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(-) Description

Title :  HADDOCK MODEL OF BACILLUS SUBTILIS L,D-TRANSPEPTIDASE IN COMPLEX WITH A PEPTIDOGLYCAN HEXAMUROPEPTIDE
 
Authors :  P. Schanda, S. Triboulet, C. Laguri, C. Bougault, I. Ayala, M. Callon, M J. Simorre
Date :  02 Sep 14  (Deposition) - 14 Jan 15  (Release) - 14 Jan 15  (Revision)
Method :  SOLID-STATE NMR
Resolution :  NOT APPLICABLE
Chains :  Asym. Unit :  A,B,C,D,E,F,G  (5x)
Biol. Unit 1:  A,B,C,D,E,F,G  (1x)
Keywords :  Transpeptidase, Peptidoglycan Biosynthesis, Transferase-Structural Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Schanda, S. Triboulet, C. Laguri, C. M. Bougault, I. Ayala, M. Callon, M. Arthur, J. P. Simorre
Atomic Model Of A Cell-Wall Cross-Linking Enzyme In Complex With An Intact Bacterial Peptidoglycan.
J. Am. Chem. Soc. V. 136 17852 2014
PubMed-ID: 25429710  |  Reference-DOI: 10.1021/JA5105987

(-) Compounds

Molecule 1 - PUTATIVE L,D-TRANSPEPTIDASE YKUD
    Chains: A
    EC Number: 2.-.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET2818
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 2-167
    Gene: BSU14040, Y647_14120, YKUD
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 224308
    Strain: 168
    Synonym: SPORE PROTEIN YKUD
 
Molecule 2 - INTACT BACTERIAL PEPTIDOGLYCAN
    Chains: B, C, D, E, F, G
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

  1234567
Asymmetric Unit (5x): ABCDEFG
Biological Unit 1 (1x): ABCDEFG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 30)

Asymmetric Unit (5, 30)
No.NameCountTypeFull Name
1AMU6Ligand/IonBETA-N-ACETYLMURAMIC ACID
2API6Mod. Amino Acid2,6-DIAMINOPIMELIC ACID
3DAL6Mod. Amino AcidD-ALANINE
4FGA6Mod. Amino AcidGAMMA-D-GLUTAMIC ACID
5NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (5, 30)
No.NameCountTypeFull Name
1AMU6Ligand/IonBETA-N-ACETYLMURAMIC ACID
2API6Mod. Amino Acid2,6-DIAMINOPIMELIC ACID
3DAL6Mod. Amino AcidD-ALANINE
4FGA6Mod. Amino AcidGAMMA-D-GLUTAMIC ACID
5NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:2 , LYS A:3 , LEU A:4 , THR A:6 , GLN A:8 , LYS A:10 , ASP A:13 , ASP A:21 , SER A:45 , ASP A:53 , TYR A:55 , THR A:93 , PRO A:94 , THR A:95 , GLU A:97 , TYR A:99 , GLN A:121 , ALA B:3 , ALA C:9 , FGA C:10 , ALA D:15 , FGA D:16 , ALA E:21 , ALA F:27 , FGA F:28 , API F:29 , ALA G:33 , FGA G:34BINDING SITE FOR CHAIN E OF POLYSACCHARIDE RESIDUES 101 TO 112

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2MTZ)

(-) 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:169
                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....hhhhhhhhh..hhhhhhhhh...........eeeeeeee......eeeeee....eeeeee..eeeeeee..ee.........eee..eeee........eeee.......ee...hhhhh..ee....ee.hhhhhhhhhhhh....eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2mtz A   1 GRKLLTYQVKQGDTLNSIAADFRISTAALLQANPSLQAGLTAGQSIVIPGLPDPYTIPYHIAVSIGAKTLTLSLNNRVMKTYPIAVGKILTQTPTGEFYIINRQRNPGGPFGAYWLSLSKQHYGIHGTNNPASIGKAVSKGCIRMHNKDVIELASIVPNGTRVTINRGS 169
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160         


Chain B from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 2mtz B   3 Axkx   6
                             |||
                             4-FGA
                              5-API
                               6-DAL


Chain C from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 2mtz C   9 Axkx  12
                             |||
                             |||
                            10-FGA
                             11-API
                              12-DAL


Chain D from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 2mtz D  15 Axkx  18
                             |||
                             |||
                            16-FGA
                             17-API
                              18-DAL


Chain E from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 2mtz E  21 Axkx  24
                             |||
                             |||
                            22-FGA
                             23-API
                              24-DAL


Chain F from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 2mtz F  27 Axkx  30
                             |||
                             |||
                            28-FGA
                             29-API
                              30-DAL


Chain G from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 2mtz G  33 Axkx  36
                             |||
                             |||
                            34-FGA
                             35-API
                              36-DAL
   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 2MTZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

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 Related Entries

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

UniProtKB/Swiss-Prot
        YKUD_BACSU | O34816: 1y7m 3zqd 4a1i 4a1j 4a1k 4a52

(-) Related Entries Specified in the PDB File

3zqd HADDOCK STARTING STRUCTURE