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(-) Description

Title :  NMR STRUCTURE OF THE CATALYTIC DOMAIN FROM E. FAECIUM L,D-TRANSPEPTIDASE ACYLATED BY ERTAPENEM
 
Authors :  L. Lecoq, S. Triboulet, V. Dubee, C. Bougault, J. E. Hugonnet, M. Arthur J. P. Simorre
Date :  18 Dec 12  (Deposition) - 24 Apr 13  (Release) - 12 Feb 14  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Transferase, Transpeptidation, Peptidoglycan Biosynthesis, Antibiotic Resistance (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Lecoq, S. Triboulet, V. Dubee, C. Bougault, J. E. Hugonnet, M. Arthur, J. P. Simorre
The Structure Of Enterococcus Faecium L, D---Transpeptidase Acylated By Ertapenem Provides Insight Into The Inactivation Mechanism.
Acs Chem. Biol. V. 8 1140 2013
PubMed-ID: 23574509  |  Reference-DOI: 10.1021/CB4001603

(-) Compounds

Molecule 1 - ERFK/YBIS/YCFS/YNHG
    Chains: A
    EC Number: 2.3.2.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETTEV
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN, RESIDUES 341-466
    Organism Scientific: ENTEROCOCCUS FAECIUM
    Organism Taxid: 1352
    Other Details: ERTAPENEM ANTIBIOTIC IS COVALENTLY LINKED TO THE CYSTEINE OF THE ENZYME.
    Synonym: LDTFM-ERTAPENEM

 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
11RG1Ligand/Ion(4R,5S)-3-({(3S,5S)-5-[(3-CARBOXYPHENYL)CARBAMOYL]PYRROLIDIN-3-YL}SULFANYL)-5-[(1S,2R)-1-FORMYL-2-HYDROXYPROPYL]-4-METHYL-4,5-DIHYDRO-1H-PYRROLE-2-CARBOXYLIC ACID
NMR Structure * (1, 1)
No.NameCountTypeFull Name
11RG1Ligand/Ion(4R,5S)-3-({(3S,5S)-5-[(3-CARBOXYPHENYL)CARBAMOYL]PYRROLIDIN-3-YL}SULFANYL)-5-[(1S,2R)-1-FORMYL-2-HYDROXYPROPYL]-4-METHYL-4,5-DIHYDRO-1H-PYRROLE-2-CARBOXYLIC ACID

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:393 , THR A:396 , ASN A:397 , ASP A:398 , GLY A:400 , TYR A:403 , TRP A:410 , GLY A:417 , VAL A:418 , HIS A:440 , GLY A:441 , CYS A:442BINDING SITE FOR RESIDUE 1RG A 130

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ZGP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ZGP)

(-) 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:129
 aligned with Q3Y185_ENTFC | Q3Y185 from UniProtKB/TrEMBL  Length:466

    Alignment length:135
                                   341       351       361       371       381       391       401       411       421       431       441       451       461     
         Q3Y185_ENTFC   332 GTTADHPLIEDTYIEVDLENQHMWYYKDGKVALETDIVSGKPTTPTPAGVFYVWNKEEDATLKGTNDDGTPYESPVNYWMPIDWTGVGIHDSDWQPEYGGDLWKTRGSHGCINTPPSVMKELFGMVEKGTPVLVF 466
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .----.--...eeeeee...eeeeeee..eeeeeee.............eeee..eee..eeeee.....eeeee..eeee.......eee..........hhhhhh....eee.hhhhhhhhhhh...eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zgp A 338 G----H--MEDTYIEVDLENQHMWYYKDGKVALETDIVSGKPTTPTPAGVFYVWNKEEDATLKGTNDDGTPYESPVNYWMPIDWTGVGIHDSDWQPEYGGDLWKTRGSHGCINTPPSVMKELFGMVEKGTPVLVF 466
                            |    | 341       351       361       371       381       391       401       411       421       431       441       451       461     
                            |  339  |                                                                                                                              
                          338     340
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZGP)

(-) Gene Ontology  (3, 3)

NMR Structure(hide GO term definitions)
Chain A   (Q3Y185_ENTFC | Q3Y185)
molecular function
    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.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/TrEMBL
        Q3Y185_ENTFC | Q3Y185: 1zat 2hkl 3zg4

(-) Related Entries Specified in the PDB File

3zg4 NMR STRUCTURE OF THE CATALYTIC DOMAIN FROM E. FAECIUM L,D-TRANSPEPTIDASE