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(-) Description

Title :  CATALYTIC DOMAIN OF CD27L ENDOLYSIN TARGETING CLOSTRIDIA DIFFICILE
 
Authors :  M. J. Mayer, V. Garefaliki, R. Spoerl, A. Narbad, R. Meijers
Date :  12 Jan 11  (Deposition) - 28 Dec 11  (Release) - 28 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Amidase A/B Fold, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Mayer, V. Garefalaki, R. Spoerl, A. Narbad, R. Meijers
Structure-Based Modification Of A Clostridium Difficile-Targeting Endolysin Affects Activity And Host Range.
J. Bacteriol. V. 193 5477 2011
PubMed-ID: 21803993  |  Reference-DOI: 10.1128/JB.00439-11

(-) Compounds

Molecule 1 - ENDOLYSIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21 DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN
    Organism Scientific: CLOSTRIDIUM PHAGE PHICD27
    Organism Taxid: 559189

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 18)

Asymmetric Unit (2, 18)
No.NameCountTypeFull Name
1PO414Ligand/IonPHOSPHATE ION
2ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1PO43Ligand/IonPHOSPHATE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1PO44Ligand/IonPHOSPHATE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 3)
No.NameCountTypeFull Name
1PO43Ligand/IonPHOSPHATE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 4 (1, 4)
No.NameCountTypeFull Name
1PO44Ligand/IonPHOSPHATE ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:9 , GLU A:26 , HIS A:84 , PO4 A:181 , HOH A:1468 , HOH A:1469BINDING SITE FOR RESIDUE ZN A 180
02AC2SOFTWAREGLU A:26 , HIS A:84 , LEU A:85 , ASN A:86 , GLU A:144 , ZN A:180 , HOH A:1468 , HOH A:1469BINDING SITE FOR RESIDUE PO4 A 181
03AC3SOFTWAREARG A:42 , ASP A:49 , VAL A:50 , LYS A:93 , LYS A:120 , HOH A:531 , HOH A:619 , HOH A:993 , HOH A:1162BINDING SITE FOR RESIDUE PO4 A 182
04AC4SOFTWAREARG A:42 , LYS A:47 , VAL A:48 , LYS A:120 , HOH A:213 , HOH A:220 , HOH A:619 , HOH A:912BINDING SITE FOR RESIDUE PO4 A 183
05AC5SOFTWAREHIS B:9 , GLU B:26 , HIS B:84 , PO4 B:181 , HOH B:909 , HOH B:1470BINDING SITE FOR RESIDUE ZN B 180
06AC6SOFTWAREGLU B:26 , HIS B:84 , LEU B:85 , ASN B:86 , ALA B:87 , GLU B:144 , ZN B:180 , HOH B:286 , HOH B:909 , HOH B:990 , HOH B:1470BINDING SITE FOR RESIDUE PO4 B 181
07AC7SOFTWARESER B:101 , LYS B:103 , THR B:139 , HOH B:223 , HOH B:773 , HOH B:1308 , HOH B:1372 , LYS C:137BINDING SITE FOR RESIDUE PO4 B 182
08AC8SOFTWAREARG B:42 , LYS B:47 , VAL B:48 , LYS B:120 , HOH B:216 , HOH B:1035 , HOH B:1148BINDING SITE FOR RESIDUE PO4 B 183
09AC9SOFTWAREARG B:42 , ASP B:49 , VAL B:50 , LYS B:93 , LYS B:120 , HOH B:998 , HOH B:1139 , HOH B:1161BINDING SITE FOR RESIDUE PO4 B 184
10BC1SOFTWAREHIS C:9 , GLU C:26 , HIS C:84 , PO4 C:181 , HOH C:1471BINDING SITE FOR RESIDUE ZN C 180
11BC2SOFTWAREHIS C:9 , GLU C:26 , HIS C:84 , LEU C:85 , ASN C:86 , GLU C:144 , ZN C:180 , HOH C:1471BINDING SITE FOR RESIDUE PO4 C 181
12BC3SOFTWAREARG C:42 , ASP C:49 , VAL C:50 , LYS C:93 , LYS C:120 , HOH C:227 , HOH C:705 , HOH C:1121 , HOH C:1228BINDING SITE FOR RESIDUE PO4 C 182
13BC4SOFTWAREARG C:42 , LYS C:47 , VAL C:48 , LYS C:120 , HOH C:1122 , HOH C:1374BINDING SITE FOR RESIDUE PO4 C 183
14BC5SOFTWAREHIS D:9 , GLU D:26 , HIS D:84 , PO4 D:181 , HOH D:1472BINDING SITE FOR RESIDUE ZN D 180
15BC6SOFTWAREHIS D:9 , GLU D:26 , HIS D:84 , LEU D:85 , GLU D:144 , ZN D:180 , HOH D:248 , HOH D:1198 , HOH D:1472BINDING SITE FOR RESIDUE PO4 D 181
16BC7SOFTWARELYS A:137 , SER D:101 , LYS D:103 , THR D:139 , HOH D:187 , HOH D:501 , HOH D:1074 , HOH D:1319BINDING SITE FOR RESIDUE PO4 D 182
17BC8SOFTWAREARG D:42 , LYS D:47 , VAL D:48 , LYS D:120 , HOH D:211 , HOH D:1128BINDING SITE FOR RESIDUE PO4 D 183
18BC9SOFTWARESER A:101 , LYS A:103 , THR A:139 , LYS D:137 , HOH D:576 , HOH D:702 , HOH D:1406BINDING SITE FOR RESIDUE PO4 D 184

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QAY)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3QAY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QAY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3QAY)

(-) Exons   (0, 0)

(no "Exon" information available for 3QAY)

(-) Sequences/Alignments

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:180
 aligned with B6SBV8_9CAUD | B6SBV8 from UniProtKB/TrEMBL  Length:270

    Alignment length:180
                             1                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179
         B6SBV8_9CAUD     - -MKICITVGHSILKSGACTSADGVVNEYQYNKSLAPVLADTFRKEGHKVDVIICPEKQFKTKNEEKSYKIPRVNSGGYDLLIELHLNASNGQGKGSEVLYYSNKGLEYATRICDKLGTVFKNRGAKLDKRLYILNSSKPTAVLIESFFCDNKEDYDKAKKLGHEGIAKLIVEGVLNKNIN 179
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.................hhhhhhhhhhhhhhhhhhhh..eeeee..........hhhhhhhhhhhhhh...eeeeeeee........eeeee.hhhhhhhhhhhhhhhh....eeeeee...hhhhhh...eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3qay A   0 HMKICITVGHSILKSGACTSADGVVNEYQYNKSLAPVLADTFRKEGHKVDVIICPEKQFKTKNEEKSYKIPRVNSGGYDLLIELHLNASNGQGKGSEVLYYSNKGLEYATRICDKLGTVFKNRGAKLDKRLYILNSSKPTAVLIESFFCDNKEDYDKAKKLGHEGIAKLIVEGVLNKNIN 179
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179


Chain B from PDB  Type:PROTEIN  Length:180
 aligned with B6SBV8_9CAUD | B6SBV8 from UniProtKB/TrEMBL  Length:270

    Alignment length:180
                             1                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179
         B6SBV8_9CAUD     - -MKICITVGHSILKSGACTSADGVVNEYQYNKSLAPVLADTFRKEGHKVDVIICPEKQFKTKNEEKSYKIPRVNSGGYDLLIELHLNASNGQGKGSEVLYYSNKGLEYATRICDKLGTVFKNRGAKLDKRLYILNSSKPTAVLIESFFCDNKEDYDKAKKLGHEGIAKLIVEGVLNKNIN 179
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.................hhhhhhhhhhhhhhhhhhhh..eeeee.........hhhhhhhhhhhhhhh...eeeeeeee........eeeee.hhhhhhhhhhhhhhhh....eeeeee...hhhhhh...eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3qay B   0 HMKICITVGHSILKSGACTSADGVVNEYQYNKSLAPVLADTFRKEGHKVDVIICPEKQFKTKNEEKSYKIPRVNSGGYDLLIELHLNASNGQGKGSEVLYYSNKGLEYATRICDKLGTVFKNRGAKLDKRLYILNSSKPTAVLIESFFCDNKEDYDKAKKLGHEGIAKLIVEGVLNKNIN 179
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179


Chain C from PDB  Type:PROTEIN  Length:180
 aligned with B6SBV8_9CAUD | B6SBV8 from UniProtKB/TrEMBL  Length:270

    Alignment length:180
                             1                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179
         B6SBV8_9CAUD     - -MKICITVGHSILKSGACTSADGVVNEYQYNKSLAPVLADTFRKEGHKVDVIICPEKQFKTKNEEKSYKIPRVNSGGYDLLIELHLNASNGQGKGSEVLYYSNKGLEYATRICDKLGTVFKNRGAKLDKRLYILNSSKPTAVLIESFFCDNKEDYDKAKKLGHEGIAKLIVEGVLNKNIN 179
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.................hhhhhhhhhhhhhhhhhhhh..eeeee.........hhhhhhhhhhhhh.....eeeeeeee........eeeee.hhhhhhhhhhhhhhhh....eeeeee...hhhhhh....eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3qay C   0 HMKICITVGHSILKSGACTSADGVVNEYQYNKSLAPVLADTFRKEGHKVDVIICPEKQFKTKNEEKSYKIPRVNSGGYDLLIELHLNASNGQGKGSEVLYYSNKGLEYATRICDKLGTVFKNRGAKLDKRLYILNSSKPTAVLIESFFCDNKEDYDKAKKLGHEGIAKLIVEGVLNKNIN 179
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179


Chain D from PDB  Type:PROTEIN  Length:180
 aligned with B6SBV8_9CAUD | B6SBV8 from UniProtKB/TrEMBL  Length:270

    Alignment length:180
                             1                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179
         B6SBV8_9CAUD     - -MKICITVGHSILKSGACTSADGVVNEYQYNKSLAPVLADTFRKEGHKVDVIICPEKQFKTKNEEKSYKIPRVNSGGYDLLIELHLNASNGQGKGSEVLYYSNKGLEYATRICDKLGTVFKNRGAKLDKRLYILNSSKPTAVLIESFFCDNKEDYDKAKKLGHEGIAKLIVEGVLNKNIN 179
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.................hhhhhhhhhhhhhhhhhhhh..eeeee.........hhhhhhhhhhhhhhh...eeeeeeee........eeeee.hhhhhhhhhhhhhhhh....eeeeee...hhhhhh...eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3qay D   0 HMKICITVGHSILKSGACTSADGVVNEYQYNKSLAPVLADTFRKEGHKVDVIICPEKQFKTKNEEKSYKIPRVNSGGYDLLIELHLNASNGQGKGSEVLYYSNKGLEYATRICDKLGTVFKNRGAKLDKRLYILNSSKPTAVLIESFFCDNKEDYDKAKKLGHEGIAKLIVEGVLNKNIN 179
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179
   Legend:   → Mismatch (orange background)
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  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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3QAY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QAY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3QAY)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (B6SBV8_9CAUD | B6SBV8)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    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.

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  3qay
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 Related Entries

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        B6SBV8_9CAUD | B6SBV8: 4cu5

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