2VO9 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE ENZYMATICALLY ACTIVE DOMAIN OF THE LISTERIA MONOCYTOGENES BACTERIOPHAGE 500 ENDOLYSIN PLY500

Authors :   I. P. Korndoerfer, A. Kanitz, A. Skerra

Date :   09 Feb 08 (Deposition) - 19 Feb 08 (Release) - 05 Jul 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Cell Wall Biogenesis/Degradation, Secreted, Cell Wall, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. P. Korndorfer, A. Kanitz, J. Danzer, M. Zimmer, M. J. Loessner, A. Skerra
Structural Analysis Of The L-Alanoyl-D-Glutamate Endopeptidase Domain Of Listeria Bacteriophage Endolysin Ply500 Reveals A New Member Of The Las Peptidase Family.
Acta Crystallogr. , Sect. D V. 64 644 2008
PubMed-ID: 18560152 | Reference-DOI: 10.1107/S0907444908007890

Molecule 1 - L-ALANYL-D-GLUTAMATE PEPTIDASE
	Chains	:	A, B, C
	EC Number	:	3.4.24.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PEACE500.7
	Expression System Strain	:	JM83
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALYTIC DOMAIN, RESIDUES 1-167
	Organism Scientific	:	BACTERIOPHAGE A500
	Organism Taxid	:	40522
	Synonym	:	EAD500

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 9)

No.	Name	Count	Type	Full Name
1	SO4	6	Ligand/Ion	SULFATE ION
2	ZN	3	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:80 , ASP A:87 , HIS A:133	BINDING SITE FOR RESIDUE ZN A 501
2	AC2	SOFTWARE	ARG A:50 , GLN A:55 , THR A:71 , SER A:78 , HIS A:80 , HOH A:2080 , HOH A:2131 , HOH A:2132	BINDING SITE FOR RESIDUE SO4 A 502
3	AC3	SOFTWARE	TRP A:7 , LYS A:11 , LYS A:96 , HOH A:2085 , HOH A:2133 , LYS B:126 , PHE B:128 , LYS B:129	BINDING SITE FOR RESIDUE SO4 A 503
4	AC4	SOFTWARE	HIS B:80 , ASP B:87 , HIS B:133 , HOH B:2146	BINDING SITE FOR RESIDUE ZN B 501
5	AC5	SOFTWARE	ARG B:50 , GLN B:55 , THR B:71 , SER B:78 , HIS B:80 , HOH B:2092 , HOH B:2147 , HOH B:2148	BINDING SITE FOR RESIDUE SO4 B 502
6	AC6	SOFTWARE	LYS A:126 , PHE A:128 , LYS A:129 , TRP B:7 , LYS B:11 , LYS B:96 , HOH B:2097 , HOH B:2149	BINDING SITE FOR RESIDUE SO4 B 503
7	AC7	SOFTWARE	HIS C:80 , ASP C:87 , HIS C:133	BINDING SITE FOR RESIDUE ZN C 501
8	AC8	SOFTWARE	ARG C:50 , GLN C:55 , THR C:71 , SER C:78 , HIS C:80 , HOH C:2048	BINDING SITE FOR RESIDUE SO4 C 502
9	AC9	SOFTWARE	TRP C:7 , LYS C:11 , LYS C:96 , LYS C:126 , SER C:127 , PHE C:128 , LYS C:129 , HOH C:2051 , HOH C:2087	BINDING SITE FOR RESIDUE SO4 C 503

(no "SS Bond" information available for 2VO9)

(no "Cis Peptide Bond" information available for 2VO9)

(no "SAP(SNP)/Variant" information available for 2VO9)

(no "PROSITE Motif" information available for 2VO9)

(no "Exon" information available for 2VO9)

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:149
 aligned with AEPE_BPA50 | Q37979 from UniProtKB/Swiss-Prot  Length:289

    Alignment length:149
                             1                                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139         
           AEPE_BPA50     - -MALTEAWLIEKANRKLNAGGMYKITSDKTRNVIKKMAKEGIYLCVAQGYRSTAEQNALYAQGRTKPGAIVTNAKGGQSNHNYGVAVDLCLYTNDGKDVIWESTTSRWKKVVAAMKAEGFKWGGDWKSFKDYPHFELCDAVSGEKIPAA 148
               SCOP domains -d2vo9a1 A:1-148 L-alanyl-D-glutamate peptidase Ply                                                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhh................hhhhhh.eeeeeee......ee....hhhhhhhhhhhhhh..ee.hhh.......eee..hhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vo9 A   0 AMALTEAWLIEKANRKLNAGGMYKITSDKTRNVIKKMAKEGIYLCVAQGYRSTAEQNALYAQGRTKPGAIVTNAKGGQSNHNYGVAVDLCLYTNDGKDVIWESTTSRWKKVVAAMKAEGFKWGGDWKSFKDYPHFELCDAVSGEKIPAA 148
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139

Chain B from PDB  Type:PROTEIN  Length:149
 aligned with AEPE_BPA50 | Q37979 from UniProtKB/Swiss-Prot  Length:289

    Alignment length:149
                             1                                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139         
           AEPE_BPA50     - -MALTEAWLIEKANRKLNAGGMYKITSDKTRNVIKKMAKEGIYLCVAQGYRSTAEQNALYAQGRTKPGAIVTNAKGGQSNHNYGVAVDLCLYTNDGKDVIWESTTSRWKKVVAAMKAEGFKWGGDWKSFKDYPHFELCDAVSGEKIPAA 148
               SCOP domains d2vo9b_ B: automated matches                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhh................hhhhhh.eeeeeee......ee....hhhhhhhhhhhhhh..ee.hhh.......eee............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vo9 B   0 AMALTEAWLIEKANRKLNAGGMYKITSDKTRNVIKKMAKEGIYLCVAQGYRSTAEQNALYAQGRTKPGAIVTNAKGGQSNHNYGVAVDLCLYTNDGKDVIWESTTSRWKKVVAAMKAEGFKWGGDWKSFKDYPHFELCDAVSGEKIPAA 148
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139

Chain C from PDB  Type:PROTEIN  Length:149
 aligned with AEPE_BPA50 | Q37979 from UniProtKB/Swiss-Prot  Length:289

    Alignment length:149
                             1                                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139         
           AEPE_BPA50     - -MALTEAWLIEKANRKLNAGGMYKITSDKTRNVIKKMAKEGIYLCVAQGYRSTAEQNALYAQGRTKPGAIVTNAKGGQSNHNYGVAVDLCLYTNDGKDVIWESTTSRWKKVVAAMKAEGFKWGGDWKSFKDYPHFELCDAVSGEKIPAA 148
               SCOP domains d2vo9c_ C: automated matches                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------VanY-2vo9C01 C:18-148                                                                                                               Pfam domains (1)
           Pfam domains (2) ------------------VanY-2vo9C02 C:18-148                                                                                                               Pfam domains (2)
           Pfam domains (3) ------------------VanY-2vo9C03 C:18-148                                                                                                               Pfam domains (3)
         Sec.struct. author ....hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhh................hhhhhh.eeeeeee......ee....hhhhhhhhhhhhhh..ee.hhh.......eee............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vo9 C   0 AMALTEAWLIEKANRKLNAGGMYKITSDKTRNVIKKMAKEGIYLCVAQGYRSTAEQNALYAQGRTKPGAIVTNAKGGQSNHNYGVAVDLCLYTNDGKDVIWESTTSRWKKVVAAMKAEGFKWGGDWKSFKDYPHFELCDAVSGEKIPAA 148
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139

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: Hedgehog/DD-peptidase (29)

Superfamily: Hedgehog/DD-peptidase (29)

Family: VanY-like (2)

Protein domain: automated matches (1)

Bacteriophage a500 [TaxId: 40522] (1)

1a	d2vo9b_	B:
1b	d2vo9c_	C:

Protein domain: L-alanyl-D-glutamate peptidase Ply (1)

Listeria phage A500 [TaxId: 40522] (1)

d2vo9a1

A:1-148

(no "CATH Domain" information available for 2VO9)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_MD (20)

Family: VanY (1)

Listeria phage A500 (Bacteriophage A500) (1)

1a	VanY-2vo9C01	C:18-148
1b	VanY-2vo9C02	C:18-148
1c	VanY-2vo9C03	C:18-148

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (AEPE_BPA50 | Q37979)

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.
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.
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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Biological Units
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Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 9)

Sites (9, 9)

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