1R77 - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE CELL WALL TARGETING DOMAIN OF PEPTIDYLGLYCAN HYDROLASE ALE-1

Authors :   J. Z. Lu, T. Fujiwara, H. Komatsuzawa, M. Sugai, J. Sakon

Date :   20 Oct 03 (Deposition) - 12 Apr 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

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

Keywords :   Sh3B Domain, Cell Wall Targeting Domain, Lysostaphin, Peptidoglycan Hydrolase, Glycylglycine Endopeptidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Z. Lu, T. Fujiwara, H. Komatsuzawa, M. Sugai, J. Sakon
Cell Wall-Targeting Domain Of Glycylglycine Endopeptidase Distinguishes Among Peptidoglycan Cross-Bridges.
J. Biol. Chem. V. 281 549 2006
PubMed-ID: 16257954 | Reference-DOI: 10.1074/JBC.M509691200
(for further references see the PDB file header)

Molecule 1 - CELL WALL TARGETING DOMAIN OF GLYCYLGLYCINE ENDOPEPTIDASE ALE-1
	Chains	:	A, B
	EC Number	:	3.4.24.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTF479
	Expression System Taxid	:	562
	Fragment	:	CELL WALL TARGETING DOMAIN
	Mutation	:	YES
	Organism Scientific	:	STAPHYLOCOCCUS CAPITIS
	Organism Taxid	:	29388
	Strain	:	EPK1

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1R77)

(no "Site" information available for 1R77)

(no "SS Bond" information available for 1R77)

(no "Cis Peptide Bond" information available for 1R77)

(no "SAP(SNP)/Variant" information available for 1R77)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SH3B	PS51781	SH3b domain profile.	ALE1_STACP	282-350	2	A:282-350 B:282-350

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SH3B	PS51781	SH3b domain profile.	ALE1_STACP	282-350	1	A:282-350 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SH3B	PS51781	SH3b domain profile.	ALE1_STACP	282-350	1	- B:282-350

(no "Exon" information available for 1R77)

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:99
 aligned with ALE1_STACP | O05156 from UniProtKB/Swiss-Prot  Length:362

    Alignment length:173
                                   199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359   
           ALE1_STACP   190 NDGVHRQWYMHLSKFNVKVGDRVKAGQIIGWSGSTGYSTAPHLHFQRMTNSFSNNTAQDPMPFLKSAGYGSNSTSSSNNNGYKTNKYGTLYKSESASFTANTDIITRLTGPFRSMPQSGVLRKGLTIKYDEVMKQDGHVWVGYNTNSGKRVYLPVRTWNESTGELGPLWGTIK 362
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hh------------------hhh..--------------------------------------------------------.ee.....eeeeeeeeeee...eeee.........eeeee....eeeeeeeeee..eeeeeee.....eeeeeeee............eeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------SH3B  PDB: A:282-350 UniProt: 282-350                                ------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r77 A 264 DD------------------DKVKL--------------------------------------------------------YKTNKYGTLYKSESASFTANTDIITRLTGPFRSMPQSGVLRKGLTIKYDEVMKQDGHVWVGYNTNSGKRVYLPVRTWNESTGELGPLWGTIK 362
                             |       -         -|   |    -         -         -         -         -         - |     279       289       299       309       319       329       339       349       359   
                             |                266 270                                                      271                                                                                           
                           265

Chain B from PDB  Type:PROTEIN  Length:103
 aligned with ALE1_STACP | O05156 from UniProtKB/Swiss-Prot  Length:362

    Alignment length:232
                                   140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360  
           ALE1_STACP   131 NYKKGYGYGPYPLGINGGNHYGVDFFMNVGTPVRAISDGKIVEAGWTNYGGGNEIGLVENDGVHRQWYMHLSKFNVKVGDRVKAGQIIGWSGSTGYSTAPHLHFQRMTNSFSNNTAQDPMPFLKSAGYGSNSTSSSNNNGYKTNKYGTLYKSESASFTANTDIITRLTGPFRSMPQSGVLRKGLTIKYDEVMKQDGHVWVGYNTNSGKRVYLPVRTWNESTGELGPLWGTIK 362
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------------------------------------------------SH3_5-1r77B01 B:279-344                                           ------------------ Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------------------------------------------SH3_5-1r77B02 B:279-344                                           ------------------ Pfam domains (2)
         Sec.struct. author ...-------------------------------------------------------.hh------------------hhh..--------------------------------------------------------.ee.....eeeeeeeeeee...eeee.........eeeee....eeeeeeeeee..eeeeeee.....eeeeeeee............eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------SH3B  PDB: B:282-350 UniProt: 282-350                                ------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r77 B 260 DYK-------------------------------------------------------DDD------------------DKVKL--------------------------------------------------------YKTNKYGTLYKSESASFTANTDIITRLTGPFRSMPQSGVLRKGLTIKYDEVMKQDGHVWVGYNTNSGKRVYLPVRTWNESTGELGPLWGTIK 362
                              |      -         -         -         -         -       264|        -       266   |     -         -         -         -         -         -|      280       290       300       310       320       330       340       350       360  
                            262                                                     263 |                266 270                                                      271                                                                                           
                                                                                      265

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 '\|'

(no "SCOP Domain" information available for 1R77)

(no "CATH Domain" information available for 1R77)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: SH3 (175)

Family: SH3_5 (1)

Staphylococcus capitis (1)

1a	SH3_5-1r77B01	B:279-344
1b	SH3_5-1r77B02	B:279-344

Asymmetric Unit(hide GO term definitions)

Chain A,B (ALE1_STACP | O05156)

molecular function
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008237	metallopeptidase activity	Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
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:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
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.

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	1r77
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