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(-) Description

Title :  NMR STRUCTURE OF THE IMIPENEM-ACYLATED L,D-TRANSPEPTIDASE FROM BACILLUS SUBTILIS
 
Authors :  L. Lecoq, J. P. Simorre, C. Bougault, M. Arthur, J. Hugonnet, C. Veckerl O. Pessey
Date :  24 Oct 11  (Deposition) - 30 May 12  (Release) - 15 Jan 14  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Transferase, Peptidoglycan, Antibiotic Resistance, Cysteine Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Lecoq, C. Bougault, J. Hugonnet, C. Veckerle, O. Pessey, M. Arthur, J. P. Simorre
Dynamics Induced By Beta-Lactam Antibiotics In The Active Site Of Bacillus Subtilisl, D-Transpeptidase.
Structure V. 20 850 2012
PubMed-ID: 22579252  |  Reference-DOI: 10.1016/J.STR.2012.03.015

(-) Compounds

Molecule 1 - PUTATIVE L, D-TRANSPEPTIDASE YKUD
    ChainsA
    EC Number2.-.-.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantPREP4GROESL
    Expression System VectorPET2818
    Expression System Vector TypePLASMID
    FragmentRESIDUES 2-164
    Organism ScientificBACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168
    Organism Taxid224308
    SynonymSPORE PROTEIN YKUD, IMIPENEM-LDTBS

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x)A
NMR Structure * (1x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

NMR Structure (1, 1)
No.NameCountTypeFull Name
1IM21Ligand/Ion(5R)-5-[(1S,2R)-1-FORMYL-2-HYDROXYPROPYL]-3-[(2-{[(E)-IMINOMETHYL]AMINO}ETHYL)SULFANYL]-4,5-DIHYDRO-1H-PYRROLE-2-CARBOXYLIC ACID
NMR Structure * (1, 1)
No.NameCountTypeFull Name
1IM21Ligand/Ion(5R)-5-[(1S,2R)-1-FORMYL-2-HYDROXYPROPYL]-3-[(2-{[(E)-IMINOMETHYL]AMINO}ETHYL)SULFANYL]-4,5-DIHYDRO-1H-PYRROLE-2-CARBOXYLIC ACID

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:115 , HIS A:122 , LYS A:140 , CYS A:142 , ARG A:144BINDING SITE FOR RESIDUE IM2 A1142

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4A52)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4A52)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4A52)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LYSMPS51782 LysM domain profile.YKUD_BACSU2-45  1A:5-48
NMR Structure * (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LYSMPS51782 LysM domain profile.YKUD_BACSU2-45  1A:5-48

(-) Exons   (0, 0)

(no "Exon" information available for 4A52)

(-) Sequences/Alignments

NMR Structure
   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
 aligned with YKUD_BACSU | O34816 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:169
                               1                                                                                                                                                                164  
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157      |  
           YKUD_BACSU     - ---MLTYQVKQGDTLNSIAADFRISTAALLQANPSLQAGLTAGQSIVIPGLPDPYTIPYHIAVSIGAKTLTLSLNNRVMKTYPIAVGKILTQTPTGEFYIINRQRNPGGPFGAYWLSLSKQHYGIHGTNNPASIGKAVSKGCIRMHNKDVIELASIVPNGTRVTINR--   -
               SCOP domains d4a52a1 A:1-51 automated matches                   d4a52a2 A:52-169 automated matches                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....hhhhhhh....hhhhhhhhhhhhhh......eeee...........eeeee....eeeeee..eeeeeee.............eeee.ee...........eee......eeee...............eeehhhhhhhhhhhh...eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----LYSM  PDB: A:5-48 UniProt: 2-45             ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a52 A   1 GRKLLTYQVKQGDTLNSIAADFRISTAALLQANPSLQAGLTAGQSIVIPGLPDPYTIPYHIAVSIGAKTLTLSLNNRVMKTYPIAVGKILTQTPTGEFYIINRQRNPGGPFGAYWLSLSKQHYGIHGTNNPASIGKAVSKGCIRMHNKDVIELASIVPNGTRVTINRGS 169
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160         

   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  (2, 2)

NMR Structure

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4A52)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4A52)

(-) Gene Ontology  (8, 8)

NMR Structure(hide GO term definitions)
Chain A   (YKUD_BACSU | O34816)
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:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
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:0009252    peptidoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0030435    sporulation resulting in formation of a cellular spore    The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.
cellular component
    GO:0031160    spore wall    The specialized envelope lying outside the cell membrane of a spore.

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 Related Entries

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

UniProtKB/Swiss-Prot
        YKUD_BACSU | O348161y7m 2mtz 3zqd 4a1i 4a1j 4a1k

(-) Related Entries Specified in the PDB File

1y7m CRYSTAL STRUCTURE OF THE B. SUBTILIS YKUD PROTEIN AT 2 ARESOLUTION
3zqd B. SUBTILIS L,D-TRANSPEPTIDASE
4a1i YKUD FROM B.SUBTILIS
4a1j YKUD L,D-TRANSPEPTIDASE FROM B.SUBTILIS
4a1k YKUD L,D-TRANSPEPTIDASE