	GO:0008745	N-acetylmuramoyl-L-alanine amidase activity	Catalysis of the hydrolysis of the link between N-acetylmuramoyl residues and L-amino acid residues in certain bacterial cell-wall glycopeptides.
	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.
biological process
	GO:0071555	cell wall organization	A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
	GO:0030420	establishment of competence for transformation	The process in which a naturally transformable bacterium acquires the ability to take up exogenous DNA. This term should be applied only to naturally transformable bacteria, and should not be used in the context of artificially induced bacterial transformation.
	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:0030435	sporulation resulting in formation of a cellular spore	The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Asymmetric Unit
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Biological Unit
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	1h8g
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	3.5.1.28
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	ALYS_STRPN \| P06653	:	1gvm 1hcx 2bml 4ivv 4x36 5ctv

(no "Related Entries Specified in the PDB File" available for 1H8G)

Description

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Ligands, Modified Residues, Ions (2, 12)

Sites (6, 6)

SS Bonds (0, 0)

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