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(-) Description

Title :  HIGH RESOLUTION STRUCTURE OF M23 PEPTIDASE LYTM WITH SUBSTRATE ANALOGUE
 
Authors :  M. Grabowska, E. Jagielska, H. Czapinska, M. Bochtler, I. Sabala
Date :  21 May 15  (Deposition) - 21 Oct 15  (Release) - 21 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
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 :  Lytm, Lysostaphin, Peptidoglycan Amidase, Peptidase, Hydrolase, Tetraglycine Phosphinate, Transition State Analogue, Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Grabowska, E. Jagielska, H. Czapinska, M. Bochtler, I. Sabala
High Resolution Structure Of An M23 Peptidase With A Substrate Analogue.
Sci Rep V. 5 14833 2015
PubMed-ID: 26437833  |  Reference-DOI: 10.1038/SREP14833

(-) Compounds

Molecule 1 - GLYCYL-GLYCINE ENDOPEPTIDASE LYTM
    ChainsA, B, C, D
    EC Number3.4.24.75
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPLASMID
    Expression System Taxid469008
    FragmentUNP RESIDUES 185-316
    GeneLYTM, SAS0252
    Organism ScientificSTAPHYLOCOCCUS AUREUS SUBSP. AUREUS NCTC 8325
    Organism Taxid93061
    SynonymAUTOLYSIN LYTM

 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  (8, 25)

Asymmetric Unit (8, 25)
No.NameCountTypeFull Name
14SQ4Ligand/IonTETRAGLYCINE PHOSPHINATE
2CA4Ligand/IonCALCIUM ION
3CL4Ligand/IonCHLORIDE ION
4EDO2Ligand/Ion1,2-ETHANEDIOL
5EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
6PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
7UNL4Ligand/IonUNKNOWN LIGAND
8ZN4Ligand/IonZINC ION
Biological Unit 1 (4, 6)
No.NameCountTypeFull Name
14SQ1Ligand/IonTETRAGLYCINE PHOSPHINATE
2CA-1Ligand/IonCALCIUM ION
3CL-1Ligand/IonCHLORIDE ION
4EDO1Ligand/Ion1,2-ETHANEDIOL
5EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
6PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
7UNL3Ligand/IonUNKNOWN LIGAND
8ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
14SQ1Ligand/IonTETRAGLYCINE PHOSPHINATE
2CA-1Ligand/IonCALCIUM ION
3CL-1Ligand/IonCHLORIDE ION
4EDO1Ligand/Ion1,2-ETHANEDIOL
5EPE-1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
6PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
7UNL-1Ligand/IonUNKNOWN LIGAND
8ZN-1Ligand/IonZINC ION
Biological Unit 3 (3, 3)
No.NameCountTypeFull Name
14SQ1Ligand/IonTETRAGLYCINE PHOSPHINATE
2CA-1Ligand/IonCALCIUM ION
3CL-1Ligand/IonCHLORIDE ION
4EDO-1Ligand/Ion1,2-ETHANEDIOL
5EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
6PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
7UNL1Ligand/IonUNKNOWN LIGAND
8ZN-1Ligand/IonZINC ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
14SQ1Ligand/IonTETRAGLYCINE PHOSPHINATE
2CA-1Ligand/IonCALCIUM ION
3CL-1Ligand/IonCHLORIDE ION
4EDO-1Ligand/Ion1,2-ETHANEDIOL
5EPE-1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
6PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
7UNL-1Ligand/IonUNKNOWN LIGAND
8ZN-1Ligand/IonZINC ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:210 , ASP A:214 , HIS A:293 , 4SQ A:409binding site for residue ZN A 401
02AC2SOFTWAREGLY A:285 , GLN A:314 , ARG A:316 , HOH A:547 , HOH A:560 , HOH A:576 , HOH A:639binding site for residue CA A 402
03AC3SOFTWAREARG A:195 , HOH A:528binding site for residue CL A 403
04AC4SOFTWAREHIS A:185 , THR A:227 , ASP A:228 , HOH A:512 , HOH A:529 , HOH A:642binding site for residue CL A 404
05AC5SOFTWAREARG A:263binding site for residue EDO A 408
06AC6SOFTWARETYR A:204 , HIS A:210 , ASP A:214 , TYR A:239 , GLY A:240 , MET A:259 , HIS A:260 , ASN A:286 , SER A:287 , THR A:288 , HIS A:291 , HIS A:293 , ASN A:303 , ZN A:401 , HOH A:514 , HOH A:521 , HOH A:522 , HOH A:586 , HOH A:594 , HOH A:619 , HOH A:662binding site for residue 4SQ A 409
07AC7SOFTWAREALA A:234 , LEU A:264 , VAL A:266 , SER A:267 , HOH A:533 , HOH A:552 , HOH A:600 , HOH A:602 , HOH A:607 , HOH A:637 , HOH A:693 , GLN D:203 , ALA D:209binding site for residue EPE A 410
08AC8SOFTWAREHIS B:210 , ASP B:214 , HIS B:293 , 4SQ B:406binding site for residue ZN B 401
09AC9SOFTWAREGLY B:285 , GLN B:314 , ARG B:316 , HOH B:530 , HOH B:540 , HOH B:589 , HOH B:653 , HOH B:711binding site for residue CA B 402
10AD1SOFTWAREGLN B:199 , GLY B:206binding site for residue CL B 403
11AD2SOFTWAREARG B:263 , LEU B:264 , THR B:265 , VAL B:266 , SER B:267binding site for residue PEG B 404
12AD3SOFTWARETYR B:239 , HOH B:600 , LYS C:248 , ASN C:251 , SER C:252 , ASN C:253binding site for residue EDO B 405
13AD4SOFTWAREGLN B:199 , TYR B:204 , HIS B:210 , ASP B:214 , TYR B:239 , GLY B:240 , MET B:259 , HIS B:260 , ASN B:286 , HIS B:291 , HIS B:293 , ASN B:303 , ZN B:401 , HOH B:512 , HOH B:519 , HOH B:532 , HOH B:559 , HOH B:560binding site for residue 4SQ B 406
14AD5SOFTWAREHIS C:210 , ASP C:214 , HIS C:293 , 4SQ C:404binding site for residue ZN C 401
15AD6SOFTWAREGLY C:285 , GLN C:314 , ARG C:316 , HOH C:533 , HOH C:575 , HOH C:582 , HOH C:663 , HOH C:711binding site for residue CA C 402
16AD7SOFTWARETYR C:204 , HIS C:210 , ASP C:214 , TYR C:239 , GLY C:240 , MET C:259 , HIS C:260 , ASN C:286 , SER C:287 , THR C:288 , HIS C:291 , HIS C:293 , ASN C:303 , ZN C:401 , HOH C:516 , HOH C:526 , HOH C:540 , HOH C:584 , HOH C:609binding site for residue 4SQ C 404
17AD8SOFTWAREGLN B:203 , ALA B:209 , ALA C:234 , LEU C:264 , VAL C:266 , SER C:267 , HOH C:517 , HOH C:593 , HOH C:704binding site for residue EPE C 405
18AD9SOFTWAREHIS D:210 , ASP D:214 , HIS D:293 , 4SQ D:404binding site for residue ZN D 401
19AE1SOFTWAREGLY D:285 , GLN D:314 , ARG D:316 , HOH D:536 , HOH D:537 , HOH D:543 , HOH D:608binding site for residue CA D 402
20AE2SOFTWAREGLN D:199 , GLY D:206binding site for residue CL D 403
21AE3SOFTWARETYR D:204 , HIS D:210 , ASP D:214 , TYR D:239 , GLY D:240 , MET D:259 , HIS D:260 , ASN D:286 , SER D:287 , THR D:288 , HIS D:291 , HIS D:293 , ASN D:303 , ZN D:401 , HOH D:502 , HOH D:525 , HOH D:557 , HOH D:561 , HOH D:582binding site for residue 4SQ D 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ZYB)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4ZYB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ZYB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ZYB)

(-) Exons   (0, 0)

(no "Exon" information available for 4ZYB)

(-) 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:133
                                                                                                                                                                     
               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.hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zyb A 184 AHAKDASWLTSRKQLQPYGQYHGGGAHYGVDYAMPENSPVYSLTDGTVVQAGWSNYGGGNQVTIKEANSNNYQWYMHNNRLTVSAGDKVKAGDQIAYSGSTGNSTAPHVHFQRMSGGIGNQYAVDPTSYLQSR 316
                                   193       203       213       223       233       243       253       263       273       283       293       303       313   

Chain B from PDB  Type:PROTEIN  Length:132
                                                                                                                                                                    
               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.hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4zyb B 185 HAKDASWLTSRKQLQPYGQYHGGGAHYGVDYAMPENSPVYSLTDGTVVQAGWSNYGGGNQVTIKEANSNNYQWYMHNNRLTVSAGDKVKAGDQIAYSGSTGNSTAPHVHFQRMSGGIGNQYAVDPTSYLQSR 316
                                   194       204       214       224       234       244       254       264       274       284       294       304       314  

Chain C from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               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.hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zyb C 184 AHAKDASWLTSRKQLQPYGQYHGGGAHYGVDYAMPENSPVYSLTDGTVVQAGWSNYGGGNQVTIKEANSNNYQWYMHNNRLTVSAGDKVKAGDQIAYSGSTGNSTAPHVHFQRMSGGIGNQYAVDPTSYLQSR 316
                                   193       203       213       223       233       243       253       263       273       283       293       303       313   

Chain D from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               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.hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zyb D 184 AHAKDASWLTSRKQLQPYGQYHGGGAHYGVDYAMPENSPVYSLTDGTVVQAGWSNYGGGNQVTIKEANSNNYQWYMHNNRLTVSAGDKVKAGDQIAYSGSTGNSTAPHVHFQRMSGGIGNQYAVDPTSYLQSR 316
                                   193       203       213       223       233       243       253       263       273       283       293       303       313   

   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 4ZYB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ZYB)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ZYB)

(-) Gene Ontology  (8, 16)

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 Related Entries

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

UniProtKB/Swiss-Prot
        LYTM_STAA8 | O335991qwy 2b0p 2b13 2b44

(-) Related Entries Specified in the PDB File

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