4B6Z

Crystal structure of metallo-carboxypeptidase from Burkholderia cenocepacia


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

High-Resolution Structure of the M14-Type Cytosolic Carboxypeptidase from Burkholderia Cenocepacia Refined Exploiting Pdb_Redo Strategies.

Rimsa, V.Eadsforth, T.C.Joosten, R.P.Hunter, W.N.

(2014) Acta Crystallogr.,Sect.D 70: 279

  • DOI: 10.1107/S1399004713026801

  • PubMed Abstract: 
  • A potential cytosolic metallocarboxypeptidase from Burkholderia cenocepacia has been crystallized and a synchrotron-radiation microfocus beamline allowed the acquisition of diffraction data to 1.9 Å resolution. The asymmetric unit comprises a tetrame ...

    A potential cytosolic metallocarboxypeptidase from Burkholderia cenocepacia has been crystallized and a synchrotron-radiation microfocus beamline allowed the acquisition of diffraction data to 1.9 Å resolution. The asymmetric unit comprises a tetramer containing over 1500 amino acids, and the high-throughput automated protocols embedded in PDB_REDO were coupled with model-map inspections in refinement. This approach has highlighted the value of such protocols for efficient analyses. The subunit is constructed from two domains. The N-terminal domain has previously only been observed in cytosolic carboxypeptidase (CCP) proteins. The C-terminal domain, which carries the Zn2+-containing active site, serves to classify this protein as a member of the M14D subfamily of carboxypeptidases. Although eukaryotic CCPs possess deglutamylase activity and are implicated in processing modified tubulin, the function and substrates of the bacterial family members remain unknown. The B. cenocepacia protein did not display deglutamylase activity towards a furylacryloyl glutamate derivative, a potential substrate. Residues previously shown to coordinate the divalent cation and that contribute to peptide-bond cleavage in related enzymes such as bovine carboxypeptidase are conserved. The location of a conserved basic patch in the active site adjacent to the catalytic Zn2+, where an acetate ion is identified, suggests recognition of the carboxy-terminus in a similar fashion to other carboxypeptidases. However, there are significant differences that indicate the recognition of substrates with different properties. Of note is the presence of a lysine in the S1' recognition subsite that suggests specificity towards an acidic substrate.


    Organizational Affiliation

    Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FAMILY M14 UNASSIGNED PEPTIDASE
A, B, C, D
405Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610)N/A
Find proteins for B4EEQ5 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610))
Go to UniProtKB:  B4EEQ5
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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A, B, C, D
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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B, C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A, B, C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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B, C, D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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D
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.164 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 62.897α = 90.00
b = 85.947β = 90.00
c = 289.016γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-27
    Type: Initial release
  • Version 1.1: 2014-02-12
    Type: Database references
  • Version 1.2: 2014-02-26
    Type: Database references