The Open Protein Structure Annotation Network
PDB Keyword


    Title Crystal structure of LD-carboxypeptidase A (YP_496704.1) from Novosphingobium aromaticivorans DSM 12444 at 1.89 A resolution. To be published
    Site JCSG
    PDB Id 3g23 Target Id 379617
    Molecular Characteristics
    Source Novosphingobium aromaticivorans dsm 12444
    Alias Ids TPS7206,SARO_25NOV03_CONTIG29_REVISED_GENE2295, 87837 Molecular Weight 29277.55 Da.
    Residues 273 Isoelectric Point 5.75
    Sequence vtrriaicapstpftredsarvialaaaefpdlslsfheqcfaseghfagsdalrlsaflecanddafe avwfvrggyganriaedalarlgraasakqylgysdagtllaalyahrigrsvhapmpvdirrpegesa vrrtlgwlagaregleptlgagapavafnlmtlamlcgtrllpdlsghvvmieevaehhyavdrllfhv tscladagiaglrlgrvsdvpendrpfgcsveemarhwchragiaflgtadighdvdnrivpfgla
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.89 Rfree 0.207
    Matthews' coefficent 2.44 Rfactor 0.171
    Waters 464 Solvent Content 49.54

    Ligand Information


    Google Scholar output for 3g23
    1. Structural and functional characterization of microcin C resistance peptidase MccF from Bacillus anthracis
    B Nocek, A Tikhonov, G Babnigg, M Gu, M Zhou - Journal of Molecular , 2012 - Elsevier

    Protein Summary

    Pfam update: This protein has now been incorporated into Peptidase_S66 which already has 12 known structures. It is deposited as UniProt:Q2G8F3_NOVAD.

    Gene Saro_1426 fromNovosphingobium aromaticivorans dsm 12444 translates into the YP_496704 protein belonging to the LD-carboxypeptidase family ( PF02016 ).

    Pre-SCOP classifies 3g23 N-terminal region (4-158) in the alpha/beta class, class I glutamine amidotransferase-like superfamily, LD-carboxyopeptidase A N-terminal domain-like family; and the C-terminal region (167-272) in the LD-carboxypeptisase A C-terminal domain-like (super)family. The protein is present as a dimer in the 3g23 structure and its crystal packing analysis suggests that this dimer should be the stable oligomeric form in solution. An unidentified ligand (UNL, blue) has been modeled at the dimeric interface.


    The final UNL modeled into the Fo-Fc difference electron density (green, at 3.0 sigma contour) calculated without the UNL shows the environment around this molecule (Note that this UNL is not in the putative active site that is discussed below):


    Other crystal structures from this Pfam are the protein from Pseudomonas aeruginosa, first solved by the Midwest Center for Structural Genomics as a protein of unknown function (PDB id PDB:1zl0) and subsequently as the wild type serine peptidase/LD-carboxypeptidase with a Ser-His-Glu catalytic triad (PDB:1zrsRef1) and the active site Ser115Ala mutant (PDB:2aum, Ref1) and His285Ala mutant (PDB:2aun, Ref1). 1zl0 structure also comes up as the top FFAS hit (link above) and FFAS does not show any other significant hit, when using 3g23 as query. A search for structural similarity using DALI returns as top hits the 1zrs, 2aum, 2aun and 1zl0 (Z=29); next is the microcin immunity protein MCCF PDB:3gjz (Z=26).


    Inspection of a 1zl0-3g23 structural superimposition indicates that the active site is conserved, i.e., Ser115, Glu217 and His285 from the PA LD-carboxypeptidase 1zl0 is present as Ser104, Glu191 and His261 (black sticks) in 3g23. Some other residues in the vicinity of the putative active site are also conserved.



    Contributed by Piotr Kozbial:

    Functional associations.

    LD-carboxypeptidase A (Saro_1426) from Novosphingobium aromaticivorans DSM 12444 is functionally associated with its genomic neighbour, an UDP-N-acetylmuramate-L-alanine ligase (EC, Saro_1425 - cytoplasmic peptidoglycan synthetase-like protein). Both proteins have similar phylogenetic co-occurrence (STRING server). LD-Carboxypeptidases (EC are named for their ability to cleave amide bonds between L- and D-amino acids, which occur naturally in bacterial peptidoglycan (Ref1). Dithiazoline Inhibitor of Escherichia coli L,D-Carboxypeptidase A causes cell lysis in stationary phase.


    Patterns resembling known catalytic sites.

    Saro_1426 has similar resideus in its putative active site than a serine carboxypeptidase II (PDB code 1bcs and 1bcr; identified with Catalytic Site Search at EBI).

    CSA entry for template Template RMSD E-value Assessment
    1bcs Serine carboxypeptidase ii 1.22 8.3e-05 Possible

    Residues in template 1bcs   Matching residues in Saro_1426 structure
    Residue name Residue number Chain   Residue name Residue number Chain
    GLY 53 A   GLY 77 B
    SER 146 A   SER 104 B
    TYR 147 A   ASP 105 B
    ASP 338 B   GLU 191 B
    HIS 397 B   HIS 261 B


    Cleft Analysis.

    Saro_1426 has similar cleft to PDB code 1zl0 (as detected by SuMO server; see below).

      Saro_1426 1ZL0 - TLA Deformation (+ coef.) Deviation (Å) Depth difference Weight
    amide   ASN 167 A   ASN 192 A 2% (7.79) 0.216 0.028 0.75
    delta_minus e2 GLU 191 A e1 GLU 217 A 1.9% (4.19) 0.173 0.032 0.6
    acyl   GLU 192 A   ASP 218 A 4% (7.21) 0.247 0.005 0.75
    delta_minus backbone VAL 193 A backbone VAL 219 A 0.65% (3.44) 0.185 0.023 0.6
    aromatic #2 HIS 261 A #2 HIS 285 A 1.2% (6.59) 0.061 0.081 0.9
    imidazole   HIS 261 A   HIS 285 A 1.2% (9.74) 0.061 0.081 0.9


    Score 3.600
    Weighted number of groups 4.5
    Number of groups 6
    Number of PDB groups 5 5
    Radius of the patches 3.54 Å 3.53 Å
    Volumes 3.6 3.6
    Global deformation 1.9%
    RMSD 0.000 Å
    Mean deviation 0.000 Å
    Depth difference 0.045


    End of Piotr Kozbial's contribution.


    1. Korza, H.J.,  Bochtler, M. (2005) Pseudomonas aeruginosa LD-carboxypeptidase, a serine peptidase with a Ser-His-Glu triad and a nucleophilic elbow. J.Biol.Chem. 280: 40802-40

    Ligand Summary

    An unidentified ligand (UNL) has been modeled at the dimeric interface. This is not at the putative active site.




    No references found.

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