5Z01 | pdb_00005z01

Native Escherichia coli L,D-carboxypeptidase A (LdcA)

• PDB DOI: https://doi.org/10.2210/pdb5Z01/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-12-18 Released: 2018-04-25 
• Deposition Author(s): Meyer, K., Tame, J.R.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.225 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Literature

The crystal structure and oligomeric form of Escherichia colil,d-carboxypeptidase A.

Meyer, K., Addy, C., Akashi, S., Roper, D.I., Tame, J.R.H.

(2018) Biochem Biophys Res Commun 499: 594-599

• PubMed: 29601819 
• DOI: https://doi.org/10.1016/j.bbrc.2018.03.195
• Primary Citation Related Structures: 
  5Z01, 5Z03


• PubMed Abstract: 
  

  Bacterial peptidoglycan is constructed by cross-linking sugar chains carrying pentapeptide building blocks with two d-alanine residues at the C-terminus. Incorporation into the polymer and subsequent breakdown of peptidoglycan releases a tetrapeptide with a single d-alanine residue. Removal of this residue is necessary for the tripeptide to receive a new D-Ala-D-Ala dipeptide in the synthetic pathway, but proteases are generally unable to work with substrates having residues of unusual chirality close to the scissile bond. Processing of the tetrapeptide is carried out by a dedicated ld-carboxypeptidase, which is of interest as a novel drug target. We describe the high resolution crystal structure of the enzyme from E. coli, and demonstrate the dimeric structure is highly conserved.

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Organizational Affiliation: 
• Graduate School of Medical Life Science, Yokohama City University, Suehiro 1-7-29, Tsurumi, Yokohama, 230-0045, Japan.
School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK.
Graduate School of Medical Life Science, Yokohama City University, Suehiro 1-7-29, Tsurumi, Yokohama, 230-0045, Japan. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 35.71 kDa 
• Atom Count: 2,583 
• Modeled Residue Count: 305 
• Deposited Residue Count: 323 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Murein tetrapeptide carboxypeptidase	A	323	Escherichia coli K-12	Mutation(s): 0  Gene Names: ldcA, ycgQ, b1192, JW1181 EC: 3.4.17.13
UniProt
Find proteins for P76008 (Escherichia coli (strain K12)) Explore P76008  Go to UniProtKB:  P76008

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.225 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.949	α = 90
b = 89.069	β = 90
c = 93.772	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-04-25 
Deposition Author(s): Meyer, K., Tame, J.R.H.

Revision History  

• Version 1.0: 2018-04-25
  Type: Initial release
  
• Version 1.1: 2018-05-02
  Changes: Data collection, Database references
• Version 1.2: 2024-03-27
  Changes: Data collection, Database references, Derived calculations