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(-) Description

Title :  TRUNCATED S. AUREUS LYTM, P41 CRYSTAL FORM
 
Authors :  M. Firczuk, A. Mucha, M. Bochtler
Date :  15 Sep 05  (Deposition) - 10 Jan 06  (Release) - 17 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Lytm, Lysostaphin, Peptidoglycan Amidase, Peptidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Firczuk, A. Mucha, M. Bochtler
Crystal Structures Of Active Lytm.
J. Mol. Biol. V. 354 578 2005
PubMed-ID: 16269153  |  Reference-DOI: 10.1016/J.JMB.2005.09.082
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLYCYL-GLYCINE ENDOPEPTIDASE LYTM
    Chains: A, B
    EC Number: 3.4.24.75
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: LYTM
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Synonym: AUTOLYSIN LYTM

 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  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1TLA2Ligand/IonL(+)-TARTARIC ACID
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1TLA1Ligand/IonL(+)-TARTARIC ACID
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1TLA1Ligand/IonL(+)-TARTARIC ACID
2ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC2SOFTWAREHIS B:210 , ASP B:214 , HIS B:293 , TLA B:500BINDING SITE FOR RESIDUE ZN B 401
2AC3SOFTWAREHIS A:210 , ASP A:214 , HIS A:260 , ASN A:286 , SER A:287 , THR A:288 , HIS A:291 , HIS A:293 , HOH A:518 , HOH A:544 , HOH A:576 , HOH A:581 , HOH A:631BINDING SITE FOR RESIDUE TLA A 501
3AC4SOFTWARETYR B:204 , HIS B:210 , ASP B:214 , HIS B:260 , ASN B:286 , SER B:287 , THR B:288 , HIS B:291 , HIS B:293 , ZN B:401 , HOH B:529 , HOH B:540 , HOH B:544 , HOH B:549BINDING SITE FOR RESIDUE TLA B 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2B13)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2B13)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2B13)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2B13)

(-) Exons   (0, 0)

(no "Exon" information available for 2B13)

(-) 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:131
 aligned with LYTM_STAA8 | O33599 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:131
                                   194       204       214       224       234       244       254       264       274       284       294       304       314 
           LYTM_STAA8   185 HAKDASWLTSRKQLQPYGQYHGGGAHYGVDYAMPENSPVYSLTDGTVVQAGWSNYGGGNQVTIKEANSNNYQWYMHNNRLTVSAGDKVKAGDQIAYSGSTGNSTAPHVHFQRMSGGIGNQYAVDPTSYLQS 315
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh..eee..ee.....ee..eeee.....eee....eeeeeeee......eeeeeee....eeeeeeee.........ee....eeee..........eeeeeeee...hhh.ee.hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b13 A 185 HAKDASWLTSRKQLQPYGQYHGGGAHYGVDYAMPENSPVYSLTDGTVVQAGWSNYGGGNQVTIKEANSNNYQWYMHNNRLTVSAGDKVKAGDQIAYSGSTGNSTAPHVHFQRMSGGIGNQYAVDPTSYLQS 315
                                   194       204       214       224       234       244       254       264       274       284       294       304       314 


Chain B from PDB  Type:PROTEIN  Length:131
 aligned with LYTM_STAA8 | O33599 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:131
                                   194       204       214       224       234       244       254       264       274       284       294       304       314 
           LYTM_STAA8   185 HAKDASWLTSRKQLQPYGQYHGGGAHYGVDYAMPENSPVYSLTDGTVVQAGWSNYGGGNQVTIKEANSNNYQWYMHNNRLTVSAGDKVKAGDQIAYSGSTGNSTAPHVHFQRMSGGIGNQYAVDPTSYLQS 315
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh..eee..ee.....ee..eeee.....eee....eeeeeeeee....eeeeeeee....eeeeeeee.........ee....eeee..........eeeeeeee...hhh.ee.hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b13 B 185 HAKDASWLTSRKQLQPYGQYHGGGAHYGVDYAMPENSPVYSLTDGTVVQAGWSNYGGGNQVTIKEANSNNYQWYMHNNRLTVSAGDKVKAGDQIAYSGSTGNSTAPHVHFQRMSGGIGNQYAVDPTSYLQS 315
                                   194       204       214       224       234       244       254       264       274       284       294       304       314
   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 2B13)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2B13)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2B13)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (LYTM_STAA8 | O33599)
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:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    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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  2b13
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  3.4.24.75
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        LYTM_STAA8 | O33599: 1qwy 2b0p 2b44 4zyb

(-) Related Entries Specified in the PDB File

1qwy FULL-LENGTH LYTM
2b0p TRUNCATED S. AUREUS LYTM, P212121 CRYSTAL FORM
2b44 TRUNCATED S. AUREUS LYTM, P 32 2 1 CRYSTAL FORM