Crystal structure of a ld-carboxypeptidase a (saro_1426) from novosphingobium aromaticivorans dsm at 1.89 A resolution

Experimental Data Snapshot

  • Resolution: 1.89 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report

This is version 1.5 of the entry. See complete history


Structure and function of a novel LD-carboxypeptidase a involved in peptidoglycan recycling.

Das, D.Herve, M.Elsliger, M.A.Kadam, R.U.Grant, J.C.Chiu, H.J.Knuth, M.W.Klock, H.E.Miller, M.D.Godzik, A.Lesley, S.A.Deacon, A.M.Mengin-Lecreulx, D.Wilson, I.A.

(2013) J Bacteriol 195: 5555-5566

  • DOI: https://doi.org/10.1128/JB.00900-13
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Approximately 50% of cell wall peptidoglycan in Gram-negative bacteria is recycled with each generation. The primary substrates used for peptidoglycan biosynthesis and recycling in the cytoplasm are GlcNAc-MurNAc(anhydro)-tetrapeptide and its degradation product, the free tetrapeptide. This complex process involves ∼15 proteins, among which the cytoplasmic enzyme ld-carboxypeptidase A (LdcA) catabolizes the bond between the last two l- and d-amino acid residues in the tetrapeptide to form the tripeptide, which is then utilized as a substrate by murein peptide ligase (Mpl). LdcA has been proposed as an antibacterial target. The crystal structure of Novosphingobium aromaticivorans DSM 12444 LdcA (NaLdcA) was determined at 1.89-Å resolution. The enzyme was biochemically characterized and its interactions with the substrate modeled, identifying residues potentially involved in substrate binding. Unaccounted electron density at the dimer interface in the crystal suggested a potential site for disrupting protein-protein interactions should a dimer be required to perform its function in bacteria. Our analysis extends the identification of functional residues to several other homologs, which include enzymes from bacteria that are involved in hydrocarbon degradation and destruction of coral reefs. The NaLdcA crystal structure provides an alternate system for investigating the structure-function relationships of LdcA and increases the structural coverage of the protagonists in bacterial cell wall recycling.

  • Organizational Affiliation

    Joint Center for Structural Genomics‡

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LD-carboxypeptidase A
A, B
274Novosphingobium aromaticivorans DSM 12444Mutation(s): 0 
Gene Names: Saro_1426YP_496704.1
Find proteins for Q2G8F3 (Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 / F199))
Explore Q2G8F3 
Go to UniProtKB:  Q2G8F3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2G8F3
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B]
O4 S
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
O [auth A]
P [auth A]
Q [auth A]
AA [auth B],
BA [auth B],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
Z [auth B]
C3 H8 O3
Query on UNL

Download Ideal Coordinates CCD File 
T [auth B]Unknown ligand
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.628α = 90
b = 91.042β = 90
c = 145.744γ = 90
Software Package:
Software NamePurpose
MolProbitymodel building
SCALAdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
MOSFLMdata reduction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-02-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Source and taxonomy, Version format compliance
  • Version 1.2: 2014-09-24
    Changes: Database references
  • Version 1.3: 2017-11-01
    Changes: Refinement description
  • Version 1.4: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.5: 2023-02-01
    Changes: Database references, Derived calculations