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(-) Description

Title :  CRYSTAL STRUCTURE OF STAPHYLOCOCCUS PEPTIDOGLYCAN HYDROLASE AMIE
 
Authors :  S. Zoll, T. Stehle
Date :  07 Jan 10  (Deposition) - 23 Mar 10  (Release) - 31 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Amidase, Atle, Autolysin, Peptidoglycan Hydrolase, Cell Wall Biogenesis/Degradation, Multifunctional Enzyme, Secreted, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Zoll, B. Patzold, M. Schlag, F. Gotz, H. Kalbacher, T. Stehle
Structural Basis Of Cell Wall Cleavage By A Staphylococcal Autolysin
Plos Pathog. V. 6 E1000 2010
PubMed-ID: 20300605  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1000807

(-) Compounds

Molecule 1 - BIFUNCTIONAL AUTOLYSIN
    Chains: A, B
    EC Number: 3.5.1.28
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX 4T-3
    Expression System Strain: ROSETTA 2 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 303-515
    Gene: ATLE
    Organism Scientific: STAPHYLOCOCCUS EPIDERMIDIS
    Organism Taxid: 1282
    Strain: O-47
    Synonym: PEPTIDOGLYCAN HYDROLASE AMIE, ATLE, N- ACETYLMURAMOYL-L-ALANINE AMIDASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 20)

Asymmetric Unit (4, 20)
No.NameCountTypeFull Name
1BU13Ligand/Ion1,4-BUTANEDIOL
2CL1Ligand/IonCHLORIDE ION
3IMD2Ligand/IonIMIDAZOLE
4ZN14Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1BU11Ligand/Ion1,4-BUTANEDIOL
2CL-1Ligand/IonCHLORIDE ION
3IMD1Ligand/IonIMIDAZOLE
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1BU12Ligand/Ion1,4-BUTANEDIOL
2CL-1Ligand/IonCHLORIDE ION
3IMD1Ligand/IonIMIDAZOLE
4ZN-1Ligand/IonZINC ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:176 , ASP B:61 , HIS B:177 , ASP B:179 , ZN B:216 , ZN B:218 , BU1 B:222 , CL B:224BINDING SITE FOR RESIDUE IMD A 214
02AC2SOFTWAREHIS A:60 , HIS A:165 , ASP A:179 , ZN A:216 , HOH A:372BINDING SITE FOR RESIDUE ZN A 215
03AC3SOFTWAREHIS A:177 , ASP A:179 , ZN A:215 , HOH A:372 , IMD B:214 , BU1 B:222BINDING SITE FOR RESIDUE ZN A 216
04AC4SOFTWAREASP A:152 , HOH A:375 , HOH A:376 , HOH A:377 , HOH A:378 , HOH A:379BINDING SITE FOR RESIDUE ZN A 217
05AC5SOFTWAREGLU A:36 , GLU B:96 , HOH B:274 , HOH B:277BINDING SITE FOR RESIDUE ZN A 218
06AC6SOFTWAREGLU A:96 , HOH A:454 , HOH A:457 , GLU B:36BINDING SITE FOR RESIDUE ZN A 219
07AC7SOFTWAREASP A:65 , HIS A:124 , ZN A:221 , HOH A:367BINDING SITE FOR RESIDUE ZN A 220
08AC8SOFTWAREHIS A:124 , ZN A:220BINDING SITE FOR RESIDUE ZN A 221
09AC9SOFTWARESER A:67 , GLY A:71 , GLU A:72 , PHE A:75 , HOH A:419 , HOH A:438 , ASN B:82BINDING SITE FOR RESIDUE BU1 A 222
10BC1SOFTWAREASP A:61 , HIS A:177 , ASP A:179 , ZN A:216 , ASP B:176 , ZN B:217 , BU1 B:222 , CL B:224BINDING SITE FOR RESIDUE IMD B 214
11BC2SOFTWAREHIS B:60 , HIS B:165 , ASP B:179 , ZN B:216 , HOH B:312BINDING SITE FOR RESIDUE ZN B 215
12BC3SOFTWAREIMD A:214 , HIS B:177 , ASP B:179 , ZN B:215 , BU1 B:222 , HOH B:312BINDING SITE FOR RESIDUE ZN B 216
13BC4SOFTWAREASP A:61 , THR A:62 , HOH A:374 , ASP B:176 , IMD B:214BINDING SITE FOR RESIDUE ZN B 217
14BC5SOFTWAREASP A:176 , IMD A:214 , ASP B:61 , THR B:62 , HOH B:314BINDING SITE FOR RESIDUE ZN B 218
15BC6SOFTWAREASP B:152 , HOH B:315 , HOH B:316 , HOH B:317 , HOH B:318 , HOH B:319BINDING SITE FOR RESIDUE ZN B 219
16BC7SOFTWAREASP B:65 , HIS B:124 , ZN B:221BINDING SITE FOR RESIDUE ZN B 220
17BC8SOFTWAREHIS B:124 , ZN B:220BINDING SITE FOR RESIDUE ZN B 221
18BC9SOFTWAREALA A:63 , HIS A:177 , IMD A:214 , ZN A:216 , ALA B:63 , HIS B:177 , IMD B:214 , ZN B:216 , HOH B:312BINDING SITE FOR RESIDUE BU1 B 222
19CC1SOFTWAREASN A:82 , HOH A:250 , HOH A:343 , SER B:67 , GLU B:72 , PHE B:75 , HOH B:341BINDING SITE FOR RESIDUE BU1 B 223
20CC2SOFTWAREALA A:178 , IMD A:214 , ALA B:178 , IMD B:214BINDING SITE FOR RESIDUE CL B 224

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asp A:179 -Pro A:180
2Asp B:179 -Pro B:180

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3LAT)

(-) 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:207
 aligned with ATL_STAEP | O33635 from UniProtKB/Swiss-Prot  Length:1335

    Alignment length:207
                                   318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       
            ATL_STAEP   309 SSLPKYTPKVNSSINNYIRKKNMKAPRIEEDYTSYFPKYGYRNGVGRPEGIVVHDTANDNSTIDGEIAFMKRNYTNAFVHAFVDGNRIIETAPTDYLSWGAGPYGNQRFINVEIVHTHDYDSFARSMNNYADYAATQLQYYNLKPDSAENDGRGTVWTHAAISNFLGGTDHADPHQYLRSHNYSYAELYDLIYEKYLIKTKQVAPWG 515
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhh......eee...................eeeeee......hhhhhhhhhhhh.......eee....eee..........hhhhhhh.eeeeee....hhhhhhhhhhhhhhhhhhhhhhh..............eeehhhhhhhh.......hhhhhhhh..hhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lat A   7 SSLPKYTPKVNSSINNYIRKKNMKAPRIEEDYTSYFPKYGYRNGVGRPEGIVVHDTANDNSTIDGEIAFMKRNYTNAFVHAFVDGNRIIETAPTDYLSWGAGPYGNQRFINVEIVHTHDYDSFARSMNNYADYAATQLQYYNLKPDSAENDGRGTVWTHAAISNFLGGTDHADPHQYLRSHNYSYAELYDLIYEKYLIKTKQVAPWG 213
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       


Chain B from PDB  Type:PROTEIN  Length:207
 aligned with ATL_STAEP | O33635 from UniProtKB/Swiss-Prot  Length:1335

    Alignment length:207
                                   318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       
            ATL_STAEP   309 SSLPKYTPKVNSSINNYIRKKNMKAPRIEEDYTSYFPKYGYRNGVGRPEGIVVHDTANDNSTIDGEIAFMKRNYTNAFVHAFVDGNRIIETAPTDYLSWGAGPYGNQRFINVEIVHTHDYDSFARSMNNYADYAATQLQYYNLKPDSAENDGRGTVWTHAAISNFLGGTDHADPHQYLRSHNYSYAELYDLIYEKYLIKTKQVAPWG 515
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------Amidase_2-3latB01 B:46-183                                                                                                                ------------------------------ Pfam domains (1)
           Pfam domains (2) ---------------------------------------Amidase_2-3latB02 B:46-183                                                                                                                ------------------------------ Pfam domains (2)
         Sec.struct. author ...........hhhhhhhhhh......eee...................eeeeee......hhhhhhhhhhhh.......eee....eee..........hhhhhhh.eeeeee....hhhhhhhhhhhhhhhhhhhhhhh..............eeehhhhhhhh.......hhhhhhhh..hhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lat B   7 SSLPKYTPKVNSSINNYIRKKNMKAPRIEEDYTSYFPKYGYRNGVGRPEGIVVHDTANDNSTIDGEIAFMKRNYTNAFVHAFVDGNRIIETAPTDYLSWGAGPYGNQRFINVEIVHTHDYDSFARSMNNYADYAATQLQYYNLKPDSAENDGRGTVWTHAAISNFLGGTDHADPHQYLRSHNYSYAELYDLIYEKYLIKTKQVAPWG 213
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Amidase_2] (23)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ATL_STAEP | O33635)
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:0004040    amidase activity    Catalysis of the reaction: a monocarboxylic acid amide + H2O = a monocarboxylate + NH3.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0033925    mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity    Catalysis of the endohydrolysis of the N,N'-diacetylchitobiosyl unit in high-mannose glycopeptides and glycoproteins containing the -[Man(GlcNAc)2]Asn-structure. One N-acetyl-D-glucosamine residue remains attached to the protein; the rest of the oligosaccharide is released intact.
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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    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.
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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        ATL_STAEP | O33635: 4epc

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